@article {pmid42426176, year = {2026}, author = {Latorre, F and Jaillon, O and Sieracki, ME and Cruaud, C and Massana, R and Logares, R}, title = {Global population structure in MAST-4 unicellular marine predators.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10607-z}, pmid = {42426176}, issn = {2399-3642}, support = {CTM2015-69936-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; PID2022-137508NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RYC-2013-12554//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; CEX2019-000928-S//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; 240904//Norges Forskningsråd (Research Council of Norway)/ ; }, abstract = {Marine heterotrophic flagellates (HFs) are key unicellular predators in marine food webs. Understanding their diversity and distributions is crucial for comprehending ocean ecosystems. MAST-4, an uncultured clade of Marine Stramenopiles, comprises a key group of bacterivorous heterotrophic flagellates (HFs) in the ocean microbiome. While we know that temperature is a major driver of MAST-4's biogeography, the population structure of MAST-4 species remains poorly known, limiting our ability to understand their ecology and adaptations. Here, we investigate the global population diversity and structure of MAST-4 species A, B, C, and E using metagenomics and single-cell genomics data from the Tara Oceans expedition. We find substantial population divergence in MAST-4A and C, with lower divergence in species B and E. Temperature and salinity are the primary factors structuring these populations. Analyses of positively selected genes reveal genomic regions likely involved in population adaptation to different environments. Our findings enhance the understanding of the population diversity and structure of these critical unicellular predators, providing insights into their ecological roles and adaptations in the global ocean. They also contribute to our general understanding of microbial populations, a largely unexplored dimension of biodiversity that plays a crucial role in grasping the impacts of global change.}, }
@article {pmid42426205, year = {2026}, author = {Wang, RH and Pan, G and Wang, S and Wang, J and Li, SC}, title = {High-quality phage assembly from metagenomes with PALACE.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42426205}, issn = {1546-1696}, abstract = {Millions of phage genomes have been mined from metagenomic data recently but the genome completeness remains poor because of the limitations of existing phage detection methods, which rely on metagenomic contigs that fragment phage genomes. Here, we present PALACE, a conjugate-graph-based framework for assembling high-quality phage genomes from metagenomes. PALACE incorporates homology-based and deep-learning-based methods to detect phage signals and constructs a conjugate graph from the metagenomic sample. On simulated data, PALACE generates accurate and complete phage genomes, achieving an F1 score of 0.92-1.00 across simulation settings, outperforming the second-best method by 0.21-0.48. Applying PALACE to 914 gut metagenomic samples from healthy controls and participants with colorectal cancer (CRC) yielded 5,306 high-quality phage genomes, outperforming the second-best benchmark method by 55.98% in median genome completeness. We observed a high degree of functional organization for genes within phage genomes. Phages from participants with CRC exhibited a notable enrichment of metabolic factors, suggesting their adaptation to nutrient availability in the CRC gut environment.}, }
@article {pmid42426353, year = {2026}, author = {Marszałek, K and Kowalski, MB and Jagiełło, A and Woźniak, A and Herda, K and Płoski, R and Ossowski, A and Oliveira, M and Zbieć-Piekarska, R and Łabaj, PP and Branicki, W}, title = {Evaluation of targeted Massively Parallel Sequencing methods for forensic metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13944-5}, pmid = {42426353}, issn = {1432-0614}, abstract = {Massively Parallel Sequencing (MPS) is effective for monitoring the microbial composition of environmental samples. Soil microbial signatures are critical for pinpointing the geographic location of forensic evidence, but standard 16S rRNA methods lack species-level resolution. Targeted sequencing panels, consisting of informative DNA fragments, can overcome this shortcoming and are highly desirable for forensic investigations. To address this, we evaluated three target enrichment methods for metagenomic analysis. First, we used Whole Metagenome Sequencing (WMS) data from 134 soil samples across 46 locations in Poland to extract a set of 200 markers. Using these markers, we created prototype targeted sequencing panels to compare two amplicon capture-based methods (Thermo Fisher AmpliSeq™ and Integrated DNA Technologies xGen™) and one hybridization capture-based method (Roche KAPA HyperPlus). The comparison of the technologies was guided by the results of classification of sample origin by machine learning classifier trained on feature profiles from WMS. The methods were assessed on technical parameters including data quality, reproducibility, sensitivity, and practical implementation for forensic laboratories. The performance and precision varied depending on technology and DNA concentration. The Roche KAPA HyperPlus hybridization capture-based method consistently demonstrated superior performance. Across various DNA input quantities, it showed the highest correlation with WMS data and achieved an exceptional F1 score of 0.94 at 5 ng, significantly outperforming the amplicon-based methods. This indicates that hybridization capture is a more robust and accurate approach for forensic soil microbiome profiling, particularly for low-template evidence, providing a highly reliable tool for predicting geographic origin. KEY POINTS: • Targeted Massively Parallel Sequencing methods for forensic soil microbial analysis • Targeted sequencing allowed the determination of the place of origin of soil samples • Roche KAPA HyperPlus: the most accurate classification of the soil samples origin.}, }
@article {pmid42426489, year = {2026}, author = {Dimri, A and Sharma, P and Vishvakarma, R and Sharma, S}, title = {Effect of Probiotics on the Gut-Mammary Pathway: Implications on Infant Microbiota Transfer and Development.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {42426489}, issn = {2161-3311}, mesh = {Humans ; *Probiotics/administration &amp; dosage/pharmacology ; Female ; *Gastrointestinal Microbiome ; Infant, Newborn ; Milk, Human/microbiology ; Lactobacillus ; Bifidobacterium ; Pregnancy ; Infant ; *Gastrointestinal Tract/microbiology ; Lactation ; *Mammary Glands, Human/microbiology ; }, abstract = {PURPOSE OF REVIEW: Transfer of microbiota from the maternal gut, during lactation, takes place via breastmilk, which establishes an intricate beneficial microbial ecosystem in the gut of the newborn. A healthy gut microbiota influences and enhances the neonatal health, and aids in multidimensional development-metabolically, immunologically, neurologically, and hormonally. Several microorganisms like Lactobacillus and Bifidobacterium get transferred to the infant gut and play a key role in its colonization and programming. Administration of such microbes, or probiotics, to the mother can assist in improving the benefits imparted by breastmilk to the infant, and can also provide health benefits to the mother. In recent years, there has been a focus on related metagenomic studies and the immunological effects of individual genera have also been studied in detail. In this review, we observe the gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios. We also analyze the level of evidence of potential of some promising probiotic strains in the transfer, establishment, and development of infant gut microbiota based on recently conducted studies.<br><br>RECENT FINDINGS: The analysis of recent metagenomic studies proved that strains like Bifidobacterium infantis, Lactobacillus rhamnosus, and Limosilactobacillus reuteri exibit a high level of evidence in benefitting the microbiota transfer as well as establishment, diversification, and development of the infant gut ecosystem. Hence, these strains in particular, can be given as supplements to mothers during pregnancy and lactation, in order to improve their inherent immunity and the overall health of the mother-infant dyad. With the advent of metagenomics, the roles, functions and effects of microbes in the gut-mammary pathway have been re-examined. This review, critically evaluates the recent studies related to gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios with particular emphasis on the strength and quality of their evidence.}, }
@article {pmid42426596, year = {2026}, author = {Bunga, S and Tan, A and Roos, M and Kuersten, S}, title = {RiboZAP: a species-agnostic pipeline for rRNA depletion probe design in metatranscriptomics.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06533-w}, pmid = {42426596}, issn = {1471-2105}, abstract = {BACKGROUND: Metatranscriptomic (MetaT) sequencing provides insights into gene expression and functional activity within microbial communities, but its utility is limited by the high abundance of ribosomal RNA (rRNA), which often accounts for ≥ 90% of total RNA. Efficient rRNA depletion is therefore essential to maximize mRNA coverage and sequencing efficiency. Commercial rRNA depletion kits can effectively reduce rRNA content; they are typically optimized for specific host microbiomes and often underperform in others. For example, probes designed for the human gut microbiome frequently show reduced efficiency when applied to non-human samples such as mouse cecal donor samples-a common model in microbiome research. Regardless of the depletion strategy used, designing rRNA removal probes solely based on a microbiome's taxonomic composition often requires an extensive number of probes, making the approach expensive and difficult to manufacture. To address these challenges, we developed RiboZAP, a species-agnostic computational pipeline that designs custom RNase H depletion probes directly from MetaT sequencing data without prior knowledge of sample composition.<br><br>RESULTS: RiboZAP-designed probe sets achieved 43-62% predicted rRNA depletion across both design and independent mouse cecal MetaT samples. Probes performed effectively on non-design samples, with depletion performance consistent with those observed in the design samples. Read composition and taxonomic diversity of residual rRNA, calculated using Shannon diversity indices, showed no evidence of probe-induced bias following depletion. In silico predictions were consistent with previously reported experimental depletion results [1-3], where RiboZAP designed probes improved mRNA recovery up to ~&#x2009;75% (P&#x2009;<&#x2009;0.01). Comprehensive downstream validation demonstrated no bias in differential gene expression (R[2] = 0.96), metabolic pathway profiling (&#x3c1; = ~0.92-0.95), or taxonomic composition.<br><br>CONCLUSION: In this study, we demonstrate a data-driven, in silico approach for designing additional rRNA depletion probes that perform consistently across samples of the same sample type. Probe sets designed from a subset of samples can be applied to independent samples of the same type. This approach enables estimation of rRNA depletion prior to synthesis, reducing experimental costs, and improving the efficiency of MetaT profiling from complex microbial communities.}, }
@article {pmid42426749, year = {2026}, author = {Zhan, S and Zheng, Y and Wu, T and Hou, X and Li, J and Ma, S and Gai, W and Shen, N and Zheng, J}, title = {Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08597-x}, pmid = {42426749}, issn = {1479-5876}, support = {F252052//Beijing Natural Science Foundation/ ; BYSYJC2023005//Peking University Third Hospital Fund for Interdisciplinary Research/ ; 2025-VHR-O-SY-21//State Key Laboratory of Vascular Homeostasis and Remodeling Open Research Fund/ ; 2025YFC2609702 and 2025YFC2609700//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Bloodstream infections (BSIs) are leading causes of sepsis-related mortality. Although metagenomic next-generation sequencing (mNGS) enables culture-independent pathogen detection, its clinical utility in plasma is limited by the overwhelming abundance of host cell-free DNA (cfDNA) and labor-intensive manual workflows.<br><br>METHODS: A plasma host DNA depletion mNGS (HD-mNGS) assay was developed which integrated nucleosome-targeted host DNA depletion with automated DNA extraction and library preparation. Analytical performance was evaluated through limit of detection, linearity, precision, and contamination control. Clinical performance was assessed in a cohort of 107 patients with suspected BSI and benchmarked against blood culture (BC), conventional microbiological testing (CMT), and standard mNGS without host depletion, using a composite clinical reference standard.<br><br>RESULTS: Nucleosome depletion markedly reduced host DNA background by an average of 66-fold, consequently enriching microbial reads by approximately 46.73-fold. The automated HD-mNGS assay exhibited robust analytical sensitivity, with limits of detection (LoD) ranging from 9.1 to 38 genome equivalents (GE) /mL for bacteria and fungi, and from 283 to 321 GE/mL for viruses and excellent linearity across tested concentrations (R[2]&#x2009;=&#x2009;0.915-0.989). Furthermore, the automated workflow maintained strong quantitative correlation with manual protocols while significantly reducing common skin and environmental contaminants by 71.7% and 83.7%, respectively. In a cohort of 107 patients, HD-mNGS demonstrates improved diagnostic performance for BSI, achieving a significantly higher pathogen detection rate (64.49%) and clinical positive percent agreement (PPA: 95.24%) than standard mNGS, BC, and CMT (P&#x2009;<&#x2009;0.001). Crucially, HD-mNGS demonstrates enhanced performance in detecting rare, fastidious, and intracellular pathogens (such as Mycobacterium tuberculosis and Rickettsia) that yield extremely low concentrations of circulating DNA, overcoming the limitations of traditional methods while maintaining high overall diagnostic total percent agreement (TPA: 88.79%).<br><br>CONCLUSIONS: Nucleosome-targeted host DNA depletion integrated with a fully automated mNGS platform significantly enhances microbial detection in plasma and provides a scalable approach for standardized BSI diagnostics.}, }
@article {pmid42426884, year = {2026}, author = {Lei, Y and Xu, Y and Yan, Y and Zhang, J and Zhang, T and Huang, J and Huang, Y and Zhong, J and Wang, X and Zhang, K and Chen, Y}, title = {Multi-omics and functional validation reveal that Methanobrevibacter-derived L-3-aminoisobutyrate alleviates subclinical mastitis in dairy goats via the HSPA1B-p65 signaling pathway.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02464-z}, pmid = {42426884}, issn = {2049-2618}, abstract = {BACKGROUND: Subclinical mastitis (SCM) is prevalent in dairy livestock and compromises milk quality and lactation performance. Although often attributed to bacterial infection, many cases lack identifiable pathogens, suggesting alternative mechanisms. While evidence supports a gut-mammary gland axis, the microbial drivers and microbiota-derived metabolites linking gut dysbiosis to SCM remain unclear. Here, we aimed to identify SCM-associated gut microbial markers, prioritize candidate therapeutic metabolites and define the underlying mechanism.<br><br>RESULTS: Based on differences in somatic cell count (SCC) and inflammatory phenotypes across a cohort of 167 mid-lactation Saanen dairy goats, we selected 6 healthy and 6 SCM goats for downstream analyses. By integrating metagenomics, metabolomics, cross-species fecal microbiota transplantation (FMT) and functional validation in vitro and in vivo, we found that SCM was accompanied by reduced milk yield and heightened inflammatory signatures. Compared with the Healthy group, SCM goats exhibited marked remodelling of the gut microbiota, with enrichment of opportunistic taxa (Eubacterium and Blautia) and a pronounced depletion of archaeal Methanobrevibacter spp. Notably, FMT from SCM donors recapitulated mammary inflammatory phenotypes in mice, supporting a causal contribution of gut dysbiosis to mammary inflammation. Joint metagenomic functional profiling and metabolomics further identified the branched-chain amino-acid-derived metabolite L-3-aminoisobutyrate (BAIBA) as significantly enriched in the gut of healthy goats. Moreover, Methanobrevibacter spp. harboured key enzyme genes (vorA, vorB and vorD) implicated in BAIBA biosynthesis. In an LPS-challenged MAC-T model, BAIBA attenuated mammary epithelial inflammation by activating endoplasmic reticulum protein quality control programmes and restoring HSPA1B expression, thereby suppressing NF-&#x3ba;B activation and reducing pro-inflammatory cytokine production. Finally, in naturally infected goats, intramammary administration of BAIBA lowered SCC, highlighting translational potential.<br><br>CONCLUSIONS: This study identifies BAIBA as a microbiota-derived metabolite that protects against SCM by restraining mammary inflammation via the HSPA1B-NF-&#x3ba;B axis, establishing a mechanistic gut-mammary link and highlighting a potential non-antibiotic intervention strategy. Video Abstract.}, }
@article {pmid42426896, year = {2026}, author = {Tóth, GE and Nagy, A and Costales, JA and Camacho, MA and Burneo, SF and Petersen, M and Bialonski, A and Baum, H and Horváth, B and Heitmann, A and Lühken, R and Schmidt, M and Schmidt-Chanasit, J and Tauber, Z and Cadar, D}, title = {A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, doi = {10.1186/s12985-026-03251-w}, pmid = {42426896}, issn = {1743-422X}, mesh = {Humans ; *Flavivirus/genetics/isolation &amp; purification/classification ; Germany ; *High-Throughput Nucleotide Sequencing/methods ; *Genome, Viral ; *Flavivirus Infections/virology ; Workflow ; Blood Donors ; RNA, Viral/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65-98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.}, }
@article {pmid42427046, year = {2026}, author = {Guo, YF and Zhan, QY and Huang, LN}, title = {[Clinical characteristics, diagnosis and treatment strategies, and prognostic factors in 47 patients with pulmonary mucormycosis].}, journal = {Zhonghua nei ke za zhi}, volume = {65}, number = {7}, pages = {734-742}, doi = {10.3760/cma.j.cn112138-20260201-00069}, pmid = {42427046}, issn = {0578-1426}, support = {2025ZD01902400//National Science and Technology Major Project/ ; }, mesh = {Humans ; *Mucormycosis/diagnosis ; Male ; Prognosis ; *Lung Diseases, Fungal/diagnosis ; Middle Aged ; Retrospective Studies ; Female ; Antifungal Agents ; Risk Factors ; Adult ; Voriconazole ; }, abstract = {Objective: To summarize the clinical characteristics, diagnostic and therapeutic strategies, and prognostic factors in patients with pulmonary mucormycosis. Methods: The patients with pulmonary mucormycosis admitted to the Department of Respiratory and Critical Care Medicine and the Lung Transplantation Department of China-Japan Friendship Hospital from January 2016 to March 2023 were retrospectively evaluated. High-risk factors, clinical manifestations, imaging findings, microbiological tests, therapeutic interventions, and clinical outcomes were analyzed, and variables were compared between survivors and non-survivors. Intergroup statistical analyses were performed using the chi-squared test, or Fisher's exact test, etc. Results: Of the 47 patients (21 confirmed, 26 clinically diagnosed), 32 (68.1%) were male, and the mean age of the cohort was (48±17) years. High-risk factors were present in 87.2% (41/47) of patients, primarily diabetes mellitus (53.2%, 25/47) and immunosuppression (42.6%, 20/47); 53.2% (25/47) had a history of voriconazole exposure. Hemoptysis occurred in 57.4% (27/47) of patients, of whom 17.0% (8/47) experienced massive hemoptysis; 48.9%(23/47) required interventional or surgical management. Chest CT scans revealed large consolidative opacities (70.2%, 33/47) and thick-walled cavities (48.9%, 23/47), and contrast-enhanced CT identified vascular involvement. The positive rate for lower respiratory tract fungal culture was only 17.1% (6/35), and that of smear microscopy was 18.2% (6/33), whereas the positive rate of metagenomic next-generation sequencing (mNGS) reached 76.0% (19/25), with mNGS of bronchoalveolar lavage fluid reaching 85.0% (17/20). Overall, 34.0% (16/47) of patients were diagnosed exclusively via mNGS. Conventional amphotericin B formulations were administered to 68.1% (32/47) of patients (including 10 who received liposomal amphotericin B); these formulations were associated with an adverse drug reaction rate of 86.7% (26/30), which contributed to only 40.7% (11/27) of these treated patients receiving a full therapeutic dose. Azoles were administered to 91.5% (43/47) of patients (15 received azoles alone), and among those treated with posaconazole, 88.0% (22/25) achieved target plasma concentrations; 48.9% (23/47) received combination therapy consisting of an amphotericin B formulation plus an azole. The survival rate among patients who underwent surgical intervention combined with antifungal therapy was 11/12, which was higher than that of patients who received antifungal therapy alone (28/35). Compared with survivors, non-survivors demonstrated significantly higher incidences of dyspnea (8/8 vs. 14/39, P=0.001), uncontrolled fever (6/8 vs. 12/39, P=0.027), pleural effusion (8/8 vs. 17/39, P=0.003), atelectasis (5/8 vs. 6/39, P=0.016), and severe complications (7/8 vs. 13/39, P=0.015). Furthermore, a significantly lower proportion of non-survivors received adequate antifungal dosing (1/8 vs. 21/39, P=0.037). Conclusions: Pulmonary mucormycosis predominantly occurs in high-risk populations such as those with diabetes mellitus or immunosuppression. Hemoptysis is a prominent clinical manifestation, while imaging findings commonly include large areas of consolidation, thick-walled cavities, and signs of vascular invasion. Early execution of contrast-enhanced chest CT, along with bronchoscopy with bronchoalveolar lavage fluid mNGS, improves the diagnostic yield. Adequate antifungal therapy combined with aggressive surgical intervention may contribute to improved prognosis. Severe complications, dyspnea, uncontrolled fever, pleural effusion, atelectasis, and inadequate antifungal treatment are associated with a poor prognosis, underscoring the need for early recognition and management.}, }
@article {pmid42427959, year = {2026}, author = {Wang, L and Ding, K and Yu, S and Guo, Z and Wang, Y and Zeng, L and Yuan, W}, title = {Atypical congenital toxoplasmosis presenting with neonatal jaundice and central nervous system involvement: a case report and therapeutic challenges to limited access to first-line anti-toxoplasma medications.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1874973}, pmid = {42427959}, issn = {2296-2360}, abstract = {BACKGROUND: Congenital toxoplasmosis (CT) is a vertically transmitted infection with a variable clinical spectrum, ranging from asymptomatic infection at birth to severe neurological and ocular sequelae. While the classic triad of hydrocephalus, intracranial calcifications, and chorioretinitis is well characterized, isolated neonatal hyperbilirubinemia as the initial presenting feature is uncommon and may delay diagnosis. We report a case of CT in a Chinese neonate who presented with jaundice and was subsequently found to have subclinical active chorioretinitis, cerebral edema, and bilateral central auditory pathway dysfunction. The case also illustrates therapeutic challenges related to the availability of first-line anti-parasitic agents.<br><br>CASE PRESENTATION: A 9-day-old term male infant was admitted for persistent jaundice. He was born at 39&#x2009;[+]&#x2009;[4] weeks' gestation, with a prenatal history notable only for maternal cat exposure and treated hypothyroidism. Initial serological testing at the referring hospital revealed positive Toxoplasma gondii IgM and IgG. After transfer, two consecutive blood metagenomic next-generation sequencing (mNGS) tests detected T. gondii DNA (reads: 6 and 7). The combination of negative first-trimester maternal serology, postpartum maternal IgM/IgG positivity, neonatal IgM positivity, and repeated detection of T. gondii DNA in neonatal blood strongly supported congenital toxoplasmosis. Cerebrospinal fluid (CSF) analysis showed pleocytosis and elevated protein, while CSF mNGS was negative, possibly reflecting low pathogen burden or compartmentalized infection. Further evaluation demonstrated bilateral active chorioretinitis on fundoscopic examination, abnormal brainstem auditory evoked potentials consistent with bilateral central auditory pathway dysfunction, and brain MRI showing cerebral edema with punctate hemorrhages. Due to initial unavailability of pyrimethamine, azithromycin followed by trimethoprim-sulfamethoxazole was administered; however, no clear improvement in CSF inflammatory indices was observed during this period. After initiation of standard therapy with pyrimethamine, sulfadiazine, and folinic acid, the patient demonstrated rapid clinical improvement and radiological resolution of brain lesions on follow-up MRI, with marked improvement of chorioretinal scars.<br><br>CONCLUSIONS: Clinicians should consider congenital toxoplasmosis in neonates with unexplained jaundice, even in the absence of classic clinical manifestations. Comprehensive multi-organ evaluation, including neuroimaging, ophthalmologic examination, and auditory testing, is essential for early disease characterization. Standard pyrimethamine-sulfadiazine-folinic acid therapy may be associated with better clinical and radiological outcomes and should be used when available. Long-term multidisciplinary follow-up is necessary to monitor potential sequelae.}, }
@article {pmid42428097, year = {2026}, author = {Hanze Villavicencio, KL and Tanes, C and Malekshahi, C and Cutillo, D and Knoll, MD and Prosperi, C and Kalaycioglu, M and Harris, M and Utz, PJ and Mattei, LM and Beiting, DP}, title = {Microbial and immune determinants of disease severity and death in pediatric pneumonia.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.02.26356561}, pmid = {42428097}, abstract = {Pneumonia is a leading cause of death globally and disproportionately affects children in lower- and middle-income countries. To explore microbial and immune correlates of disease and death, we performed metagenomic sequencing of upper respiratory tract (URT) microbiome in 309 children in Mali with pneumonia and 150 age- and season- and site-matched controls. We show that the URT microbiome matures throughout early life and is influenced by breastfeeding. URT microbiome maturation was disrupted during pneumonia resulting in loss of commensal species and expansion of pathobionts, which was linked to disease severity and death. Analysis of serum antibody levels revealed that low levels of passively acquired antibody from mothers, deficient antibody responses to RSV, and persistent autoantibody to cytokines were associated with pneumonia mortality in an age-dependent manner. These findings underscore the complex nature of pneumonia and identify microbial and immune factors for risk stratification and therapeutic interventions in pediatric pneumonia.}, }
@article {pmid42428114, year = {2026}, author = {Wang, Q and Wang, BY and Wilus, D and Xie, H}, title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {42428114}, abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced bleeding on probing and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of microbial community. Established periodontal pathogens, including Porphyromonas gingivalis and Tannerella forsythia , as well as the emerging pathogen Escherichia coli , decreased following treatment, whereas health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus , increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified treatment-associated differences in several carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.}, }
@article {pmid42428252, year = {2026}, author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y}, title = {The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.}, journal = {Environmental health perspectives}, volume = {134}, number = {3}, pages = {335-350}, pmid = {42428252}, issn = {1552-9924}, mesh = {Humans ; *Air Pollution/adverse effects/statistics &amp; numerical data ; *Gastrointestinal Microbiome/drug effects ; Aged ; Particulate Matter/adverse effects ; Ozone ; Male ; Female ; *Cognition/drug effects ; *Cognitive Dysfunction/epidemiology ; *Air Pollutants ; *Environmental Exposure/statistics &amp; numerical data ; }, abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway given their crucial role in the gut-brain axis. OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circulating metabolites in the association of residential PM2.5 and O3 exposure with cognitive dysfunction. METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated by using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-Mental State Examination and Hasegawa Dementia Scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes. RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and l-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase. CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation.}, }
@article {pmid42429397, year = {2026}, author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Bobay, L-M and Raymann, K}, title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0121326}, doi = {10.1128/spectrum.01213-26}, pmid = {42429397}, issn = {2165-0497}, abstract = {UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits.<br><br>IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.}, }
@article {pmid42429454, year = {2026}, author = {Di Leo, D and Nilsson, E and Westmeijer, G and Pinhassi, J and Lundin, D}, title = {nf-core/magmap: Map metatranscriptomes to large collections of genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag501}, pmid = {42429454}, issn = {1367-4811}, abstract = {SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.<br><br>The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42429456, year = {2026}, author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K}, title = {Exploring life's hidden majority: microbial dark matter symposium highlights.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0058725}, doi = {10.1128/msphere.00587-25}, pmid = {42429456}, issn = {2379-5042}, abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.}, }
@article {pmid42429485, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Multi-omics Analysis Identify Novel Microbiome-Metabolome Signatures Associated with Obesity.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag172}, pmid = {42429485}, issn = {1365-2672}, abstract = {AIMS: Explore the potential microbiome and serum metabolome factors and their interactions associated with obesity.<br><br>METHODS AND RESULTS: We performed a systematic multi-omics analysis using paired metagenomic and metabolomic profiles-including untargeted serum metabolomics, lipidomics, and short-chain fatty acids (SCFAs) with body mass index (BMI) from a cohort of 495 US men. Single omics analysis identified 52 gut bacteria species and 31 serum metabolites for potential associations with BMI. Among the identified bacteria, Collinsella stercoris (C.stercoris) (Coef.=-0.147, P=0.015) was negatively associated, whereas Bacteroides fragilis (B.fragilis) (Coef.=0.294, P=1.22E-04) and Veillonella dispar (V.dispar) (Coef.=0.135, P=0.001) were positively associated, these results were further validated by an independent Chinese cohort. Several of the identified metabolites including gamma-glutamylglycine (Coef.=-0.713, P=4.53E-06), asparagine (Coef.=-0.629, P=3.53E-05), glycine (Coef.=-0.952, P=5.28E-09) and serotonin (Coef.=0.566, P=1.78E-04) were associated with these significant bacteria (P<0.05).<br><br>CONCLUSION: This multi-omics study identifies key gut bacteria and serum metabolites that interact to associate with host obesity, providing systemic insight into microbiome-host metabolic interactions.}, }
@article {pmid42429570, year = {2026}, author = {Sánchez-Nieto, E and Martínez-Abarca, F and Millán, V and Molina-Sánchez, MD and García-Rodríguez, FM and Toro, N}, title = {A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0038126}, doi = {10.1128/spectrum.00381-26}, pmid = {42429570}, issn = {2165-0497}, abstract = {Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large reverse transcriptase (RT)-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with podovirus-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.IMPORTANCEIn this study, we report the functional characterization of a UG5-large reverse transcriptase-associated defense system (DRT11) encoded on the pSymA megaplasmid of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Using a combination of phylogenetic, metagenomic, genomic, and experimental approaches, we demonstrate that DRT11 functions as a bona fide antiviral defense module, providing protection against naturally occurring rhizosphere phages through a minimal reverse transcriptase-nitrilase architecture. This work establishes direct functional evidence for antiviral activity within the UG5 family and clarifies the evolutionary placement of UG5-associated systems within the broader UG radiation.}, }
@article {pmid42429609, year = {2026}, author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA}, title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0002726}, doi = {10.1128/msphere.00027-26}, pmid = {42429609}, issn = {2379-5042}, abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS vaginal carriage is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokines at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences, with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to eight pro-inflammatory cytokines post-GBS infection. Diabetic mice exhibited decreased proportions of uterine neutrophils and, following GBS exposure, also displayed an expanded vaginal γδ T cell compartment compared with controls. Pairing cytokine observations with GBS colonization revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS phenotypes. Intravaginal supplementation with rIL-1α resolved GBS burden differences between diabetic mice and controls, confirming that deficient vaginal cytokines contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention.IMPORTANCEPeople with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances the colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes in the vaginal microbiome but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.}, }
@article {pmid42429615, year = {2026}, author = {Jiang, K and Xiong, F and Peng, Y and Meng, L and Wang, X and Xu, Y and Tang, T and Gao, H}, title = {Intermittent Fasting Restores Cardiac Lipid Homeostasis in Diabetic Cardiomyopathy in Association With Akkermansia Muciniphila and 1-methyl-L-histidine.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76528}, doi = {10.1002/advs.76528}, pmid = {42429615}, issn = {2198-3844}, support = {22274115//National Natural Science Foundation of China/ ; 21974096//National Natural Science Foundation of China/ ; LZ26C010002//Zhejiang Provincial Natural Science Foundation of China/ ; LQN26C010004//Zhejiang Provincial Natural Science Foundation of China/ ; }, abstract = {Diabetic cardiomyopathy (DCM) is a major cardiovascular complication of diabetes with limited effective interventions. Using a streptozotocin-induced insulin-deficient, type 1 diabetes-like DCM mouse model, we show that intermittent fasting (IF) improves cardiac function and attenuates myocardial remodeling. Antibiotic-mediated microbiota depletion largely abolished these benefits, whereas fecal microbiota transplantation from IF-treated donors recapitulated cardioprotection, supporting a causal role of the gut microbiota. Metagenomic profiling identified Akkermansia muciniphila (A. muciniphila) as a prominent IF-responsive taxon, and A. muciniphila supplementation alleviated cardiac injury without obvious improvement in glycaemia. Integrated serum and heart metabolomics identified 1-methyl-L-histidine as a microbiota-associated metabolite reduced in diabetes but restored by IF and A. muciniphila. In vitro and ex vivo assays further supported an L-anserine-linked microbial route for 1-methyl-L-histidine generation. Importantly, oral 1-methyl-L-histidine supplementation recapitulated key cardioprotective effects, remodeled cardiac lipid homeostasis, and reduced lipid peroxidation and oxidative injury. Together, these findings support a gut microbiota-metabolite-lipid axis associated with IF-related cardioprotection in DCM and highlight microbial metabolites as tractable targets to complement dietary intervention.}, }
@article {pmid42429677, year = {2026}, author = {Sarkar, M and Maddheshiya, A and Tailor, P and Nath, S and Makkar, N and ,  and Misra, S and Desiraju, BK and Wadhwa, N and Bhatnagar, S and Kshetrapal, P and Mukherjee, S}, title = {Longitudinal shifts in oral microbiome composition and metabolic pathways associated with preterm birth.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0018426}, doi = {10.1128/msystems.00184-26}, pmid = {42429677}, issn = {2379-5077}, abstract = {Oral dysbiosis in pregnant women with oral diseases has been associated with adverse pregnancy outcomes. However, the inter-individual variability in oral microbiome composition of pregnant women without any oral disease, and its role in preterm birth, has not been studied yet. Here, we have collected saliva from 20 term birth (TB) and 20 preterm birth (PTB) delivering women without any self-reported oral disease at three trimesters (n = 120). Microbial DNA was subjected to 16S rRNA gene sequencing for taxonomic classification, and microbial pathways were investigated by PICRUSt2. In a subset of samples, shotgun metagenomic sequencing was done to identify microbial species, their gene families, and their pathways. TB and PTB women were distributed into three distinct oral community types (OCTs). Haemophilus parainfluenzae and Rothia mucilaginosa were associated with TB and PTB, respectively. The chorismate biosynthesis pathway, essential for folic acid biosynthesis, was significantly enriched in TB, whereas the enterobactin biosynthesis pathway that produces iron chelators (siderophores) was significantly enriched in PTB. The heterolactic fermentation pathway that reduces oral pH was enriched in PTB. Our data suggest that oral microbiome changes might have an impact on birth outcomes in women even without any history of self-reported oral disease during the pregnancy period.IMPORTANCEThe importance of this study lies in demonstrating that compositional and functional shifts in the oral microbiome are associated with pregnancy outcomes. Using a longitudinal design across three trimesters in an Indian cohort, we show that pregnant women segregate into distinct oral community types with consistent associations to term birth (TB) and preterm birth (PTB). Importantly, the TB-associated microbiome was enriched in taxa and pathways linked to vitamin and amino acid biosynthesis, including chorismate and threonine metabolism, which are critical for fetal growth. In contrast, PTB was associated with pathways related to iron scavenging and acidification of the oral environment, suggesting a metabolically stressed and dysbiotic state. These findings highlight the oral microbiome as a previously underappreciated, modifiable factor in pregnancy outcomes and underscore its potential relevance for early risk stratification and preventive strategies against PTB.}, }
@article {pmid42429741, year = {2026}, author = {Koraimann, G and Hölzl, N and Koller, M and Zarfel, G and Treiber, F}, title = {A complete Candidatus walczuchella monophlebidarum genome assembled from citrus leaf metagenomic sequences.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0062026}, doi = {10.1128/mra.00620-26}, pmid = {42429741}, issn = {2576-098X}, abstract = {We present the complete de novo assembly of a Candidatus Walczuchella monophlebidarum genome (286,606 bp), a flavobacterial endosymbiont of the giant-scale insect Icerya purchasi. The genome was assembled from metagenomic short read Illumina sequences obtained from DNA of citrus leaves collected in Carinthia, Austria in November 2024.}, }
@article {pmid42429749, year = {2026}, author = {Cluett, H and Chandler, JC and Bisha, B}, title = {A coding-complete genome sequence of bovine-like coronavirus identified in white-tailed deer (Odocoileus virginianus) in the United States.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0050026}, doi = {10.1128/mra.00500-26}, pmid = {42429749}, issn = {2576-098X}, abstract = {Bovine coronavirus within the Embecovirus subgenus causes respiratory and enteric diseases in domestic cattle. We report a coding-complete genome of bovine-like coronavirus from a white-tailed deer (Odocoileus virginianus) in New Jersey, USA. This genome is 30,988 bp with a guanine-cytosine content of 37%.}, }
@article {pmid42429762, year = {2026}, author = {Putman, T and Abdel-Hamid, AM and Galbraith, E and Schimmel, P and Kim, H and Yasuma, T and Alhawsawi, MAB and Boateng, KA and Holmes, J and Duersteler, M and D'Alessandro-Gabazza, CN and Fujimoto, H and Kobayashi, T and Walden, KKO and Rendon, G and Fields, CJ and Zuckermann, FA and Mackie, RI and Son, S and Leistikow, KR and Gabazza, EC and King, MR and Cann, I}, title = {A Bacillus-based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella-infected pigs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0097226}, doi = {10.1128/aem.00972-26}, pmid = {42429762}, issn = {1098-5336}, abstract = {Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus-based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella-infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella-only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella-only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health.IMPORTANCEAntibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus, as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella-infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus-based DFM could improve outcomes along the gut-lung axis under realistic co-infection conditions.}, }
@article {pmid42429885, year = {2026}, author = {Delik, A and Ülger, Y and Albayrak, F and Orhan, U and Unal, U and Gov, E and Dinçer, S}, title = {Machine learning integration of tissue-specific metagenomic signatures for colorectal cancer diagnosis.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, pmid = {42429885}, issn = {2190-3883}, abstract = {Colorectal cancer (CRC) represents a significant global health burden. Leveraging machine learning (ML) with metagenomic and tissue-specific data presents new opportunities for improving diagnostic accuracy and understanding the microbiome's role in CRC. This study was conducted to enhance diagnostic efficiency and identify crucial bacterial biomarkers in CRC using various ML models applied to metagenomic data. A total of 33 samples were analyzed, comprising 20 healthy controls and 13 CRC patients. Each sample included demographic data (age, gender) and bacterial information (Bacteroides, Enterococcus, Faecalibacterium, Proteobacteria, Gammaproteobacteria, Firmicutes, Enterobacteriaceae, Clostridia). Six models: Logistic Regression, Naive Bayes, Decision Tree, Support Vector Machine (SVM) with both linear and polynomial kernels and Multilayer Perceptron (MLP) were employed. Performance was evaluated using leave-one-out cross-validation (LOOCV). To address the class imbalance, F1-score was utilized as the primary metric for feature selection. A consensus-based feature elimination strategy, where bacterial features were iteratively removed only if their exclusion improved or maintained the F1-score across the majority of the models was implemented. For the MLP, a grid search was integrated into each iteration to optimize hidden layer architectures and solvers, thereby ensuring that robust performance was achieved for each feature subset. The analysis was conducted using a 10-feature initial set consisting of 2 demographic and 8 microbial features. Model performances were optimized through a consensus-based feature elimination strategy, and it was determined that diagnostic success increased with the exclusion of the Faecalibacterium, Age, and Enterobacteriaceae features during the process. The highest performance was achieved with the SVM model with Linear kernel when Bacteroides was excluded from the 9-feature subset (Table 4), reaching an accuracy of 87.88% and an F1-score of 83.33%. Within the final biomarker set, Enterococcus and Firmicutes were identified as the most critical predictive features due to the sharpest declines in F1-score observed in their absence. This study demonstrates that the systematic elimination of initial clinical and metagenomic features maximizes CRC diagnostic accuracy and model stability. The process, initiated with a 10-feature baseline set was subsequently refined to establish a high-precision diagnostic mechanism with an F1-score of 83.33%. The identified final microbial signatures, consisting of 5-6 taxa, provide a clinically applicable, non-invasive diagnostic foundation with low input requirements.}, }
@article {pmid42429927, year = {2026}, author = {Lirio, CPT and Albino, EED and Nisnisan, KKS and Castro, AE}, title = {Gut bacterial community profile of the endemic catfish Arius manillensis from Pasig River, Philippines.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0037026}, doi = {10.1128/mra.00370-26}, pmid = {42429927}, issn = {2576-098X}, abstract = {The Pasig River is a highly urbanized waterway, yet the microbial ecology of its native fauna remains poorly understood. This study provides the first report of the gut bacterial community of the catfish Arius manillensis, revealing bacterial taxa and underscoring the need to study host-associated microbiomes in urban aquatic ecosystems.}, }
@article {pmid42430134, year = {2026}, author = {Laureano, G and Lal, V and Mitchell, L and Santillan Olea, E and Tovar, J and Scoles, A and Arun, A}, title = {Meta-genome assembled genome of Agrobacterium oryzihabitans associated with the cultivated yellow-green alga Vaucheria bursata.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0047325}, doi = {10.1128/mra.00473-25}, pmid = {42430134}, issn = {2576-098X}, abstract = {We report a draft metagenome-assembled genome (MAG) of an Agrobacterium species from Vaucheria bursata. The MAG is 89% complete (CheckM2 v1.1.0) with 3,281 predicted genes, providing a basis to explore bacteria-algae interactions and their role in the Vaucheria microbiome.}, }
@article {pmid42430136, year = {2026}, author = {Aoki, M and Wakui, N and Hayashi, K and Syutsubo, K}, title = {High-quality metagenome-assembled genome sequences of Bacteroidota and Pseudomonadota bacteria, assembled from a manganese(II)-oxidizing biofilm reactor.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0058826}, doi = {10.1128/mra.00588-26}, pmid = {42430136}, issn = {2576-098X}, abstract = {We report five high-quality, potentially novel metagenome-assembled genomes (MAGs) recovered from a manganese(II)-oxidizing biofilm reactor. Affiliated with Bacteroidota and Pseudomonadota, these MAGs provide a genomic basis for understanding the ecology and metabolic potential of Mn(II)-oxidizing systems and represent a valuable resource for future functional studies of biofilm-mediated metal cycling.}, }
@article {pmid42419832, year = {2026}, author = {Chaurasia, A and Ponangi, K}, title = {The microbiome of the head and neck region.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {25-51}, doi = {10.1016/bs.ai.2026.03.002}, pmid = {42419832}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; }, abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.}, }
@article {pmid42419833, year = {2026}, author = {Jams, J and Jayasinghe, RD}, title = {Introduction.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {3-23}, doi = {10.1016/bs.ai.2026.03.005}, pmid = {42419833}, issn = {1557-8445}, mesh = {Humans ; *Microbiota ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Biofilms ; Animals ; *Head and Neck Neoplasms/microbiology/etiology/immunology ; Host Microbial Interactions ; Host-Pathogen Interactions ; }, abstract = {Microorganisms colonize nearly all anatomical sites of the human body, with the oral cavity hosting one of the most diverse, accessible, and densely populated microbial ecosystems. The oral microbiome comprises a complex consortium of bacteria, fungi, viruses, archaea, and protozoa that inhabit distinct ecological niches. Each niche provides unique physicochemical conditions that shape microbial composition, structure, and function. In addition to oral and dental sites, oral biofilms frequently develop on dental materials, appliances, and prostheses, where surface characteristics such as roughness, hydrophobicity, and chemical composition further influence microbial adhesion and biofilm maturation, leading to marked differences at species and strain levels. Advances in culture-independent molecular technologies, particularly 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics approaches, have greatly enhanced understanding of oral microbial diversity, functional capacity, and host-microbe interactions beyond the limitations of conventional culture-based methods. In health, the oral microbiome exists in a state of dynamic equilibrium, or eubiosis, which contributes to local and systemic homeostasis. This balance is modulated by host factors such as saliva composition, immune responses, and oral hygiene practices, as well as environmental influences including diet, tobacco use, and alcohol consumption. Disruption of this equilibrium, termed dysbiosis, has been increasingly implicated in the pathogenesis of head and neck cancers. Emerging evidence suggests that microbial dysbiosis may promote carcinogenesis through chronic inflammation, immune modulation, production of carcinogenic metabolites, and direct interactions with epithelial cells. Understanding the microbiology of head and neck cancer therefore provides critical insights into disease initiation, progression, and potential diagnostic and therapeutic strategies.}, }
@article {pmid42420265, year = {2026}, author = {Vilar Geraldi, M and Dwibedi, C and Jaiswal, R and Gregori, G and Zhou, X and Lv, B and Zheng, Y and Wang, X and Wu, H and Axelsson, KF and Bäckhed, F and Tremaroli, V and Lorentzon, M}, title = {Gut microbiota associates with frailty in older women.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42420265}, issn = {2041-1723}, support = {2023-01976, 2023-01976, 2022-06725, 2018-05973, 2024-03723,//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Lorentzon, 2023-2024//Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse (King Gustaf V and Queen Victoria's Foundation of Freemasons)/ ; 2024-0104//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; Lorentzon, 2016//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, mesh = {Humans ; Female ; Aged ; *Frailty/microbiology/mortality ; Aged, 80 and over ; *Gastrointestinal Microbiome/genetics/physiology ; Sweden/epidemiology ; Frail Elderly ; Bacteria/classification/genetics/isolation &amp; purification ; Cohort Studies ; }, abstract = {Frailty is a multifactorial geriatric condition linked to increased mortality and adverse health outcomes and is associated with gut microbiome features that differ from those observed in healthy ageing. We analyze gut metagenomic profiles in relation to estimated frailty severity and frailty-related clinical outcomes assessed with an internally developed and validated Frailty Mortality Index (FMI) in the SUPERB cohort, comprising 2,081 Swedish women aged 75-80 years. The FMI is a composite measure that integrates functional, physiological and psychological dimensions associated with frailty and mortality risk, and shows stronger associations with mortality compared to the Charlson Comorbidity Index in the SUPERB cohort. The FMI is inversely associated with microbial diversity, gene richness, and predicted functional capacity, which are linked to physical function, mortality and fall-related injuries. A total of 404 bacterial species are significantly associated with FMI, and most show concordant associations in a Chinese cohort of 1,448 older adults. Here we show microbial signatures linked to frailty and mortality across different continents.}, }
@article {pmid42420666, year = {2026}, author = {Ounjai, S and Liu, H and Zhou, Z and Correia, MP and Creedy, TJ and Andújar, C and Arribas, P and Vogler, AP}, title = {Phylogenetic Authentication of Amplicon Sequence Variants in Single-Specimen Metabarcoding of Tropical Insects.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70178}, doi = {10.1111/1755-0998.70178}, pmid = {42420666}, issn = {1755-0998}, support = {//Institute for the Promotion of Teaching Science and Technology/ ; //Biodiversity Initiative of the Natural History Museum/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods/standards ; *Phylogeny ; *Coleoptera/classification/genetics ; Tropical Climate ; *Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA ; Genetic Variation ; DNA, Mitochondrial/genetics ; }, abstract = {High-throughput sequencing (HTS) allows large-scale DNA barcoding of individually tagged specimens ('megabarcoding'), but deep amplicon sequencing produces a mixture of authentic mitochondrial sequences together with nuclear pseudogenes (NUMTs), environmental and cross-sample contaminants, and sequencing artefacts. Standard approaches relying on read clustering or dominant-read selection often fail to classify these types, leading to incorrect taxonomic identifications and species counts. We developed an authentication framework by integrating abundance filtering, phylogenetic placement and taxonomic congruence. The workflow was applied to 18,533 morphospecies of tropical beetles (Coleoptera) from multiple biogeographic regions, which were imaged for family-level identification, prior to individual Illumina barcoding. Sequencing yielded > 36 million reads and 64,544 unique ASVs, which were evaluated against a reference phylogeny of > 13,000 mitogenomes. Authentication succeeded for 86.5% of quality-passing specimens (15,901 ASVs). Non-authentic sequences were technical artefacts (58.0%), environmental contamination including prey DNA (14.2%), intra-individual variants (NUMTs, heteroplasmy; 11.3%) and cross-sample contamination (7.5%). Authentication success and the proportions of failure categories varied markedly across trap types, sampling campaigns, taxonomic groups and sequencing runs. We identified 930 confirmed NUMTs based on consistent co-occurrence patterns and phylogenetic proximity to authenticated haplotypes. Single-specimen HTS data contain substantial biological and technical complexity not resolved by standard filtering methods. Our pipeline-agnostic, phylogenetically informed authentication framework achieves robust recovery of validated barcodes while retaining informative secondary variants, improving the accuracy of molecular ASV data to a standard sufficient for inclusion in barcode reference databases and the phylogenetically informed DNA barcoding of tropical insects.}, }
@article {pmid42420833, year = {2026}, author = {Luo, D and Lu, F and Yang, L and Gan, Z and Zhang, X and Zhao, Z and Dong, R}, title = {Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-13161-4}, pmid = {42420833}, issn = {1471-2164}, support = {GZSTYYCYJSTX-202605//Guizhou Modern Agricultural Industry Technology System of China/ ; 2024 (No. 079//the Guizhou Provincial Key Technology R&amp;D Program/ ; 32460918//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed.<br><br>RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT&#x2012;qPCR and ELISA.<br><br>CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.}, }
@article {pmid42421628, year = {2026}, author = {Chen, X and Jamieson, L and Weyrich, LS and Nath, S}, title = {Global Landscape of Publicly Available Human Oral Microbiome Data.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345261456612}, doi = {10.1177/00220345261456612}, pmid = {42421628}, issn = {1544-0591}, abstract = {Despite rapid growth in oral microbiome research, it remains unclear how well publicly available data reflect the diversity of the global human population. This study systematically evaluated the geographic and sampling-type representativeness of publicly available human oral microbiome data. A global meta-research analysis of publicly available human oral microbiome records in the NCBI BioSample database released up to December 31, 2025, was conducted. Records were retrieved, harmonized, and analyzed across 4 dimensions: geographic origin, oral sampling type, temporal trends, and population-adjusted representation using a derived representation index (RI). A total of 222,454 BioSamples from 1,600 studies were identified, spanning 92 countries and 4 major oral sampling-type groups: oral fluids, oral mucosa and surfaces, dental plaque and calculus, and special or lesion-associated sites. Geographic distribution was highly concentrated; nearly half of all geographically annotated samples originated from the United States and China, while 61% of countries worldwide contributed no samples. Low- and middle-income regions, including Central and Southern Asia (RI = -12.76) and Sub-Saharan Africa (RI = -11.21), were underrepresented relative to their population sizes. Sampling-type distribution was similarly uneven, with saliva samples comprising more than half of all samples. In contrast, disease-relevant sites, including carious lesions, periapical lesions, and the dental pulp, each represented less than 0.2% of the dataset. Together, these findings underscore that publicly available human oral microbiome data remain unevenly distributed across geographic origin and sampling types, reflecting structural and practical factors that have persisted over time. Deliberate efforts to improve global representation, sampling diversity, and metadata standardization are needed to build a more scientifically robust oral microbiome evidence base.}, }
@article {pmid42421935, year = {2026}, author = {Memida, T and Jaar, JC and Chen, T and Cao, G and Kuriki, N and Abdolahinia, ED and Okamoto, M and Shindo, S and Yamashita, S and He, X and Suzuki, M and Vardar, S and Kawai, T and Han, X}, title = {Hyperglycemia and systemic inflammation differentially shape immune dysregulation, tissue destruction, and microbiota in experimental periodontitis and peri-implantitis in diabetic mice.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847456}, pmid = {42421935}, issn = {1664-3224}, mesh = {Animals ; *Peri-Implantitis/immunology/microbiology/pathology/etiology ; *Periodontitis/immunology/microbiology/pathology/etiology ; Mice ; *Hyperglycemia/immunology/microbiology ; *Microbiota/immunology ; *Diabetes Mellitus, Experimental/immunology/complications/microbiology ; *Inflammation/immunology ; Disease Models, Animal ; Cytokines/metabolism ; Male ; }, abstract = {AIM: To investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.<br><br>MATERIALS AND METHODS: After implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.<br><br>RESULTS: Liraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3[+] Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.<br><br>CONCLUSIONS: Diabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.}, }
@article {pmid42421950, year = {2026}, author = {Lu, W and Wang, Y and Zhang, J and Li, Y and Huang, L and Yang, W and Zhou, S and Zhou, M and Chen, Y and Wu, R and Wang, Y and Zhang, H and Wan, J and Xia, F and Zhang, Z and Shen, L}, title = {Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1871586}, pmid = {42421950}, issn = {1664-3224}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immunotherapy/adverse effects/methods ; *Metabolome ; Metabolomics ; Multiomics ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/metabolism/microbiology/immunology ; Treatment Outcome ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Immunotherapy-based total neoadjuvant therapy (iTNT) is a promising strategy for microsatellite-stable locally advanced rectal cancer (LARC), yet therapeutic response and treatment-related toxicity remain heterogeneous. Integrated fecal microbiome and metabolome profiling may provide non-invasive biomarkers and functional clues for optimizing iTNT.<br><br>METHODS: We conducted a longitudinal fecal multi-omics study using samples from patients with microsatellite-stable LARC enrolled in the TORCH trial (NCT04518280). A total of 102 fecal samples were collected before treatment, during treatment, and after completion of iTNT. Metagenomic sequencing and untargeted metabolomics were integrated to characterize longitudinal microbial and metabolic changes. We also examined baseline features associated with therapeutic response, and multi-omics signatures linked to hematologic and gastrointestinal toxicities. A murine tumor model treated with radiotherapy plus immunotherapy, with or without GABA supplementation, was used for functional testing of the response-associated metabolite.<br><br>RESULTS: iTNT induced longitudinal gut microbiome remodeling. This remodeling was characterized by altered community structure, increased alpha diversity, enhanced microbial network connectivity, enrichment of Firmicutes-associated taxa, and depletion of Bacteroidetes and Proteobacteria. Fecal metabolomic profiles also shifted during treatment, with prominent changes in amino acid-related pathways and significant concordance between microbial and metabolic profiles. Responders were enriched in several Firmicutes-associated genera, including Ruminococcus, Anaerostipes, and Coprobacillus. In contrast, non-responders showed enrichment of Klebsiella and response-associated metabolites including gamma-aminobutyric acid (GABA). Microbial functional and metabolomic pathway analyses showed convergent enrichment of arginine and proline metabolism, which includes an alternative GABA-related metabolic route. Functionally, GABA supplementation weakened the antitumor efficacy of radiotherapy plus immunotherapy and was accompanied by systemic T cell dysfunction. In addition, specific microbial taxa and fecal metabolic features were associated with hematologic toxicity and diarrhea severity, with baseline metabolites showing exploratory potential for toxicity stratification.<br><br>CONCLUSION: This study provides a longitudinal fecal microbiome-metabolome resource for iTNT in LARC and identifies candidate microbial and metabolic features associated with treatment response and toxicity. GABA was functionally supported as a response-associated immunomodulatory metabolite, while candidate microbial functional signals warrant further mechanistic validation.}, }
@article {pmid42422444, year = {2026}, author = {Lu, T and Sun, S and Teng, T and Zhang, J and Cao, Q and Ren, H}, title = {Bartonella henselae mediastinal lymphadenitis mimicking malignancy with critical airway compression in a child: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1871232}, pmid = {42422444}, issn = {2296-2360}, abstract = {Cat-scratch disease, caused by Bartonella henselae, is usually a self-limited infection presenting with regional lymphadenopathy in children. Thoracic involvement is uncommon, and mediastinal lymphadenitis with clinically significant airway compression may closely mimic malignancy. We report a previously healthy 6-year-old boy who presented with persistent fever, mild cough, weight loss, and cervical lymphadenopathy. Chest computed tomography revealed necrotic mediastinal lymphadenopathy forming a mass-like lesion with compression of the right middle lobe bronchus and associated atelectasis. Bronchoscopy showed severe bronchomalacia with approximately 90% luminal narrowing, despite only mild respiratory symptoms. Initial antimicrobial therapy failed to improve the clinical or radiologic abnormalities. Because of constitutional symptoms and a necrotic mediastinal mass, lymphoma was strongly suspected; however, bone marrow examination was unrevealing. During biopsy of the mediastinal lesion, purulent material was encountered. Histopathology demonstrated necrotizing granulomatous inflammation, and metagenomic next-generation sequencing identified Bartonella henselae, establishing the diagnosis of cat-scratch disease. Treatment with doxycycline and rifampin led to prompt resolution of fever and marked radiologic improvement, with substantial relief of airway compression. This case highlights that Bartonella henselae infection can present as a necrotic mediastinal mass with severe but reversible airway compression in children. Cat-scratch disease should be considered in the differential diagnosis of pediatric mediastinal masses, particularly when inflammatory features, cat exposure, and discordant respiratory symptoms are present. Integration of imaging, bronchoscopy, pathology, and molecular testing may prevent misdiagnosis as malignancy and underestimation of airway risk.}, }
@article {pmid42422454, year = {2026}, author = {Wang, X and Zhang, Y and Ye, M and Kong, C and Diao, M}, title = {Clinical and stool microbiome correlates of simple post-ERCP hyperamylasemia in children undergoing therapeutic ERCP for pancreatobiliary obstructive disorders: an exploratory pilot study.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1851821}, pmid = {42422454}, issn = {2296-2360}, abstract = {BACKGROUND: Simple post-ERCP hyperamylasemia is a common biochemical finding after therapeutic endoscopic retrograde cholangiopancreatography (ERCP), but pediatric data integrating procedural characteristics with stool microbiome features remain limited.<br><br>METHODS: We performed an exploratory single-center observational pilot study of 24 successful therapeutic ERCP procedures in children younger than 18 years with pancreatobiliary obstructive disorders between January 2024 and December 2025. The primary endpoint was simple post-ERCP hyperamylasemia, defined as serum amylase >3 times the upper limit of normal within 24&#x2005;h after ERCP without new or worsening abdominal pain. Baseline clinical variables, predefined stool microbiome features derived from pre-ERCP metagenomic data (Shannon diversity, Enterococcus abundance, and Bifidobacterium abundance), and intraprocedural variables were compared between groups. Exploratory signal prioritization was used only to identify candidate associations for future validation.<br><br>RESULTS: Hyperamylasemia occurred in 8/24 procedures (33.3%). Compared with non- hyperamylasemia group, the affected children had higher baseline gamma-glutamyl transferase and C-reactive protein, longer procedure time, more difficult cannulation, more inadvertent pancreatic duct cannulation, more pancreatic contrast injection, and more rescue precut access. Stool microbiome features in the hyperamylasemia group included lower Shannon diversity, higher Enterococcus abundance, and lower Bifidobacterium abundance. Procedure time and Shannon diversity emerged as the most interpretable combined signals, but all model estimates should be viewed cautiously because of the small event count.<br><br>CONCLUSION: In this pilot dataset, simple post-ERCP hyperamylasemia clustered with technically demanding procedures and a low-diversity, Enterococcus-enriched stool microbiome profile. These findings are hypothesis-generating and require prospective multicenter validation before they can inform pediatric ERCP surveillance or risk-stratification research.}, }
@article {pmid42422751, year = {2026}, author = {Wang, H and Han, Y and Chen, C and Chen, K and Zhang, Y and Wang, Z and Qi, L}, title = {Moisture-mediated resource availability shapes rhizosphere and bulk soil microbial structure and function post-rainfall.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1752099}, pmid = {42422751}, issn = {1664-302X}, abstract = {INTRODUCTION: Rainfall pulses drive rapid ecological changes in alpine grasslands, but their compartment-specific effects on short-term soil microbial dynamics remain unclear.<br><br>METHODS: We investigated the structural and functional responses of rhizosphere versus bulk soil microbiomes associated with Poa alpigena in the Qinghai Lake Basin. Paired soil samples were collected before rainfall and 2 h after a heavy rainfall event and analyzed by shotgun metagenomic DNA sequencing.<br><br>RESULTS: Rainfall triggered compartment-specific shifts in microbial community assembly. In the rhizosphere, rainfall significantly reduced alpha diversity (Chao1 and Richness indices) but enhanced community evenness (Simpson and Shannon indices), whereas bulk soil diversity remained relatively stable. DNA-based functional profiling revealed a short-term shift in the rhizosphere from a pre-rain "carbon-oriented" metabolic potential to increased relative abundance of genes involved in central carbon pathways, amino acid degradation, and chemotaxis post-rainfall. Notably, sequences affiliated with Paraburkholderia were significantly enriched in the nitrogen-limited rhizosphere immediately after rainfall, suggesting a potential link to nitrogen cycling. In contrast, bulk soil communities shifted toward gene categories for labile carbon utilization and bacterial secretion systems. Co-occurrence network analysis indicated that rainfall simplified microbial interactions and weakened the coupling between microbial communities and soil physicochemical properties.<br><br>DISCUSSION: These findings demonstrate that rainfall pulses trigger rapid, niche-dependent changes in soil microbiomes at the DNA level, driven by moisture-mediated shifts in resource availability, and highlight distinct ecological strategies in rhizosphere and bulk soil compartments.}, }
@article {pmid42422832, year = {2026}, author = {Wang, H and Zhu, Y and Cheng, AX and Zhang, C}, title = {Acute retinal necrosis presenting exudative retinal detachment: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1746774}, pmid = {42422832}, issn = {2296-858X}, abstract = {BACKGROUND: Acute retinal necrosis (ARN) is a severe, rapidly progressive viral retinitis that is commonly complicated by rhegmatogenous retinal detachment in its late stage. However, the presentation of ARN with exudative retinal detachment (ERD) in the early phase is exceptionally rare, particularly when caused by varicella zoster virus (VZV) in an adult patient. This report highlights this atypical presentation, which initially occurred without definite evidence of retinal necrosis, posing a diagnostic challenge.<br><br>CASE PRESENTATION: A 43-year-old woman presented with acute blurred vision, eye redness, and ocular pain in the left eye of 3&#x202f;days' duration. Initial clinical examination revealed ciliary congestion, vitritis, optic disc swelling, and a non-rhegmatogenous retinal detachment. Optical coherence tomography demonstrated optic disc and macular edema with intraretinal cystic spaces and a serous retinal detachment temporal to the fovea. Given the atypical presentation, the patient was initially treated with corticosteroids. Two days later, characteristic peripheral retinal necrotic lesions appeared, prompting immediate aqueous humor sampling. Metagenomic testing confirmed VZV infection. The patient was then treated aggressively with systemic intravenous acyclovir, intravitreal ganciclovir injections, and systemic corticosteroids. This regimen led to rapid resolution of the retinal detachment and complete resolution of the retinal lesions, with stable visual acuity maintained at 1&#x202f;month of follow-up.<br><br>CONCLUSION: Exudative retinal detachment is a rare manifestation of early-stage ARN. In uveitis patients presenting with ERD who show a poor response to initial anti-inflammatory therapy, viral infection (particularly VZV) should be considered in the differential diagnosis. Aggressive combined systemic and intravitreal antiviral therapy, alongside corticosteroids, is critical for achieving favorable anatomical and visual outcomes in these challenging cases.}, }
@article {pmid42422873, year = {2026}, author = {Pithia, N and Kesavan, K and Lee, A and Yang, S and Kaur, I}, title = {Clinical impact of plasma cell-free DNA metagenomic next-generation sequencing testing in neonatal and infant populations.}, journal = {Antimicrobial stewardship &amp; healthcare epidemiology : ASHE}, volume = {6}, number = {1}, pages = {e201}, pmid = {42422873}, issn = {2732-494X}, abstract = {OBJECTIVE: Plasma cell-free DNA metagenomic next-generation sequencing (cf-mNGS) tests offer the ability to detect microbial DNA from a single blood sample; however, its clinical utility in infants remains incompletely characterized. This study aims to evaluate the real-world clinical impact of plasma cf-mNGS testing in the neonatal and infant population.<br><br>DESIGN: Retrospective cohort study.<br><br>SETTING: A large academic medical center in Los Angeles, California.<br><br>PATIENTS: 95 hospitalized neonates and infants (&#x2264;12 months of age).<br><br>METHODS: Clinical impact was adjudicated using predefined criteria.<br><br>RESULTS: We reviewed 95 unique plasma cf-mNGS testing episodes performed between February 2018 and August 2024. The mean age at testing was 4.2 months (SD, 3.8). All patients were hospitalized in the intensive care unit at the time of testing. Tests were most frequently performed for evaluation of "culture-negative sepsis" (30.5%), unexplained hospital-onset fevers (25.3%), and multiorgan failure (21.1%). Plasma cf-mNGS testing did not influence clinical management in the majority of cases (86.3%; 95% CI, 78.0%-91.8%). Positive clinical impact occurred in 5/95 cases (5.3%; 95% CI, 2.3%-11.7%), where plasma mNGS results assisting in antimicrobial de-escalation/discontinuation or earlier/new diagnoses. Negative clinical impact occurred in 4/95 cases (4.2%; 95% CI, 1.6%-10.3%), with plasma cf-mNGS results prompting unnecessary investigations or treatment.<br><br>CONCLUSIONS: Our findings do not support the routine use of plasma cf-mNGS testing for indications including "culture-negative sepsis" in neonatal and infant populations.}, }
@article {pmid42423254, year = {2026}, author = {Irshad, F and Nazir, A}, title = {Metagenomic exploration of indigenous bacteria with their bioaugmentation for enhanced phytobial remediation of tannery effluent with Lemna minor.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/15226514.2026.2698048}, pmid = {42423254}, issn = {1549-7879}, abstract = {Despite the toxic and persistent nature of tannery effluent (TE), limited research studies have evaluated Lemna minor-based phytobial remediation in real TE. The current study aimed at TE remediation using L. minor with the assistance of indigenous heavy metals (HMs) tolerant bacterial strains. Five coded TE indigenous bacterial strains (S1WC4, S2WC3, S2WC2, S3WC1 and S1WC2), isolated from TE samples were applied in combination with L. minor for treatment of TE dilutions (2%, 5%, 10% and 15%), while pond water (PW) treatments were used as a control. The bacterial community was also profiled through 16S rRNA metagenomic amplicon sequencing. Results showed that treatments aided by consortia demonstrated higher efficiencies for metal removal, i.e., Pb removal ∼80-95%, Cr removal ∼80-90%, Cu removal ∼55-83%, Cd removal ∼70-85%. The consortia treatments also enhanced bioaccumulation factors (e.g.,BAF up to 18.4 for Pb and 8.2 for Cr in 5% TE), with higher biomass and SPAD values compared to control treatments. The TE bacterial community was dominated by stress tolerant bacterial taxa, and the ecological importance of these taxa was evaluated with PICRUSt2-analysis, predicting pathways associated with community survival under HMs stress conditions. Biologically driven removal was confirmed in logistic modeling that showed time-dependent HMs removal. Results of the study, therefore, conclude that bioaugmentation had a significant effect on the performance of the remediation system when compared with control treatments (plant-only treatments).}, }
@article {pmid42423734, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {Upper Respiratory Tract Resistome Exhibits SARS-CoV-2-associated Antimicrobial Resistance Patterns.}, journal = {Current microbiology}, volume = {83}, number = {9}, pages = {}, pmid = {42423734}, issn = {1432-0991}, mesh = {Humans ; *SARS-CoV-2/drug effects/genetics/isolation &amp; purification ; *COVID-19/virology/microbiology ; India ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects ; }, abstract = {SARS-CoV-2 infection can influence the antimicrobial resistance (AMR) profiles of the upper respiratory tract (URT), although the extent and nature of these alterations remain insufficiently understood. In this study, we analysed 95 URT swab samples, including 48 SARS-CoV-2-positive cases and 47 RT-PCR-negative controls, collected from five districts of central India. Metagenomic DNA sequencing was performed on the Illumina NextSeq 550 platform, and the data were analysed using the Chan Zuckerberg Initiative (CZ ID) pipeline. Alpha diversity indices (Chao1, Shannon, and Simpson) did not differ significantly (p = 0.264, 0.985, and 0.902, respectively). Beta-diversity analysis revealed distinct clustering of SARS-CoV-2 and control resistomes. Differential resistome analysis identified 22 significantly altered AMR genes, of which 21 were enriched in the SARS-CoV-2 group. Pathogen-of-origin analysis linked several AMR genes to opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. Bayesian regression analysis identified SARS-CoV-2 infection as a significant factor associated with increased AMR abundance (β = 1.549, HDI [1.409, 1.691]), whereas age and location were not significantly associated. Results demonstrate an association between SARS-CoV-2 infection and alterations in the URT resistome, warranting further investigation into the mechanisms linking viral infection and antimicrobial resistance.}, }
@article {pmid42423979, year = {2026}, author = {Hu, C and Zeng, X and Wu, X and Yan, D and Yuan, J and Qu, L and Dou, M and Yang, Y}, title = {Mechanistic insights into iron cycling-driven nitrogen removal from biogas slurry via coupled iron-based denitrification and Feammox.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {10}, pages = {}, pmid = {42423979}, issn = {1573-2983}, support = {52300222//National Natural Science Foundation of China/ ; 221100320200//Key Science and Technology Project of Henan Province/ ; 242300421224//Natural Science Foundation of Henan Province/ ; 25A610006//Applied Research Plan of Key Scientific Research Projects in Colleges and Universities of Henan Province/ ; }, mesh = {*Denitrification ; *Nitrogen/metabolism/isolation &amp; purification ; *Biofuels ; *Iron/metabolism/chemistry ; Bioreactors/microbiology ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; Ferrous Compounds/metabolism ; }, abstract = {In this study, ferrous-based denitrification was combined with Feammox (Fe(III) reduction coupled with anaerobic ammonium oxidation) to trigger NH4[+] removal through intermittently adding NOx[-] (NO2[-] and NO3[-]) into biogas slurry. The results showed that NOx[-] oxidized Fe(II), then the generated Fe(III) was reduced to Fe(II) again, resulting in a continuous iron cycling and nitrogen removal. On day 35, the total nitrogen removal efficiencies in the NO2[-] (67.52%) and NO3[-]-added (52.32%) groups were significantly higher than that of the control (without NOx[-]) (P < 0.05). Nitrifying and Anammox microorganisms were not detected in the NOx[-]-added reactors, while Feammox functional microorganisms (iron-reducing bacteria) were enriched (1.08%-1.51%), and the electron transfer capacities were also increased by 7.69%-16.08%. Metagenomic analysis showed that the NO3[-] group had more nitrate reductase genes but fewer downstream denitrification genes than the control group, indicating that NO2[-] accumulated as a key intermediate. NO3[-] could not directly oxidize Fe(II), and no nitrate-dependent Fe(II)-oxidizing microorganisms were detected. Moreover, the Fe(II) oxidation products in the NO3[-]-added reactors were identical to those generated by abiotic NO2[-] oxidation, suggesting that NO2[-] produced via partial denitrification was likely responsible for Fe(II) oxidation. Based on this, a possible metabolic pathway coupling nitrogen and iron transformations was proposed, in which partial NO3[-] reduction to NO2[-] may contribute to Fe(II) oxidation and subsequent Fe(III)-mediated NH4[+] removal via Feammox. This study provided a method for dealing with biogas slurry, and also offers a new approach for simultaneously removing NOx[-] and NH4[+].}, }
@article {pmid42424147, year = {2026}, author = {Ebel, ER and Kulkarni, AS and Mongad, DS and Olm, MR and Devi, SI and Mir, BA and Ozarkar, S and Sonnenburg, ED and Shouche, YS and Sonnenburg, JL and Dhotre, DP}, title = {Gut microbiomes of tribal communities in India vary with dairy and grain consumption.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2694242}, doi = {10.1080/19490976.2026.2694242}, pmid = {42424147}, issn = {1949-0984}, mesh = {Humans ; India ; Feces/microbiology ; *Diet ; *Edible Grain/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Dairy Products ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Tract/microbiology ; }, abstract = {Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%-47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.}, }
@article {pmid42424326, year = {2026}, author = {Brown, CR and Yacoub, MN and Bogan, JE and Buehler, MD and Hoffman, ML and Krumbeck, JA and Loughman, ZJ}, title = {Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0350824}, doi = {10.1371/journal.pone.0350824}, pmid = {42424326}, issn = {1932-6203}, mesh = {Animals ; *Cloaca/microbiology/parasitology ; *Cryptosporidium/isolation &amp; purification ; *Snakes/microbiology/parasitology ; *Microbiota ; *Cryptosporidiosis/microbiology/parasitology ; Animals, Wild/microbiology ; }, abstract = {The Eastern Indigo Snake (EIS; Drymarchon couperi), a federally threatened species native to the southeastern United States, serves as a valuable model for examining the effects of captivity and infection on gastrointestinal microbial composition in reptiles. As an alternative to direct gut sampling, we examined the cloacal microbiomes of EISs to evaluate changes in microbial community structure across our study groups. This study assessed the cloacal microbiome of wild and captive EISs using shotgun metagenomic sequencing. Samples were divided into three groups for comparative microbiome analysis: captive snakes positive for Cryptosporidium serpentis (C. serpentis), captive snakes negative for C. serpentis, and wild snakes. Alpha (Shannon index, paired Wilcoxon test) and beta diversity (Bray-Curtis dissimilarity, PERMANOVA, CAP) metrics were used to assess microbial diversity and community composition across groups. Furthermore, a linear discriminant analysis effect size (LEfSe) was used to identify microbial taxa significantly enriched in C. serpentis-positive versus C. serpentis-negative captive snakes. Bacterial, fungal, bacteriophage, nematode, and protozoan taxa were significantly enriched in C. serpentis-positive snakes compared with C. serpentis-negative captive snakes, based on a linear discriminant analysis (LDA) score ≥ 2.5 and p ≤ 0.05. Total taxa species Shannon diversity was consistent between C. serpentis-positive and negative captive snakes (p = 0.55) while wild snake samples were significantly more diverse (p = 0.026). Wild snakes also exhibited a significantly increased Shannon diversity of fungi (p = 0.044), protozoa (p = 0.012), and nematodes (p = 0.008) compared to their captive counterparts. This study offers the first in-depth characterization of the cloacal microbiome in reptiles, specifically in EISs, using shotgun metagenomic sequencing. The findings establish a foundation for exploring microbiota-host interactions with implications for reptile health, disease ecology, and conservation management.}, }
@article {pmid42424815, year = {2026}, author = {Tang, Q and Zhang, Y and Garza, DR and Ruan, C and Liu, B and Rocha, U and Shen, P and Wei, Y and Deng, Y and Zhang, J and Richnow, HH}, title = {Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.}, journal = {Water research}, volume = {305}, number = {}, pages = {126401}, doi = {10.1016/j.watres.2026.126401}, pmid = {42424815}, issn = {1879-2448}, abstract = {Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.}, }
@article {pmid42425006, year = {2026}, author = {Hao, Q and Jiang, L and Yu, H and Chen, C and Deng, Z and Zhou, H and Deng, Y and Lai, H and Cao, J and Zhang, C}, title = {Hydrostatic pressure drives metabolic strategies for anaerobic hydrocarbon degradation in cold seep sediments: from autonomy to syntrophic cooperation revealed by metagenomics.}, journal = {Marine environmental research}, volume = {221}, number = {}, pages = {108254}, doi = {10.1016/j.marenvres.2026.108254}, pmid = {42425006}, issn = {1879-0291}, abstract = {Petroleum pollution poses a significant threat to marine ecosystems, extending its impact to deep-sea environments. Cold seeps represent unique deep-sea ecosystems and are natural hotspots for studying anaerobic hydrocarbon degradation, yet the specific influence of hydrostatic pressure on the microbial process remains poorly understood. In this study, we established incubation systems with sediments from the Haima cold seep, enriched with n-hexadecane and naphthalene under varying hydrostatic pressures (0.1, 5, and 11 MPa). After seven months, naphthalene degradation consistently exceeded that of n-hexadecane across all pressures, yet was suppressed under high-pressure conditions. Notably, pressure selectively shaped the community structure: Marinobacter and Desulfoscipio were enriched at 0.1 MPa, while Halomonas and Sulfitobacter maintained stable dominance under high pressure. Metagenomic analysis revealed 0.1-bin.35, a bacterium affiliated with Desulfotomaculia, as a key hydrocarbon degrader encoding self-sufficient pathways for hydrocarbon degradation and dissimilatory sulfite reduction. However, under high pressure, dominant Sulfitobacter (5-bin.13, 11-bin.4) likely relied on syntrophy with sulfate-reducing bacteria to complement its incomplete catabolic pathways for hydrocarbons. This study reveals key hydrocarbon degraders in cold seep environments, advancing our understanding of deep-sea hydrocarbon-degrading microbiomes. Moreover, it unveils a possible pressure-induced adaptation strategy from autonomous degradation to syntrophic cooperation, providing insights into their ecological significance and potential applications in deep-sea oil pollutant bioremediation.}, }
@article {pmid42425460, year = {2026}, author = {Feng, B and Chen, J and Wang, C and Fu, J and Wang, R and Zhang, J and Zhang, B and Cheng, C}, title = {Fate of antibiotic resistance genes during rural domestic wastewater treatment: Anaerobic unit as enrichment hotspot versus aerobic unit as attenuation zone.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135356}, doi = {10.1016/j.biortech.2026.135356}, pmid = {42425460}, issn = {1873-2976}, abstract = {Rural domestic wastewater treatment systems are important but understudied reservoirs for antibiotic resistance genes (ARGs), whose full-process migration mechanisms remain unclear. Herein, the contribution of each treatment unit of ARGs was investigated using metagenomic methods across two seasons in typical rural domestic wastewater treatment systems. Although a removal efficiency (69 % in winter and 22 % in summer) was observed for ARGs, higher antibiotic residues and temperature dramatically induced ARG occurrence in wastewater and horizontal gene transfer (HGT) risk during wastewater treatment. The ARG abundances in the anaerobic unit increased by 1.6-2.1 fold compared to the regulating pool, primarily driven by elevated mobile genetic element (MGE) activity. In sharp contrast, ARG reduction was achieved through ARG host removal and suppressed HGT potential in the aerobic unit. Notably, mobile ARGs were dominated by tetracycline resistance genes in winter and co-dominated by tetracycline and sulfonamide genes in summer, with most flanked by transposases. Key pathogenic hosts, including Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa carrying ARG-MGE complexes, were primarily concentrated in the regulating pool and the influent, forming high-risk upstream sources of dissemination. Partial least-squares path model highlighted MGEs as the primary drivers, and variance partitioning analysis indicated that MGEs account for 31 % of the explained variation in ARGs during wastewater treatment. In summary, the anaerobic unit was an ARG enrichment hotspot, while the aerobic unit as ARG attenuation zone during wastewater treatment. These findings provide crucial evidence to optimize rural wastewater treatment processes and to target the control of antibiotic resistance.}, }
@article {pmid42425523, year = {2026}, author = {Post, SE and Ceisler, HS and Lal, RG and Singh, A and Deen, MA and Bonomo, LE and Cunic, LM and Brito, IL}, title = {Discovery of Novel Glycosidase-Derived Cell-Penetrating Peptides Encoded by Human Gut Commensals.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.6c00031}, pmid = {42425523}, issn = {2161-5063}, abstract = {Intracellular delivery of therapeutics remains a major challenge for modern medicine. To enhance intracellular uptake, therapeutics can be delivered with carrier proteins possessing an inherent cell-penetrating activity. There is an increasing need for new cell-penetrating carriers with diverse biophysical properties and mechanisms of action to transport a wide range of therapeutic cargo. As many cell-penetrating proteins and peptides derive from natural proteins, we sought to mine a previously unexplored community, the human gut microbiome, for cell-penetrating sequences. Here, we performed a high-throughput functional metagenomic screen to identify cell-penetrating protein fragments from the human gut microbiome. We identified protein fragments encoded within glycosidase enzymes from members of the Bacteroidetes phylum that mediate internalization into human cell lines when displayed on the surface of nonpathogenic, noninvasive Escherichia coli. We investigate one fragment, dubbed Gh_112, that adheres to human fibronectin, activates multiple endocytic pathways, and specifically promotes uptake of E. coli into multiple cancerous epithelial cell lines rather than healthy epithelial tissue in vitro. Overall, this work demonstrates that the human gut microbiome is a source of cell-penetrating sequences and expands the known repertoire of cell-penetrating carrier systems.}, }
@article {pmid42425637, year = {2026}, author = {Elsheshtawy, A and Clokie, BGJ and Saugh, S and Adler, KD and Michniewski, SM and MacKenzie, S and Clokie, MRJ and Sicheritz-Pontén, T and Albalat, A}, title = {Microbial succession and spoilage dynamics revealed by multi-omics in Norway lobster (Nephrops norvegicus) during ice storage.}, journal = {Food microbiology}, volume = {140}, number = {}, pages = {105151}, doi = {10.1016/j.fm.2026.105151}, pmid = {42425637}, issn = {1095-9998}, abstract = {The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.}, }
@article {pmid42426126, year = {2026}, author = {Barcaccia, G and Rambaldi Migliore, N and Gabelli, G and Agostini, V and Palumbo, F and Moroni, E and Nicolini, V and Gao, L and Mattutino, G and Porter, A and Palmowski, P and Procopio, N and Perego, UA and Iorizzo, M and Sharbel, TF and Baima Bollone, P and Torroni, A and Squartini, A and Achilli, A}, title = {DNA signatures preserved in the official 1978 sample collection of the Shroud of Turin.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42426126}, issn = {2045-2322}, support = {rif: 2023-1373//Fondazione Cariplo/ ; DAFNAE1-DOR-00719//University of Padova/ ; MR/Y019989/1//UKRI FLF/ ; 2022Y8BSAL//Ministero dell'Universit&#xe0; e della Ricerca/ ; }, abstract = {This research provides novel insights into the diversity of DNA extracted from samples collected from the Turin Shroud in 1978, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. We identified several human mitochondrial DNA (mtDNA) lineages, including K1a1b1a, which matches the 1978 official collector's mitogenome, H2a2 (i.e., the lineage of the mtDNA reference sequence rCRS), H1b, which is common in Western Eurasia, and the rare H33, which is also present in the Near East. Additionally, the reconstructed microbiome of the Shroud reveals a rich tapestry of multiple microbes commonly found on the human epidermis, as well as archaeal communities adapted to high salinity and fungi including molds. These findings are consistent with the preservation conditions experienced by the Shroud over the centuries. The presence of abundant Mediterranean endemic red coral, various cultivated plants (e.g., carrot, wheat, corn, bananas, and peanuts) and domesticated animals (e.g., cattle, pigs, chickens, dogs, and cats) provide a fascinating glimpse into the diverse biological sources of the contaminants that have accumulated on the Turin Shroud over time. Finally, radiocarbon dating of two distinct threads collected from the reliquary is consistent with their use in repair interventions of the Shroud carried out in 1534 and 1694 CE.}, }
@article {pmid42276012, year = {2026}, author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T}, title = {IgG4-related disease has a specific intestinal microbiota signature.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106326}, pmid = {42276012}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.<br><br>METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).<br><br>FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.<br><br>INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.<br><br>FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.}, }
@article {pmid42412829, year = {2026}, author = {Wang, S and Du, Y}, title = {VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {Supplement_1}, pages = {}, pmid = {42412829}, issn = {1367-4811}, support = {//University of Texas Systems STARs Program/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; Animals ; Humans ; *Software ; Metagenome ; Algorithms ; }, abstract = {MOTIVATION: Metagenomic Hi-C provides in situ proximity signals that can improve genome binning and enable virus-host-association analysis. However, viral genome recovery remains difficult because virus-virus Hi-C contact matrices are extremely sparse. Viral genomes are small, often low-abundance, and frequently assemble into short contigs, leaving many true within-genome links unobserved and causing viral bins to fragment.<br><br>RESULTS: We present VirBinn, a graph-diffusion framework for viral binning from metagenomic Hi-C. VirBinn enhances virus-virus connectivity through two complementary mechanisms: random-walk-with-restart enhancement on the sparse virus-virus contact graph and host-guided diffusion that propagates viral seeds through the host network to infer indirect virus-virus associations. The enhanced views are integrated and clustered using Leiden community detection to produce viral metagenome-assembled genomes (vMAGs). On dataset-specific simulation benchmarks with ground truth, VirBinn consistently recovers more high-quality vMAGs than Hi-C-based and shotgun-based baselines and substantially increases the number of near-complete genomes. On four real metagenomic Hi-C datasets spanning human gut, pig gut, sheep gut (long-read assembly), and wastewater, VirBinn yields more high-completeness vMAGs under CheckV and produces bins with strong within-cluster contact support. Finally, host linkage analysis using reconstructed host MAGs reveals habitat-specific host-association patterns and plausible host taxonomic profiles.<br><br>VirBinn is available at https://github.com/dyxstat/VirBinn. The scripts to reproduce the results and figures in this article are available at https://github.com/dyxstat/Reproduce_VirBinn.}, }
@article {pmid42412840, year = {2026}, author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW}, title = {RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {Supplement_1}, pages = {}, pmid = {42412840}, issn = {1367-4811}, support = {R35GM160134/NH/NIH HHS/United States ; R01AI173928/NH/NIH HHS/United States ; R01AI141810/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Thermodynamics ; *Nucleic Acid Hybridization/methods ; *Sequence Analysis, DNA/methods ; *Software ; Computer Simulation ; }, abstract = {MOTIVATION: Simulators that generate synthetic datasets help address the lack of ground truth for developing and benchmarking computational tools. Many read simulators assume uniform sampling across reference genomes; however, for newer capture-based sequencing technologies (e.g. TELSeq), this assumption is intentionally broken to oversample regions of interest. Along with systematic biases arising from probe multiplicity, sequence composition, and species abundances inherent to capture-based sequencing, this mismatch between modeling assumptions and the characteristics of real data necessitates the design of a new capture-based sequencing-specific simulator.<br><br>RESULTS: We present RAmpSim, a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing models of platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. RAmpSim generally outperforms a uniform baseline with respect to position-based earth mover's distance when compared against the empirical coverage distribution. Classification analysis also shows high recall in recovering empirical high-coverage regions while outperforming a uniform baseline.<br><br>AVAILABILITY: Code, example scripts, and data sources are available at https://github.com/az002/RAmpSim.git.}, }
@article {pmid42413090, year = {2026}, author = {Hidalgo, M}, title = {From microscopy to metagenomics: Evolution and challenges in clinical microbiology.}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {46}, number = {Sp. 1}, pages = {5-7}, doi = {10.7705/biomedica.8421}, pmid = {42413090}, issn = {2590-7379}, }
@article {pmid42413135, year = {2026}, author = {Hernández-Velázquez, R and Bokulich, NA}, title = {Unlocking the biotechnological potential of traditional fermented food microbiomes.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103550}, doi = {10.1016/j.copbio.2026.103550}, pmid = {42413135}, issn = {1879-0429}, abstract = {Fermented foods are a globally important source of dietary microbes, cultural heritage, and functional diversity, yet current microbiome research captures only a narrow fraction of this richness. Public sequencing datasets are heavily skewed toward a limited set of regions and fermentation types, leaving vast areas of geographic, substrate, and process diversity underrepresented. This imbalance constrains the discovery of novel microbial species, enzymes, and biosynthetic capacities, and risks accelerating homogenization through standardized starter cultures. We argue that coordinated, ethically grounded global efforts integrating metagenomics, multi-omics, standardized metadata, and biobanking are urgently needed to document, preserve, and responsibly leverage fermented food microbial diversity for sustainable food systems and innovation.}, }
@article {pmid42413264, year = {2026}, author = {Hu, N and Feng, Q and Li, C and Liu, Y and Zhu, B and Guo, T and Tong, L and Shi, J and Sanford, RA and Li, S and He, Y and Hu, Y and Jiang, Z and Jiang, Y and Zhao, L and Wang, M and Xu, M and Li, Y and Dong, Y and Shi, L}, title = {Fe(II)-driven abiotic-biotic relay alleviates denitrification bottleneck via chemical nitrite reduction and intracellular carbon.}, journal = {Water research}, volume = {304}, number = {}, pages = {126366}, doi = {10.1016/j.watres.2026.126366}, pmid = {42413264}, issn = {1879-2448}, abstract = {The coexistence of iron and nitrate (NO3[-]) in natural and engineered environments invites complex abiotic and biotic interactions, yet how such abiotic-biotic synergies operate under fluctuating carbon availability and how light modulates them remain poorly resolved. Using a nitrate-reducing, nitrite-accumulating enrichment culture derived from lake sediment, we uncovered a synergistic abiotic-biotic relay that overcame the kinetic bottleneck of denitrification. During initial heterotrophic denitrification of 2 mM NO3[-], 85.10-89.72% of the substrate was accumulated as NO2[-]. In contrast, ferrous iron (Fe(II)) amendment triggered subsequent iron-dependent nitrate reduction (IDNR) and significantly reduced NO2[-] accumulation. Abiotic controls confirmed that Fe(II) chemically reduced the accumulated NO2[-] to the downstream products. In parallel, metagenomic and metatranscriptomic analyses of the bioactive samples demonstrated that these gaseous intermediates (e.g., NO, N2O) were enzymatically reduced to N2 based on upregulated denitrification-associated genes. More importantly, when exogenous acetate was depleted, the community sustained IDNR not through strict autotrophy but via heterotrophic metabolism using intracellular poly-3-hydroxybutyrate (PHB) and microbial necromass as the carbon/energy sources. This metabolic plasticity drove a functional succession from organotrophic denitrifiers (e.g., Pseudomonas) toward PHB- and necromass-utilizing microbial consortia mainly composed of Pseudomonas, Alicycliphilus and some phototrophic populations. Supporting evidence showed that illumination further accelerated the relay via light-driven reactive oxygen species, and secondary iron minerals (e.g., bernalite, lepidocrocite, and goethite) formed as fingerprints of the Fe(II) oxidation. Collectively, this work deciphers a dual-mechanism model, abiotic nitrite reduction followed with endogenous carbon-fueled denitrification, that governed efficient nitrate reduction under carbon-limited conditions. Leveraging such abiotic-biotic relays offers promising strategies for sustainable nitrogen removal in both natural and engineered systems.}, }
@article {pmid42413404, year = {2026}, author = {Cao, Z and Gong, H and Qin, H and Wei, T and He, X and Yang, K and Li, X and Wang, Y and Jia, Y and Lan, X and He, W and Jing, X and Long, R and Li, B and Mi, J}, title = {Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142862}, doi = {10.1016/j.jhazmat.2026.142862}, pmid = {42413404}, issn = {1873-3336}, abstract = {Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.}, }
@article {pmid42413405, year = {2026}, author = {Zhang, K and Fang, Y and Zhang, L and Zhao, W and Zhang, X and Ye, L}, title = {Dissolved oxygen regulation enhances organic micropollutant removal in wastewater treatment bioreactors.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142887}, doi = {10.1016/j.jhazmat.2026.142887}, pmid = {42413405}, issn = {1873-3336}, abstract = {Organic micropollutants (OMPs) are ubiquitously detected in wastewater and pose potential risks to aquatic ecosystems and human health, making their effective removal a critical objective of wastewater treatment processes. Dissolved oxygen (DO) is a central operational parameter that governs microbial metabolism in biological wastewater treatment processes; however, its long-term role in controlling OMP removal remains insufficiently understood. Here, three bioreactors were operated for 166 days under staged DO conditions ranging from 0.8 to 4.5 mg/L to systematically evaluate the effects of DO on the removal of eight representative OMPs and associated microbial responses. Operating at a low DO level maintained stable removal of conventional pollutants while significantly enhancing the biodegradation of several OMPs, including dimetridazole, ofloxacin, trimethoprim, and sulfamethazine. Despite only minor changes in overall community composition, intermediate and rare taxa exhibited pronounced sensitivity to DO variation, suggesting their potential involvement in OMP biodegradation under low-oxygen conditions. Enzyme activity measurements combined with metagenomic and transcriptomic analyses further revealed that low DO promoted higher activity, abundance, and expression of redox-related co-metabolic enzymes, particularly peroxidases and cytochrome P450 enzymes. These results demonstrate that DO regulates OMP removal primarily by reshaping microbial functional potential and redox metabolism. Overall, this study provides both mechanistic understanding and practical guidance for applying DO regulation to achieve enhanced micropollutant removal in wastewater treatment systems.}, }
@article {pmid42413431, year = {2026}, author = {Mitra, S and Ahmed, MF and Yusuf, MA}, title = {Hidden pathways of antimicrobial resistance: A review of environmental metagenomics and exposure risks in low-resource settings.}, journal = {Journal of environmental management}, volume = {414}, number = {}, pages = {130366}, doi = {10.1016/j.jenvman.2026.130366}, pmid = {42413431}, issn = {1095-8630}, abstract = {Antimicrobial resistance (AMR) is increasingly recognised as a One Health challenge in which environmental reservoirs play an important role in the persistence and dissemination of resistance genes. Despite growing recognition that environmental antimicrobial resistance is a critical component of the One Health challenge, the pathways through which antimicrobial resistance genes (ARGs) move between environmental systems and human populations remain incompletely characterised, particularly in low- and middle-income countries where environmental exposures are greatest and surveillance capacity is limited. This review synthesises current knowledge on environmental resistomes across soil, water, sediment and groundwater systems, with a focus on metagenomic and quantitative analytical approaches that have transformed environmental AMR surveillance. Unlike traditional culture-based methods, metagenomics enables comprehensive, culture-independent profiling of microbial communities and their associated resistomes, allowing detection of both known and previously uncharacterised resistance genes, as well as insights into their genetic context and mobility. This has significantly advanced our ability to characterise environmental reservoirs and infer potential transmission pathways at ecosystem scale. Using Bangladesh as an illustrative example of environmental exposure dynamics in rapidly urbanising low- and middle-income settings, we examine how contaminated urban waterways, wastewater discharge, agricultural practices, and seasonal hydrological processes-including monsoon-driven flooding-create interconnected transmission pathways linking environmental, animal, and human microbiomes. We also consider how co-selection pressures from heavy metals and other environmental contaminants contribute to the persistence and amplification of antimicrobial resistance beyond antibiotic-driven selection alone. These dynamics are further intensified by dense surface water networks, strong hydrological connectivity, and limited wastewater treatment infrastructure, which together create high-intensity human-environment interfaces and facilitate large-scale redistribution of antimicrobial resistance genes across environmental compartments. Taken together, these features make Bangladesh an analytically distinctive and tractable model system for understanding environmental AMR dynamics, with relevance to comparable deltaic and monsoon-influenced regions in South and Southeast Asia. Key methodological challenges-including the gap between ARG detection and clinical risk interpretation, biases in resistance gene databases, sampling limitations, and the lack of harmonised environmental surveillance frameworks-are examined alongside emerging tools such as long-read sequencing, functional metagenomics and artificial intelligence-assisted bioinformatic analysis. Finally, we propose an integrated One Health framework linking environmental metagenomics, global surveillance systems and policy interventions to support harmonised, data-driven monitoring and mitigation of environmental AMR across interconnected ecosystems.}, }
@article {pmid42413842, year = {2026}, author = {Hu, Y and Shi, S and Liu, Y and Chen, H and Cui, K and Wei, L}, title = {Structure and function of the coleoptericin gene in the ladybird beetle Serangium japonicum during seasonal development.}, journal = {Developmental and comparative immunology}, volume = {181}, number = {}, pages = {105675}, doi = {10.1016/j.dci.2026.105675}, pmid = {42413842}, issn = {1879-0089}, abstract = {OBJECTIVE: This study was conducted to explain the relationship between structure and function of coleoptericin in Serangium japonicum, and importance of the differential expression patterns of it between in winter and summer, and to provide a theoretical foundation for the rational application of S. japonicum as a natural enemy in pest control.<br><br>METHOD: The full length cDNA was obtained using rapid amplification of cDNA ends (RACE) technology. Bioinformatics software was employed to predict the structure and physicochemical properties of the coleoptericin protein based on its cDNA sequence. The prokaryotic expression protein were tested activity of anti against three experimental strains of microorganisms through using the pore diffusion method. Additionally, metagenome was sequenced and analyzed to find the proteins' effect on microorganism in S.japonicum.<br><br>RESULT: The full-length cDNA sequence of coleoptericin was found to be 606 base pairs (bp) in length. Its open reading frame (ORF) spanned from nucleotide 48 to 495, totaling 447 bp, and encoded a polypeptide of 149 amino acids. Homology analysis revealed that the deduced amino acid sequence shared the highest similarity (55.1%) with the antimicrobial peptide from Tribolium castaneum. The protein had molecular weight of 17.03 kD and theoretical i-soelectric point of 9.19. Hydrophilicity analysis indicated a grand average of hydropathicity (GRAVY) score of -0.85, suggesting a hydrophilic nature. Furthermore, the protein was predicted to contain one transmembrane domain and a signal peptide. Agar well diffusion assays demonstrated that the prokaryotically expressed coleoptericin exhibited antimicrobial activity against Escherichia coli. Results from Metagenome showed that the abundance of Penicillium was significantly lower in winter compared to summer.<br><br>CONCLUSION: The coleoptericin protein from S.japonicum had a sequence of over 100 amino acid residues and an &#x3b1;-helical secondary structure. For S. japonicum, our results supported that coleoptericin protein could protect the beetle from pathogenic bacteria in winter. Some results from relative reports suggested that coleoptericin protein also could be an antifreeze energy source except for immune function.}, }
@article {pmid42413995, year = {2026}, author = {Halford, C and Toriro, R and Rowlands, E and Le Viet, T and Schaap, S and O'Shea, MK and Fletcher, T and Beeching, NJ and Woolley, S and Lukaszewski, R and Gilmour, M and Weller, SA}, title = {Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya.}, journal = {BMJ military health}, volume = {}, number = {}, pages = {}, doi = {10.1136/military-2026-003248}, pmid = {42413995}, issn = {2633-3775}, abstract = {INTRODUCTION: Traveller's diarrhoea is a common complaint among deployed military personnel. Maintaining sample integrity prior to diagnostic testing is a key challenge in resource-limited environments. We report the comparison of three long-term ambient temperature stool sample stabilisation matrices for the detection of Cryptosporidium hominis from samples collected during an outbreak among British military personnel stationed in Kenya.<br><br>METHODS: A retrospective cohort of stool samples, each stabilised for more than 12 months at ambient temperatures using Flinders Technical Associate (FTA) cards, OMNIgene GUT tubes and DNA Shield faecal collection tubes, were analysed by Nanopore-based clinical metagenomic (CMgs) DNA sequencing and quantitative real-time PCR (qPCR) in the UK. The results were compared with BioFire FilmArray Gastrointestinal Panel testing carried out at the point of sampling in Kenya.<br><br>RESULTS: Cryptosporidium DNA was detected in 13/24 (54.2%) OMNIgene GUT samples by CMg following long-term storage, compared with 9/24 (37.5%) of DNA Shield samples. Samples stored on FTA cards did not identify Cryptosporidium DNA by CMg in any sample. OMNIgene GUT samples also had the highest rate of detection of C. hominis DNA by qPCR, with 23/24 samples testing positive, compared with 21/24 and 17/20 of DNA Shield and FTA samples, respectively.<br><br>CONCLUSIONS: Samples stored in OMNIgene GUT tubes retained detectable levels of Cryptosporidium DNA in a higher proportion of samples following long-term storage. This study demonstrates the importance of selecting the optimal sample collection and stabilisation matrix for CMg and qPCR based diagnostic testing in austere environments.}, }
@article {pmid42414020, year = {2026}, author = {Clister, D and Chandra, QM and Tan, MW and Gunawan, MC and Bibi, A and Ahmed, A and Bastian, M and Meesakul, P and Cao, S and Kim, B and Nurkolis, F and Syahputra, RA}, title = {Microbiome-Based Precision Interventions in Type 2 Diabetes Mellitus: Mechanisms, Modulators, and Translational Opportunities.}, journal = {The Journal of nutrition}, volume = {156}, number = {7}, pages = {101596}, doi = {10.1016/j.tjnut.2026.101596}, pmid = {42414020}, issn = {1541-6100}, mesh = {*Diabetes Mellitus, Type 2/therapy/microbiology ; Humans ; *Precision Medicine ; Probiotics ; *Gastrointestinal Microbiome ; Prebiotics ; Fecal Microbiota Transplantation ; Synbiotics ; Dysbiosis ; Animals ; *Microbiota ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disease driven by insulin resistance, chronic low-grade inflammation, and impaired glucose regulation. Although pharmacological options have advanced, sustained glycemic control remains elusive due to heterogeneity in disease progression and therapeutic response. Precision medicine offers a framework to individualize interventions, with the gut microbiota emerging as a central determinant of host metabolic and immune regulation. Dysbiosis has been implicated in T2DM through altered microbial metabolites-including short-chain fatty acids, bile acids, branched-chain amino acids, and indole derivatives-that shape insulin sensitivity, inflammatory pathways, and glucose homeostasis. This review critically examined microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and personalized nutrition, alongside advances in metagenomics and machine learning for biomarker discovery. By integrating mechanistic and translational insights, we highlight opportunities and challenges in implementing microbiome-based precision interventions, underscoring their potential to transform T2DM management.}, }
@article {pmid42414278, year = {2026}, author = {Zhao, C and Li, Z and Liu, M and Bao, L and Yuan, C and Zhao, Y and Wu, K and Qiu, M and He, Y and Zhang, N and Hu, X and Zhang, Y and Han, F and Fu, Y}, title = {Dissection of mammary cell landscape in ruminal dysbiosis-induced mastitis by single-cell RNA sequencing.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01076-7}, pmid = {42414278}, issn = {2055-5008}, support = {32402956//National Natural Science Foundation of China/ ; 32422086//National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; }, abstract = {Growing evidence has underscored the contribution of gastrointestinal dysbiosis to the onset of mastitis, however, the local cellular changes responsible for the pathological processes of ruminal dysbiosis-induced mastitis (RDIM) are still unclear. Here, we profiled mammary single-cell transcriptomes in goats with RDIM, complemented by ruminal metagenomic and untargeted metabolomic analyses of rumen fluid and serum. Our results indicated that compromised lactation and barrier integrity in LumSec were linked to RDIM. Increased inflammatory macrophages and DCs, γδT and CD4[+] TH cell populations, along with reduced Tex/Treg and B cells were implicated in RDIM. Fibroblasts exhibited increased gene expression related to the extracellular matrix, while lymphatic endothelial cells and Vas-venous structures displayed elevated inflammatory gene expression. Tight junction integrity and apelin signaling pathways were compromised in Vas-capillary during RDIM. Notably, metagenomic analysis indicated that RDIM correlated with reduced ruminal microbial diversity and shifts in microbial community composition. Key metabolic pathways including microbial tryptophan metabolism, secondary bile acid biosynthesis, and vitamin metabolism were significantly diminished during RDIM. Furthermore, tryptophan-induced AHR signaling and secondary bile acid receptor GPBAR1, primarily expressed in vascular endothelial cells and macrophages, respectively, which were reduced during RDIM. Collectively, our study provides a comprehensive atlas of mammary cell landscapes in RDIM, which may enhance the understanding of mastitis pathogenesis.}, }
@article {pmid42415156, year = {2026}, author = {Houvessou, GM and Antonieta Alfane, NW and Mahoche, M}, title = {Dynamic, transition and variation of cervicovaginal microbiome and HPV infection and cervical dysplasia and cancer: a systematic review.}, journal = {Infectious agents and cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13027-026-00777-0}, pmid = {42415156}, issn = {1750-9378}, abstract = {BACKGROUND: Cervical cancer is the fourth most common malignancy in women worldwide, with approximately 660,000 new cases and 350,000 deaths annually. The burden falls disproportionately on low- and middle-income countries. Although persistent infection with high-risk HPV (hrHPV) is the necessary cause, most infected women clear the virus spontaneously, implicating additional cofactors, including the cervicovaginal microbiome in determining oncogenic outcomes.<br><br>METHODS: PubMed was searched through September 10, 2024, to identify longitudinal studies assessing cervicovaginal microbiota in relation to HPV infection or cervical lesion outcomes at two or more time points. Methodological quality was evaluated using the Newcastle-Ottawa Scale (NOS). Given the substantial heterogeneity, a structured thematic synthesis was performed across three predefined domains: (a) baseline microbiome composition and clinical outcomes; (b) community state type (CST) dynamics and temporal stability; and (c) microbiome changes following treatment.<br><br>RESULTS: Twelve studies enrolling 1,663 women across 11 countries met inclusion criteria. NOS scores ranged from 4 to 9. Lactobacillus-dominated CSTs at baseline were consistently associated with HPV clearance and CIN regression, while Lactobacillus-depleted states showed higher transition rates and unfavourable outcomes. Prior L.iners (CST III) dominance was repeatedly linked to favourable outcomes, although evidence on this species remains conflicting. Cervicovaginal dysbiosis frequently preceded HPV persistence or lesion progression.<br><br>CONCLUSION: Sustained Lactobacillus-dominated CST stability, rather than dominance by any single species, is the most consistent microbiome factor associated with favourable HPV and cervical lesion outcomes. Standardized longitudinal designs incorporating metagenomic sequencing, frequent sampling intervals, and rigorous confounder adjustment are needed to advance mechanistic understanding.<br><br>Not applicable.}, }
@article {pmid42415193, year = {2026}, author = {Lechleiter, N and Wedemeyer, J and Junker, J and Sehl-Ewert, J and Homeier-Bachmann, T}, title = {Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology.}, journal = {Parasites &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42415193}, issn = {1756-3305}, support = {Grant No. 28KIDA001//Federal Ministry of Agriculture, Food and Regional Identity (BMLEH) - Germany/ ; }, mesh = {Animals ; *Deer/parasitology ; *Metagenomics/methods ; Feces/parasitology ; *Gastrointestinal Tract/parasitology/pathology ; *Parasites/genetics/isolation &amp; purification/classification ; Seasons ; Animals, Wild/parasitology ; *Intestinal Diseases, Parasitic/veterinary/parasitology ; }, abstract = {BACKGROUND: Some of the most common pathogens in wildlife are parasites. Since wild cervids are phylogenetically close to a lot of our livestock species, disease dynamics can arise, for example, through shared parasites. Insight into regional patterns, shaped by ecosystems and cross-species relationships, is only slowly emerging and the species-specific knowledge about lifecycle and ecology of parasites is often based on cross-sectional studies and therefore limited. Possibilities for broad and easy investigation of parasites could be the key to widen our understanding of these systems and processes.<br><br>METHODS: Here, shotgun metagenomics were investigated as a method for parasite detection in fecal samples of wild ungulates. The results were further validated by histopathological examination of gastrointestinal tissues.<br><br>RESULTS: The results from the two methods are in line with similar studies, and while not being identical, complement each other.<br><br>CONCLUSIONS: This investigation revealed parasite composition and seasonal dynamics in two species of wild cervid red deer (Cervus elaphus) and roe deer (Capreolus capreolus).}, }
@article {pmid42415408, year = {2026}, author = {Li, J and Liu, P and Zhang, Q and Zhao, R and Zhang, J and Zheng, X and Li, B and Zhang, XX}, title = {Temperate Phages Mediate Dual Adaptive Mechanisms That Enhance Microbial Resilience in Antibiotic-Contaminated Wastewater Treatment Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c07049}, pmid = {42415408}, issn = {1520-5851}, abstract = {Temperate phages play crucial ecological roles in engineered microbial communities, yet their adaptive strategies under antibiotic stress remain unclear. Here, metagenomic analysis was used to investigate how temperate phages facilitate host adaptation in activated sludge acclimated to chloramphenicol (CAP). Antibiotic stress markedly reshaped bacterial and temperate phage communities, with dominant degraders (e.g., Sphingomonas and Caballeronia) reaching relative abundances of 6.5-42.0%. Temperate phages exhibited specific adaptive responses by significantly enriching antibiotic resistance genes, including multidrug (arlR and mtrA) and peptide (bcrA) resistance genes, resulting in a 1.56-4.15-fold increase in the phage-derived resistome relative to the control. They also mediated general adaptive responses by encoding auxiliary genes involved in oxidative stress mitigation, DNA repair, biofilm formation, and antiviral defense. Host-phage linkage prediction identified 1045 phage-bacteria interactions, including 11 ARG-harboring viral operational taxonomic units associated with dominant CAP-degrading hosts. Collectively, our findings reveal that temperate phages facilitate microbial resilience in antibiotic-stressed environments by delivering mutualistic genetic traits, encompassing both specific (antibiotic resistance genes) and general (antiviral defense, metabolic, and stress mitigation) adaptive responses, highlighting their ecological significance and potential for enhancing the stability and performance of wastewater treatment systems under pharmaceutical stress.}, }
@article {pmid42415516, year = {2026}, author = {Zhou, G and Liu, J and Liu, F and Xiao, Y and Graham, EB and Kuzyakov, Y and Ye, M and Xin, X and Chen, L and Zhang, C and Ma, D and Wu, Z and Zhou, Z and Zhou, J and Liang, Y and Zhang, J}, title = {Resource-Dependent Metabolic and Biogeochemical Consequences of Viruses in Agricultural Soils.}, journal = {Global change biology}, volume = {32}, number = {7}, pages = {e70994}, doi = {10.1111/gcb.70994}, pmid = {42415516}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; SKLSSA2501//Major Program of State Key Laboratory of Soil and Sustainable Agriculture/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; DE-AC05-76RL01830//Department of Energy, Office of Science, Biological and Environmental Research program and by Pacific Northwest National Laboratory/ ; }, mesh = {*Soil Microbiology ; Agriculture ; *Soil/chemistry ; Carbon/metabolism ; *Viruses/genetics/metabolism ; Metagenome ; Fertilizers ; }, abstract = {Soil viruses are crucial for microbial life, biogeochemical cycles of carbon and nutrients, and for microbial necromass formation. We hypothesized that the effects of viruses on these processes depend on organic matter and nutrient availability in soils. Here, we combined a 34-year long-term fertilization trial, 150 sequenced soil metagenomes, and microcosm experiments to explore how viruses modulate carbon and nutrient dynamics depending on resource availability. We uncovered 2789 viral populations (vOTUs) grouping into 301 viral clusters, 91% of which were previously unknown. Organically fertilized soils harbored most lytic viruses carrying diverse element cycling-related auxiliary viral genes (AVGs) acquired through co-evolution and horizontal gene transfer. Synthesis and heterologous expression assays further indicated that four AVGs (i.e., cbhA, pel, wbpD, GT2) had higher transcript levels in Escherichia coli under nutrient rich than nutrient poor conditions. Addition of virus particles to soils raised microbial carbon use efficiency (CUE; biomass production relative to carbon uptake) and accelerated microbial turnover leading to boosted microbial necromass formation by 14%. Conversely, in soils without organic fertilizers, viruses facilitate bacterial adaptation to stress (e.g., defense system and interference competition) and accelerate microbial decomposition of organic matter. 35 days after virus addition, CO2 and N2O emissions increased by 41% and 52%, respectively. Finally, we propose the Viral Entombing-Priming (VEP) framework to describe the contrasting roles of viruses in carbon and nutrient dynamics depending on soil fertility. This work reveals the viral "Matthew effect" (the rich get richer and the poor get poorer) in resource-rich and resource-poor soils and could unlock nature-based pathways to raise carbon and nutrient retention for sustainable agriculture.}, }
@article {pmid42415518, year = {2026}, author = {Dolivet-Maréchal, M and Palacin-Lizarbe, C and Siljanen, HMP and Paul, D and Delort, A and Gervaix, J and Creuzé des Châtelliers, C and Schmidt, S and Cognat, M and Sebag, D and Taugourdeau, O and Schübert, C and Labourdette, N and Bertrand, I and Rossi, LMW and Le Roux, X and Richaume, A and Florio, A}, title = {Vegetation Increases CH4 Emissions and Methanotroph Diversity in Marine Sediments.}, journal = {Global change biology}, volume = {32}, number = {7}, pages = {e70989}, doi = {10.1111/gcb.70989}, pmid = {42415518}, issn = {1365-2486}, support = {101037097//EU Horizon2020/ ; ANR-17-EURE-0018//Graduate School H2O'Lyon/ ; }, mesh = {*Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; France ; *Zosteraceae/microbiology/metabolism ; }, abstract = {Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH4) emissions, whose microbial and environmental descriptors in Zostera noltii meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH4 fluxes, CH4-producing and consuming microbial communities and sediment physicochemical parameters in Z. noltii meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH4 fluxes were measured at low tide during daytime conditions, providing standardized estimates of peak emissions. Microbial communities were characterized using targeted metagenomics of three functional genes (mcrA, mmoX, pmoA) and quantitative PCR. CH4 fluxes were higher in vegetated than bare sediments (24.4 ± 2.6 vs. 9.4 ± 0.7 μmol m[-2] day[-1]). Mixed linear models and random forest analyses identified C accumulation rate and CO2 flux as the strongest positive descriptors of CH4 fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera (mcrA-Methanolobus, mmoX-Methylocella, pmoA-Methylococcus, Methyloglobulus) emerged as abundant, seagrass-associated, correlated with CH4 fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH4 fluxes than gene abundance or a specific genus. Findings indicate Z. noltii meadows enhance C burial and CH4 emission, with methanotroph diversity potentially mitigating CH4 emissions. Our results provide the first integrated assessment of CH4 fluxes and their descriptors in Z. noltii meadows, based on limited temporal coverage capturing the daytime peak emission conditions, highlighting the intertwined nature of C burial and CH4 emissions and the need to account for both in blue C climate assessments.}, }
@article {pmid42415914, year = {2026}, author = {Zhang, M and Jiang, J and Yang, B and Zhao, W and Zhang, J and Ma, T and Wang, H}, title = {Integrated multi-omics analysis reveals distinct microbiota-metabolite signatures and a novel HCN2-2-hydroxybutyric acid interaction in inflammatory bowel disease.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1843166}, pmid = {42415914}, issn = {2296-861X}, abstract = {INTRODUCTION: Gut microbiota-derived short-chain fatty acids (SCFAs) exert critical regulatory functions in inflammatory bowel disease (IBD). However, integrated profiling of fecal SCFA signatures alongside gut microbiota composition in ulcerative colitis (UC) and Crohn's disease (CD) remains insufficiently characterized. Furthermore, the molecular mechanisms through which microbiota metabolites engage host protein targets warrant systematic investigation.<br><br>METHODS: This study enrolled 30 patients with UC, 20 with CD, and 30 healthy controls, with paired fecal collection. Gut microbiota composition was analyzed by deep metagenomic sequencing, and SCFA concentrations were quantified by gas chromatography-mass spectrometry. Multi-omics integration, correlation network analysis, and Bayesian kernel machine regression were employed to resolve microbiota-metabolite associations. An integrated computational pipeline incorporating molecular dynamics simulations was constructed to evaluate the thermodynamic stability and binding modalities of metabolite-protein interactions.<br><br>RESULTS: Both UC and CD patients exhibited significantly reduced gut microbial &#x3b1;-diversity and characteristic community structure alterations. Fecal metabolomic profiling revealed synchronous elevation of 2-Hydroxybutyric acid (2-HB) and isocaproate in both patient groups, whereas butyrate reduction was restricted to UC. Multi-omics correlation analysis identified significant associations between 2-HB and unclassified Veillonella species as well as specific functional modules. Molecular dynamics simulations with an aggregate sampling time of 100 ns revealed a structural basis for the formation of a stable complex between 2-HB and the hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2). This interaction was primarily mediated by electrostatic interactions involving Arg659, Arg618, and Arg617 residues alongside hydrophobic contacts, suggestive of potential allosteric modulation.<br><br>CONCLUSIONS: This study identifies 2-HB and isocaproate as shared fecal metabolic markers across IBD and provides a structural rationale for the interaction between 2-HB and HCN2. The druggability profile of HCN2 supports its prioritization for mechanistic investigation, with the caveat that functional validation is prerequisite to any inference of therapeutic relevance.}, }
@article {pmid42416069, year = {2026}, author = {Wang, J and Lin, K and Zhong, Y and Wu, Z and Lu, T and Lu, W and Wang, W and Ma, C}, title = {Disseminated Mycobacterium kansasii infection with osseous involvement in anti-interferon-γ autoantibody-associated adult-onset immunodeficiency: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1841472}, pmid = {42416069}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/immunology/diagnosis/drug therapy ; *Mycobacterium kansasii/immunology ; *Interferon-gamma/immunology ; *Autoantibodies/immunology ; *Immunologic Deficiency Syndromes/immunology/complications/diagnosis ; }, abstract = {BACKGROUND: Anti-interferon-γ autoantibody-associated adult-onset immunodeficiency is a rare acquired immunodeficiency that predisposes patients to recurrent or disseminated opportunistic infections, particularly nontuberculous mycobacterial (NTM) infections. Disseminated Mycobacterium kansasii infection in this setting is uncommon and may radiologically mimic malignancy, leading to diagnostic delay.<br><br>CASE PRESENTATION: A 53-year-old Chinese man with untreated chronic hepatitis B virus (HBV) infection presented with cough, chest pain, and back pain. Chest computed tomography and ^18F-FDG PET/CT revealed a left hilar mass, mediastinal and hilar lymphadenopathy, and extensive FDG-avid skeletal lesions, initially suggesting lung cancer with bone metastases. However, repeated pathological examinations, including bronchoscopic brushing, endobronchial ultrasound-guided transbronchial needle aspiration, and cervical lymph node aspiration, failed to confirm malignancy. Targeted next-generation sequencing of bronchoalveolar lavage fluid and metagenomic next-generation sequencing of vertebral tissue both identified Mycobacterium kansasii, supporting disseminated infection with pulmonary and skeletal involvement. Subsequent immunologic testing demonstrated elevated anti-IFN-&#x3b3; autoantibodies, supporting a clinical diagnosis of AIGA-associated disseminated M. kansasii infection. Antimycobacterial therapy was initiated, but further treatment was complicated by postoperative cholestatic jaundice and high-level HBV viremia, which precluded immediate escalation to immune-directed therapy.<br><br>CONCLUSIONS: AIGA-associated disseminated Mycobacterium kansasii infection can closely mimic lung cancer with bone metastases. In patients with tumor-like pulmonary and skeletal lesions but repeatedly nondiagnostic pathology, early integration of pathogen detection and anti-IFN-&#x3b3; autoantibody testing may help shorten diagnostic delay.}, }
@article {pmid42416141, year = {2026}, author = {Chen, D and Li, X and Wang, Z and Huang, L and Qin, L}, title = {Complementary mNGS and traditional testing for bloodstream infections.}, journal = {Open medicine (Warsaw, Poland)}, volume = {21}, number = {1}, pages = {20261494}, pmid = {42416141}, issn = {2391-5463}, abstract = {Bloodstream infections (BSIs) require rapid and accurate etiological diagnosis to guide timely antimicrobial therapy. Conventional diagnostic approaches, particularly blood culture, remain indispensable for antimicrobial susceptibility testing; however, they are limited by prolonged turnaround time and reduced sensitivity, especially following prior antibiotic exposure. Metagenomic next-generation sequencing (mNGS) has emerged as a culture-independent and hypothesis-free diagnostic tool capable of detecting a broad spectrum of pathogens directly from clinical samples. This approach is particularly advantageous for identifying rare, fastidious, and polymicrobial infections, as well as infections in immunocompromised patients. However, its clinical application remains constrained by challenges in distinguishing infection from colonization, interpreting antimicrobial resistance signals, and variability in bioinformatics pipelines. Thus, in the era of integrated diagnosis, mNGS does not replace but powerfully complements traditional methods. Furthermore, we propose a dynamic evidence-weighted integrated diagnostic framework to guide real time clinical decision and improve the clinical applicability of mNGS in bloodstream infections.}, }
@article {pmid42416274, year = {2026}, author = {Dang, Y}, title = {How mNGS transforms care for non-verbal elderly stroke patients with pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1814320}, pmid = {42416274}, issn = {2235-2988}, mesh = {Humans ; Aged ; Retrospective Studies ; *Stroke/complications ; Female ; Male ; Sputum/microbiology/virology ; Aged, 80 and over ; *Pneumonia/diagnosis/microbiology/etiology/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Bacteria/isolation &amp; purification/genetics/classification ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {BACKGROUND: Stroke-associated pneumonia (SAP) is a severe complication in non-verbal elderly stroke patients, with diagnosis hindered by the low sensitivity and slow turnaround of conventional microbial culture.<br><br>METHODS: A single-center retrospective cohort study was conducted on 64 non-verbal elderly SAP patients (&#x2265;65 years) admitted to Guangxi Jiangbin Hospital from 2018 to 2022, divided into an mNGS group (n=30, sputum/BALF tested by metagenomic next-generation sequencing) and a control group (n=34, conventional culture). Propensity score matching (1:1) was used to balance baseline characteristics, and clinical outcomes and pathogen detection efficiency were compared between groups. Multivariable Cox regression adjusted for hypoalbuminemia, electrolyte disturbance and stroke severity.<br><br>RESULTS: mNGS detected more bacterial pathogens (37 vs.27 in sputum, 37 vs.21 in BALF) and identified 3 viral and 2 atypical pathogens undetectable by culture, with a negative rate of 13.3% (vs.20.0% for sputum culture, 43.3% for BALF culture). 73.3% of mNGS group patients received antimicrobial therapy adjustment. After adjustment, the mNGS group had notably higher 28-day (96.7% vs.76.5%; adjusted HR&#xa0;=&#xa0;0.32, P&#xa0;=&#xa0;0.032) and 90-day survival (76.7% vs.44.1%; adjusted HR&#xa0;=&#xa0;0.41, P&#xa0;=&#xa0;0.024), lower invasive mechanical ventilation rate (40.0% vs.64.7%, P&#xa0;=&#xa0;0.048), shorter median antibiotic duration (14 vs.21 days, P&#xa0;=&#xa0;0.016) and lower median hospitalization costs (&#xa5;32,450 vs.&#xa5;89,310, P&#xa0;<&#xa0;0.001).<br><br>CONCLUSION: mNGS enables more comprehensive pathogen detection in non-verbal elderly SAP patients, guides targeted antimicrobial therapy, and is associated with improved survival and reduced healthcare resource consumption. However, large-sample multicenter prospective studies are needed to validate these findings due to the study's limitations.}, }
@article {pmid42416386, year = {2026}, author = {Wicaksono, WA and Köberl, M and White, RA and Jansson, JK and Jansson, C and Cernava, T and Berg, G}, title = {Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface.}, journal = {Plant and soil}, volume = {523}, number = {2}, pages = {811-825}, pmid = {42416386}, issn = {0032-079X}, abstract = {AIMS: Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere.<br><br>METHODS: The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing.<br><br>RESULTS: We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific.<br><br>CONCLUSIONS: The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-07097-5.}, }
@article {pmid42416834, year = {2026}, author = {Zhao, Z and Lu, M and Ying, Y}, title = {Full-term pregnancy after severe gestational psittacosis: a case report and literature review.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1836961}, pmid = {42416834}, issn = {1663-9812}, abstract = {Gestational psittacosis is a rare but high-risk infection caused by Chlamydia psittaci, often leading to severe maternal complications and adverse fetal outcomes. We report a unique case of a 30-year-old woman at 22 + 5 weeks of gestation who presented with acute high fever and respiratory failure following bird exposure. The diagnosis of C. psittaci infection was rapidly confirmed via blood metagenomic next-generation sequencing (mNGS). Following multidisciplinary consultation involving obstetricians, infectious disease specialists, intensivists, respiratory physicians, clinical pharmacists, and neonatologists, an individualized management plan was established to balance maternal infection control, respiratory support, fetal monitoring, and medication safety during pregnancy. The patient was treated with intravenous azithromycin combined with corticosteroids, and her clinical condition stabilized within 2 weeks. Notably, the pregnancy continued to term, resulting in the delivery of a healthy male infant. To our knowledge, this represents the first reported case worldwide of a successful full-term delivery following gestational psittacosis. This case underscores the critical importance of early mNGS-based diagnosis, multidisciplinary collaboration, and appropriate antimicrobial therapy in optimizing maternal and neonatal outcomes, providing a valuable clinical reference for managing this life-threatening zoonosis during pregnancy.}, }
@article {pmid42417135, year = {2026}, author = {Walker, WB and Neven, LG}, title = {eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {4}, pages = {}, doi = {10.1093/jisesa/ieag062}, pmid = {42417135}, issn = {1536-2442}, support = {//Washington State Department of Agriculture Specialty Crops Block/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA, Environmental/analysis ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Sequence Analysis, DNA ; Insecta/genetics/classification ; Extrachromosomal DNA ; }, abstract = {Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.}, }
@article {pmid42417706, year = {2026}, author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY}, title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c02819}, pmid = {42417706}, issn = {1520-5118}, abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.}, }
@article {pmid42417716, year = {2026}, author = {Wang, Y and Luo, X and Ji, Y and Zhu, T and Zhao, Y and Tong, Y and Ni, BJ and Liu, Y}, title = {1,3-Dichloro-5,5-dimethylhydantoin (DCDMH)-Driven Sludge Pretreatment for Organic Carbon Valorization: Mechanistic Insights into Controlled Oxidative Disruption and Hormesis-Mediated Metabolic Reshaping.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16484}, pmid = {42417716}, issn = {1520-5851}, abstract = {Organic carbon valorization via anaerobic sludge fermentation is intrinsically constrained by biopolymer recalcitrance and methanogenic diversion. We introduced 1,3-Dichloro-5,5-dimethylhydantoin (DCDMH) pretreatment leveraging controlled oxidative disruption and microbial metabolic regulation to boost short-chain fatty acid (SCFA) production. At optimal dosage (0.025 g/g TSS), SCFA yield increased by 192.1%, driven by enhanced substrate liberation and biochemical conversion. Molecular docking and 2D-COS FTIR analyses collectively indicate that the N-Cl moiety of DCDMH preferentially oxidized hydrophobic proteins within extracellular polymeric substances, while the derived HClO could penetrate cells to damage intracellular components. This dual action disrupted structural integrity, accelerating macromolecular substrate release and conversion, and enriching stress-tolerant hydrolytic/acidogenic bacteria. Sustained HClO release established oxidative stress wherein reactive oxygen species (ROS) functioned as metabolic signals beyond mere damage indicators. Moderate intracellular ROS stress stimulated substrate acidogenesis while suppressing methanogenic carbon sinks, and enhanced the gene abundances associated with antioxidant defenses and acidogenic pathways. Crucially, this work reveals for the first time the hormetic effect of DCDMH-derived HClO on acidogenic metabolism, providing a new insight into the application of chlorine-containing disinfectants in related fields.}, }
@article {pmid42417728, year = {2026}, author = {Välikangas, T and Fritze, H and Pitkänen, JM and Peltoniemi, K and Järvi-Laturi, E and Christensen, TR and Väisänen, M and Lämsä, J and Paavola, R and Hultman, J}, title = {Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag072}, pmid = {42417728}, issn = {1574-6941}, abstract = {Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect soil microorganisms involved in methane (CH4) cycling and nitrous oxide (N2O) production/reduction. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH4 flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH4 fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.}, }
@article {pmid42417745, year = {2026}, author = {Antunes, TPB and Antunes, E}, title = {Next-generation molecular tools in veterinary parasitology: advances, challenges, and perspectives in the diagnosis of emerging parasites.}, journal = {Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria}, volume = {35}, number = {2}, pages = {e016525}, doi = {10.1590/S1984-29612026023}, pmid = {42417745}, issn = {1984-2961}, mesh = {Animals ; *Parasitic Diseases, Animal/diagnosis/parasitology ; *Parasitology/methods/trends ; *Communicable Diseases, Emerging/diagnosis/veterinary/parasitology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Advances in molecular technologies have revolutionized veterinary parasitology, providing highly sensitive and specific tools for the detection, characterization, and surveillance of parasites in domestic and wildlife species. Approaches such as next-generation sequencing, metabarcoding, and metagenomics have significantly enhanced the ability to identify previously unknown or uncultivable species, detect complex coinfections, and deepen our understanding of parasite genetic diversity, evolution, and population dynamics. Beyond their impact on laboratory diagnostics, these tools have proven essential for the early detection of zoonoses, environmental monitoring, and the development of integrated surveillance systems under the One Health framework. This review synthesizes the major technological advances and their practical applications in both global and Latin American contexts, particularly Brazilian, highlighting how the incorporation of these tools has the potential to transform strategies for surveillance, prevention, and response to emerging and re-emerging parasitic diseases. Challenges related to standardization, cost, infrastructure, and technology transfer are also discussed, along with future perspectives for large-scale implementation aimed at strengthening diagnostic capacity and epidemiological surveillance in the face of increasing parasitic threats in a rapidly changing world.}, }
@article {pmid42417967, year = {2026}, author = {Lin, Z and Ma, Y and Wu, H and Lu, Z and Zhuang, X and Zhao, M and Peng, S and Lin, F and Zheng, K and Li, Z}, title = {Effects of lemongrass (Cymbopogon citratus) on slaughter performance, meat quality, and intestinal health in Muscovy ducks.}, journal = {British poultry science}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/00071668.2026.2670474}, pmid = {42417967}, issn = {1466-1799}, abstract = {1. This study tested the effects of dietary lemongrass (LG) supplementation on production performance, meat quality and intestinal health of Muscovy ducks. A 42 d feeding trial used four treatment diets (0%, 2%, 4% or 6% LG) fed as part of a commercial diet after 20 d rearing from day old on a basal diet.2. The results revealed that 6% LG supplementation significantly improved slaughter performance, notably increasing full eviscerated weight (p < 0.05).3. Meat nutritional quality was enhanced by higher amino acids (cysteine and methionine in breast muscle; tyrosine in leg muscle) and beneficial polyunsaturated fatty acids (PUFA) including C22:6n3 (DHA) and C20:5n3 (EPA; p < 0.05).4. Intestinal health was improved, with LG which enhanced duodenal morphology manifested as increased villus length and villus-to-crypt ratio. There was up-regulated gene expression for intestinal barrier proteins (ZO-1, Claudin-1), immune factors (sIgA, IFN-γ) and antioxidant enzymes (SOD, GSH-Px; p < 0.05).5. Metagenomic and metabolomic analyses revealed a restructured caecal microbiota, characterised by increased commensal Ligilactobacillus spp. inhibited pathogenic Burkholderia spp. and increased production of beneficial metabolites, including butyric acid (p < 0.05), which acts as an energy source for enterocytes.6. This trial demonstrated that LG can enhance both growth performance outcomes and meat quality in Muscovy ducks through gut health modulation, supporting its application in sustainable poultry farming.}, }
@article {pmid42417977, year = {2026}, author = {Yu, SJ and Stanley, D and Van, TTH and Steel, JC and Bajagai, YS}, title = {Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13948-1}, pmid = {42417977}, issn = {1432-0614}, support = {PRO-017656//AgriFutures Australia/ ; PRO-017656//AgriFutures Australia/ ; }, abstract = {Integrating human, animal, and environmental health is crucial for combating infectious diseases, as an estimated 60 to 75% of emerging infectious diseases originate from zoonotic sources globally. In this study, we analysed 1274 shotgun metagenomic faecal samples of humans, pigs, and chickens collected across multiple countries to estimate levels of microbial sharing at the species-level genome bins (SGBs) resolution. We confirm that host species, rather than geography, significantly structures the gut microbial community, as shown by alpha and beta diversity analyses. Despite this high host specificity, we identified substantial cross-host sharing of SGBs, including taxa recognised as pathogens such as Escherichia coli, Clostridium perfringens, Clostridium innocuum, Clostridium disporicum, Enterococcus species, and Streptococcus alactolyticus. Core taxa were predominantly host-specific, while non-core taxa were more frequently shared across humans, pigs, and chickens. LEfSe analysis identified distinctive microbial signatures for each host, further supporting differences in community composition. These findings demonstrate that unrelated and geographically distant humans and livestock can harbour highly similar microbial populations with pathogenic potential. This work provides molecular evidence supporting the need for integrated One Health surveillance to better detect, manage, and prevent zoonotic and reverse zoonotic transmission events across interconnected human, animal, and environmental systems. KEY POINTS: • There is substantial cross-host sharing of species-level genome bins, including potential pathogens • Core taxa are predominantly host-specific • Non-core taxa are more likely to be shared across humans, pigs, and chickens.}, }
@article {pmid42418234, year = {2026}, author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC}, title = {Evolving strategies for virus discovery.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001785}, pmid = {42418234}, issn = {2057-5858}, mesh = {*Viruses/genetics/isolation &amp; purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; }, abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.}, }
@article {pmid42418242, year = {2026}, author = {Robinson, JM and Guentas, L and Breed, MF}, title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001777}, pmid = {42418242}, issn = {2057-5858}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; }, abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.}, }
@article {pmid42418263, year = {2026}, author = {Bai, W and Huang, G and Rao, X and Li, H and Zhou, T and Yang, Y and Wei, W}, title = {Efficacy, Safety, and Mechanism of the Qi-Lian-Xiao-Pi Prescription (WW-1) for Chronic Atrophic Gastritis After Helicobacter Pylori Eradication: Protocol for a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e90965}, doi = {10.2196/90965}, pmid = {42418263}, issn = {1929-0748}, mesh = {Humans ; *Gastritis, Atrophic/drug therapy ; *Helicobacter Infections/drug therapy ; Double-Blind Method ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; *Helicobacter pylori/drug effects ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Female ; Male ; Treatment Outcome ; }, abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is widely recognized as one of the precancerous lesions of gastric cancer. Helicobacter pylori is one of the important risk factors for CAG and gastric cancer. However, a large proportion of patients with CAG cannot avoid developing gastric cancer even after eradicating H pylori. It is necessary to find a safe and effective treatment to suppress this "inflammation-cancer" progression. The Qi-Lian-Xiao-Pi prescription (WW-1), a traditional Chinese medicine (TCM), has been reported to be effective in the treatment of CAG. However, the evidence is subject to methodological limitations.<br><br>OBJECTIVE: This study aimed to evaluate the efficacy, safety, and mechanism of the WW-1 in patients with CAG following successful H pylori eradication.<br><br>METHODS: This study is a rigorous parallel-arm, randomized, placebo-controlled, multicenter, double-blinded trial. A total of 110 eligible participants with a confirmed diagnosis of CAG after H pylori eradication are being enrolled and randomly assigned in a 1:1 ratio to either the intervention group (WW-1) or the control group (WW-1 placebo). Key eligibility criteria include confirmed CAG by histopathology, documented successful H pylori eradication, and compliance with predefined inclusion and exclusion criteria. The treatment duration is 24 weeks. Blinded histopathological assessments using the Operative Link on Gastritis Assessment and Operative Link on Gastric Intestinal Metaplasia Assessment staging systems will serve as primary outcomes. Secondary outcomes include improvement rates of gastric mucosal gland atrophy and intestinal metaplasia, as well as TCM syndrome scores. Safety will be assessed through monitoring vital signs, adverse events, blood, urine, and stool tests, liver and kidney function, and electrocardiography. Additionally, gastric mucosal DNA methylation and metagenomic sequencing of digestive tract microbiota (including saliva, tongue coating, gastric, and intestinal samples) will be analyzed to explore potential mechanisms of WW-1.<br><br>RESULTS: The funding began in November 2023. The study was officially initiated on April 20, 2025, with the enrollment of the first participant. The final study results, including efficacy outcomes, safety profiles, and mechanistic insights, are expected to be released in October 2026 after comprehensive data analysis and verification.<br><br>CONCLUSIONS: This study is designed to determine whether WW-1 can improve CAG by modulating gastric mucosal DNA methylation and the digestive tract microbiota. It represents a prospective clinical trial in TCM that aims to evaluate therapeutic effects on CAG through the regulation of microbiota homeostasis and epigenetic mechanisms. The findings of this study are expected to provide evidence regarding the efficacy and safety of WW-1 and contribute to the development of therapeutic strategies and future drug research for CAG.<br><br>DERR1-10.2196/90965.}, }
@article {pmid42418319, year = {2026}, author = {Li, Z and Chi, B and Ruan, C and Song, L and Dong, L and Li, A and Zheng, T and Wang, L and Huang, Y and Huang, J and Du, H and Zheng, X and Du, W and Dong, Z and Liu, Y and Huang, L and Dai, X}, title = {A deep-sea rare bacterium exhibits extraordinary metabolic versatility.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {117671}, doi = {10.1016/j.celrep.2026.117671}, pmid = {42418319}, issn = {2211-1247}, abstract = {The rare biosphere harbors immense microbial diversity, yet most low-abundance taxa remain uncultured and functionally enigmatic. Here, we isolated strain D14[T] from deep-sea water, and propose to classify it as a novel species, Metabolovarius oceani sp. nov., within the novel family Metabolovariaceae fam. nov. M. oceani represents the first cultivated member of the candidate family NORP267, a globally distributed but elusive alphaproteobacterial lineage known only from metagenome-assembled genomes. It possesses broad metabolic capabilities, including CO2 fixation, polyhydroxyalkanoate biosynthesis, complete denitrification and thiosulfate oxidation, and is capable of aerobic growth under both heterotrophic and autotrophic conditions and of anaerobic autotrophic denitrification via thiosulfate oxidation. Despite its versatile metabolic repertoire and global distribution, Metabolovariaceae remains consistently low in abundance across diverse habitats. The isolation of M. oceani permits direct experimental insights into the evolutionary adaptations, physiological resilience, and potential ecosystem roles of rare but metabolically versatile microorganisms within the microbial dark matter.}, }
@article {pmid42418574, year = {2026}, author = {Caceres, C and Krasovec, M and Crispi, O and Gourbiere, S and Piganeau, G}, title = {Effect of cellular nutrient economy on the evolution of genome size in phytoplankton.}, journal = {Science advances}, volume = {12}, number = {28}, pages = {eaee2207}, doi = {10.1126/sciadv.aee2207}, pmid = {42418574}, issn = {2375-2548}, mesh = {*Phytoplankton/genetics/metabolism ; *Genome Size ; Selection, Genetic ; *Evolution, Molecular ; *Nutrients/metabolism ; Genetic Drift ; INDEL Mutation ; Models, Genetic ; }, abstract = {The origin of genome size variation remains a central question in evolutionary biology. While energetic costs have been proposed to influence genome size through selection on insertions and deletions (indels), nutrient availability may be a more relevant constraint in primary producers such as phytoplankton. We derived an expression for the selection coefficient of indels based on the phosphorus and nitrogen costs of nucleotides and the cellular nutrient requirements. Selection coefficient estimates indicate that natural selection dominates over genetic drift and favors the fixation of mutations that reduce genome size in phytoplankton with low nutrient requirements. Model predictions are supported by comparative genomics and metagenomic analyses. Together, this model provides a rigorous quantitative framework for understanding genome size evolution, particularly in small cells and oligotrophic environments, highlighting how nutrient limitation drives genome streamlining.}, }
@article {pmid42418675, year = {2026}, author = {Zhang, M and Cao, Y and Yao, F and Lin, W and Lan, X and Sun, X and Wang, Y and Tan, Z and Ren, Y and Huang, Y and Sun, W}, title = {Antimonate Reduction Coupled to Anaerobic Ammonium Oxidation in Paddy Soil: Process Evidence and a Putative Syntrophic Microbial Model.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00276}, pmid = {42418675}, issn = {1520-5851}, abstract = {The coupling of metal(loid) (e.g., Fe(III) and As(V)) reduction with anaerobic ammonium oxidation (anammox) is emerging as a critical process impacting the fate of N and metal(loid)s. Despite the chemical analogs of As and Sb, Sb(V) reduction exhibits different thermodynamics from As(V) reduction, which may constrain its coupling with anammox (termed "Sbammox") and impose stricter limitations on the metabolic pathway. To determine the occurrence and mechanism of Sbammox, Sb-contaminated paddy soil was used to establish the microcosms. Using [15]N isotope tracing, we confirmed the existence of Sbammox with the synchronous [15]N-N2 and Sb(III) productions and their concurrent suppressions by the inhibitor acetylene (C2H2). In contrast to the single-species-driving Asammox and Feammox, a tripartite syntrophic consortium was proposed to mediate Sbammox by DNA-stable isotope probing (SIP) combined with amplicon sequencing and metagenomic analysis. In this consortium, Ramlibacter and Candidatus Brocadia are proposed as the candidate Sb(V) reducer and ammonium oxidizer, respectively, with Geobacter hypothesized to mediate interspecies electron transfer. This distinct microbial strategy suggests that the specific thermodynamic constraints of Sb(V) necessitate a cooperative strategy rather than a solitary metabolic pathway. These findings are essential for understanding the divergent biogeochemical behaviors of As and Sb and underscore a critical dual risk in exacerbating nitrogen loss and Sb toxicity in agro-ecosystems.}, }
@article {pmid42418904, year = {2026}, author = {Yu, J and Wan, Y and Peng, Y and Liang, S and Chan, FKL and Ng, SC and Tun, HM}, title = {Multi-cohort evidence for impaired microbial support of the methionine cycle in children with autism spectrum disorder.}, journal = {Psychiatry research}, volume = {364}, number = {}, pages = {117317}, doi = {10.1016/j.psychres.2026.117317}, pmid = {42418904}, issn = {1872-7123}, abstract = {The contribution of gut microbiota to outcomes of autism spectrum disorders (ASD) has been increasingly appreciated in recent years. With the accumulating evidence on ASD-driven alterations of the gut microbiota, heterogeneities arise across different reports. To account for variabilities in gut microbiota, clinical representations of ASD and data processing approaches, as well as limitations in sample sizes among the existing gut microbiota studies for ASD, the present multi-cohort analysis applied a standard bioinformatic and statistical pipeline on the publicly available gut metagenomic sequencing data for 674 samples, including 326 TD and 348 ASD individuals, collected from eight studies across three main geographical regions. Throughout the analysis, we identified taxonomic profiles of the gut microbiota exhibited more pronounced dysbiosis associated with ASD and between-study variations compared to functional profiles. Differentially abundant taxonomic and pathway markers were identified and validated for their consistent response to ASD across different studies. Co-occurring deficits in microbial pathways for salvaging adenosylcobalamin and S-adenosyl-L-methionine and biosynthesis of methionine in children with ASD point to a reduced microbial support for the host methionine cycle. Species from Faecalibacterium, Bacteroides, Blautia and Bifidobacterium were identified as microbial contributors to ASD-deficient microbial pathways, particularly those related to the methionine cycle. Therefore, the generalisable ASD-deficient contributors to the methionine cycle, such as Blautia wexlerae, Bacteroides stercoris and Streptococcus thermophilus, could be further investigated for their role in therapeutic applications for ASD.}, }
@article {pmid42418982, year = {2026}, author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Metagenomic insights into microbial drivers of organic micropollutant removal in wastewater-impacted riverbank filtration.}, journal = {Water research}, volume = {305}, number = {}, pages = {126421}, doi = {10.1016/j.watres.2026.126421}, pmid = {42418982}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) in wastewater treatment plant (WWTP) effluent pose persistent risks to aquatic ecosystems and drinking water sources. Riverbank filtration (RBF) is a nature-based treatment process, yet the compartment-specific roles of riverbed sediment and downstream soil in OMP attenuation remain poorly resolved under wastewater-impacted conditions. Here, we combined targeted chemical analysis, OMP property compilation, shotgun metagenomics, EnviPath-based biotransformation annotation, and exploratory network analysis to investigate OMP attenuation in a laboratory-scale RBF system treating real WWTP effluent for 10 months. Nineteen OMPs were monitored along a sequential sediment-soil filtration pathway. Sediment preferentially attenuated hydrophilic or charged compounds, including lidocaine, amantadine, and sotalol, whereas soil contributed more strongly to the attenuation of naproxen, atenolol, and losartan. Metagenomic profiling revealed distinct microbial communities and functional gene repertoires between sediment and soil after long-term operation. Sediment harbored higher relative abundances of genes associated with oxidative xenobiotic transformation, including cytochrome P450-related enzymes, demethylases, dehydrogenases, oxidases, and aromatic compound degradation pathways. An exploratory Spearman network further identified associations among microbial genera, EnviPath-annotated candidate biotransformation genes, and OMP removal rates, including 17 KO-OMP links supported by both correlation and pathway annotation. These findings indicate that sediment and soil develop complementary microbial functional potentials that may support compound-specific OMP attenuation. This study provides a mechanistic basis for optimizing sediment-soil configurations in wastewater-impacted RBF systems and for improving nature-based barriers against diverse OMP mixtures.}, }
@article {pmid42418983, year = {2026}, author = {Huang, Y and Liu, P and Wu, J and Li, J and Tuo, J and Zhang, Q and Zhang, XX}, title = {Diverse and ultraviolet-inducible phage-associated antibiotic resistance genes in wastewater treatment plants.}, journal = {Water research}, volume = {305}, number = {}, pages = {126419}, doi = {10.1016/j.watres.2026.126419}, pmid = {42418983}, issn = {1879-2448}, abstract = {Phage-mediated transduction is an underappreciated route of antibiotic resistance gene (ARG) dissemination in wastewater treatment plants (WWTPs), yet the diversity and fate of phage-associated ARGs remain poorly resolved. Here, a 5-year monthly metagenomic survey of 538 influent, activated sludge, and effluent samples from two municipal WWTPs in Nanjing, China, was combined with laboratory-scale UV dose-response experiments to profile the phage-encoded resistome and its fate along the treatment train. A total of 168 phage-associated ARG subtypes spanning 23 drug classes were recovered, approximately 1.7-fold more than catalogued for comparable environments in IMG/VR, with multidrug- and diaminopyrimidine-resistance genes dominating the catalogue and efflux pumps constituting the major resistance mechanism; 64.9 % of subtypes were WWTP-exclusive, highlighting pronounced habitat specificity. Caudoviricetes overwhelmingly carried the ARGs and were primarily putatively linked to Gammaproteobacteria, Betaproteobacteria, and Actinobacteria. Biological treatment markedly restructured the phage-associated resistome (PERMANOVA R[2] = 0.19-0.34, p = 0.001), whereas conventional UV disinfection produced no significant bulk abundance reduction (p > 0.05). Dose-response experiments across 0-80 mJ/cm[2] revealed a biphasic pattern: low-to-moderate doses (10-20 mJ/cm[2]) induced prophages and transiently elevated phage-fraction ARG concentrations by 0.3-0.8 log10 copies/L (≈2- to 6-fold), whereas higher doses (≥40 mJ/cm[2]) drove progressive inactivation. These findings expose a previously underappreciated paradoxical release of phage-associated ARGs within the operational UV window of Chinese municipal reactors and argue for coupling UV with complementary barriers to curb transduction-mediated resistance dissemination.}, }
@article {pmid42419029, year = {2026}, author = {Elmaghrabi, MM and Alghamdi, S and Alzeer, S and Magrashi, AM and Bakheet, RH and Alabden, DZ and Alshuhri, S and Abouelhoda, MM and Alrashaid, BA and Tayeb, HT}, title = {Metagenomic investigation of VIM-type metallo-β-lactamase-producing multidrug-resistant Pseudomonas aeruginosa associated with a hospital outbreak across multiple hospital units in Saudi Arabia.}, journal = {Journal of infection and public health}, volume = {19}, number = {8}, pages = {103299}, doi = {10.1016/j.jiph.2026.103299}, pmid = {42419029}, issn = {1876-035X}, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) represent a public health challenge, particularly when associated with VIM-type metallo-β-lactamases (MBLs), which limit therapeutic options. Conventional microbiological methods may underestimate resistance determinants and transmission dynamics. Long-read metagenomic sequencing is a promising approach for Pathogen detection, resistome characterization, and genomic surveillance.<br><br>OBJECTIVES: The study's objectives were to characterize the resistome, including detection of the blaVIM gene, assess genomic relatedness and potential transmission dynamics, and evaluate the diagnostic value of metagenomics compared with conventional microbiological approaches.<br><br>METHODS: This retrospective infection control investigation included seven hospitalized patients from multiple hospital units. Clinical specimens included blood, respiratory specimens, surgical tissue, and device-associated material. Conventional microbiological investigations included bacterial culture, identification, and antimicrobial susceptibility testing (AST) using the VITEK 2 automated system. Carbapenemase genes were detected using Xpert Carba-R. Long-read metagenomic sequencing was conducted using Oxford Nanopore Technologies (ONT) on the GridION platform. Bioinformatic analysis was performed using the CosmosID platform for taxonomic profiling, antimicrobial resistance gene detection, and genomic relatedness assessment.<br><br>RESULTS: Conventional microbiological methods identified carbapenem-resistant Pseudomonas aeruginosa (CRPA) in five cases, whereas ONT sequencing detected the blaVIM gene in all seven samples, demonstrating superior diagnostic sensitivity. A highly conserved resistome profile was identified across all investigated cases, including multiple &#x3b2;-lactamase and aminoglycoside, fluoroquinolone, and polymyxin-associated resistance determinants. Genomic relatedness analysis demonstrated close clustering patterns with minimal genomic variability, suggesting possible circulation of closely related MDR strains.<br><br>CONCLUSION: These findings highlight the added value of ONT sequencing in identifying concealed resistance determinants and improving transmission tracking compared with conventional diagnostic approaches. Future investigations involving larger sample sizes and environmental surveillance are needed to further clarify transmission dynamics and potential reservoirs of VIM-producing P. aeruginosa.}, }
@article {pmid42419186, year = {2026}, author = {Liu, H}, title = {Computational strategies for uncovering bacterial biocatalysts in the biodegradation of persistent organic pollutants.}, journal = {Computational biology and chemistry}, volume = {124}, number = {Pt 2}, pages = {109222}, doi = {10.1016/j.compbiolchem.2026.109222}, pmid = {42419186}, issn = {1476-928X}, abstract = {The rapid accumulation of persistent organic pollutants (POPs) in soil, sediment, and aquatic environments presents a critical global challenge that demands sustainable and efficient remediation strategies. In this context, computational enzymology has emerged as a powerful framework for accelerating the discovery, validation, and optimization of pollutant-degrading enzymes. However, prior POP-biodegradation reviews have typically treated enzymes, docking, molecular dynamics (MD), metagenomics, and artificial intelligence (AI) as separate topics (e.g., docking-focused reviews (1), metagenomics-focused reviews (2), and structural-mechanism-focused reviews (3) rather than as parts of a single bacterial-enzyme discovery pipeline. This review fills that gap by focusing specifically on bacterial biocatalysts and by integrating structure prediction, docking, MD, metagenomic mining, and machine learning-guided design into one workflow. Its main contribution is a unified framework that links sequence discovery to structural screening, dynamic validation, and experimental prioritization. This work provides a comprehensive synthesis of molecular docking, molecular dynamics (MD) simulations, and integrative artificial intelligence (AI)-driven approaches applied to biodegradation research. We highlight how molecular docking functions as a high-throughput, structure-based filter for prioritizing enzyme-pollutant interactions, while MD simulations supply the essential temporal and mechanistic resolution required to evaluate enzyme flexibility, substrate access pathways, and catalytic competence under realistic environmental conditions. Case studies across diverse pollutant classes including polycyclic aromatic hydrocarbons, organochlorine pesticides, polychlorinated biphenyls, and plastic additives demonstrate that workflows combining docking with microsecond-scale MD and MM-PBSA/GBSA free-energy calculations show markedly higher experimental reproducibility than static docking alone. Beyond individual methods, this article emphasizes the growing importance of integrative computational strategies that unite metagenomics, AI-based structure prediction, enhanced-sampling MD, and machine learning-guided directed evolution within a closed-loop Design-Build-Test-Learn (DBTL) paradigm. Such pipelines enable systematic navigation of vast biological sequence space while simultaneously balancing enzyme stability, conformational flexibility, and catalytic efficiency. Finally, we discuss prevailing challenges encompassing computational cost, structural uncertainty in apo-state predictions, force-field limitations for halogenated substrates, and the translational gap between in silico predictions and environmental field deployment, and outline future directions toward scalable, low-energy, and environmentally robust bioremediation technologies. Collectively, these advances position computational modeling as a cornerstone of next-generation, eco-friendly enzyme discovery.}, }
@article {pmid42419222, year = {2026}, author = {Liang, Y and Gao, H and Chen, F and Sun, J and Sun, G and Wang, Z and Li, Y and Liu, H and Geng, M and Li, J and Zhang, Y}, title = {Bilateral intranigral α-synuclein seeding in A53T transgenic mice drives early Parkinsonism and concurrent gut dysbiosis.}, journal = {Biochemical and biophysical research communications}, volume = {830}, number = {}, pages = {154244}, doi = {10.1016/j.bbrc.2026.154244}, pmid = {42419222}, issn = {1090-2104}, abstract = {Heterozygous A53T α-synuclein transgenic mice (M83 line) typically exhibit late-onset Parkinson's disease (PD) symptoms. This study established an accelerated PD model via bilateral intranigral injection of α-synuclein preformed fibrils (PFF) to characterize central and peripheral pathologies. Three-month-old heterozygous A53T mice received bilateral substantia nigra injections of α-synuclein PFF or PBS. Motor function was assessed monthly. Following the onset of motor deficits, the substantia nigra was harvested for immunohistochemistry and colons were harvested for H&amp;E, transcriptomic analysis and western blotting, while gut microbiota composition was assessed using metagenomic sequencing. Three months post-injection, PFF-treated mice exhibited significant motor deficits, dopaminergic neuron loss, and nigral α-synuclein aggregation, with no sex differences. Peripherally, mice displayed increased α-synuclein in colon, impaired gut motility, reduced Occludin expression indicating barrier damage, and colonic inflammation. Metagenomics identified gut dysbiosis characterized by a skewed Bacillota/Bacteroidota ratio, Lactobacillus depletion, and enrichment of inflammation-associated taxa. Bilateral intranigral α-synuclein PFF injection in A53T mice successfully induces an early-onset, progressive PD phenotype encompassing motor impairments, nigrostriatal neurodegeneration. Crucially, the model recapitulates key peripheral manifestations, including gastrointestinal dysfunction and microbial dysbiosis. These findings provide compelling evidence for a descending brain-to-gut pathological axis where central α-synuclein pathology drives distal gut alterations. This optimized model offers a valuable platform for investigating multi-system PD progression and bidirectional brain-gut communication mechanisms.}, }
@article {pmid42419237, year = {2026}, author = {Li, T and Xu, J and He, S and Zhao, Q and Liu, J and Shi, Y}, title = {Salinity of oxidation pond effluent regulates the fate of antibiotic resistance genes in the soil-leachate continuum by selecting a salt-adaptive resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142854}, doi = {10.1016/j.jhazmat.2026.142854}, pmid = {42419237}, issn = {1873-3336}, abstract = {Oxidation pond effluent (OPE) reuse can introduce antibiotic resistance genes (ARGs) into agricultural soils. Yet, how OPE salinity regulates ARG fate across the soil-leachate continuum remains poorly understood. Soil column experiments were conducted using three OPE salinity levels with electrical conductivities of 4.35, 8.24, and 13.17 dS/m, combined with high-throughput quantitative PCR and metagenomics. Results showed that although increasing OPE salinity reduced the mean ARG abundance across the soil-leachate continuum, its effects were clearly depth dependent, with slight ARG enrichment of 10.78%-17.26% in surface soil (0-30 cm), a unimodal response in the 30-60 cm layer, and marked reduction of 24.17%-42.60% in deeper soil (60-90 cm) and leachate. More importantly, increasing OPE salinity reduced total ARG abundance by about 14.13% in OPE, but ARG abundance still increased in surface soil after irrigation. Metagenomic analyses showed increasing OPE salinity selectively enriched ARGs related to antibiotic efflux and antibiotic inactivation, indicating that salt-adaptive ARG enrichment better explained topsoil ARG accumulation than total ARG input load alone under OPE irrigation. In addition, surface ARG enrichment was linked to the selection of bacterial groups capable of maintaining ARGs under saline conditions, and the co-localization of salt-tolerance genes, ARGs, and MGEs. In deeper soil and leachate, ARG attenuation was driven mainly by reduced bacterial abundance under continued salinity accumulation. These findings provide a new perspective on ARG risk under saline wastewater irrigation by showing that salinity-driven reshaping of the introduced resistome and salinity accumulation regulate ARG fate and downward transport potential.}, }
@article {pmid42419245, year = {2026}, author = {Han, Z and Zhang, Y and Luan, X and Feng, H and Wang, Y and Deng, Y and Hu, C and Yang, M}, title = {Clinically prevalent transposons contribute to erm gene dissemination in the field soil under pseudo-persistent erythromycin contamination.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142927}, doi = {10.1016/j.jhazmat.2026.142927}, pmid = {42419245}, issn = {1873-3336}, abstract = {Clinically relevant antibiotic resistance genes (ARGs) or their ancestral genes are widespread in natural soil microbiome at ultralow abundance. Whether and how long-term antibiotic pressure in soil accelerate dissemination of these ARGs remain unclear. Here, annual cycle of erythromycin exposure at levels around 5-20 μg∙kg[-1] was conducted in previously undisturbed field soil for consecutive five years, to simulate the pseudo-persistent characteristic of antibiotic contamination in soil environment. The primary clinically relevant macrolide resistance genes, rRNA methyltransferase genes (erm genes), were initially rare but gradually enriched, exhibiting a 37.8-fold increase after five years, which was greatly higher than macrolide efflux pump genes and inactivation genes (less than 2.3-fold). Among diverse mobile genetic elements, transposase gene tnpA exhibited potential association with the horizontal transfer of erm genes during long-term erythromycin exposure. From genetic and statistical evidence, enriched erm genes were presumed to locate on Bacilli with mobile transposable elements Tn554 and Tn551, which were clinically prevalent gene clusters in pathogens-Enterococcus and Staphylococcus. Thus, there may be a historical contribution of long-term erythromycin contamination to erm-carrying clinical transposable elements in soil microbiome. Our findings also demonstrated soil erythromycin exposure at levels much lower than laboratory-determined minimal selective concentrations (MSCs) still exhibits long-term effects on erm genes. Taking pseudo-persistent characteristic of antibiotic contamination, we further proposed long-term in-situ assessment with endpoint of clinically relevant ARGs to obtain a real-world MSC in the future studies.}, }
@article {pmid42419262, year = {2026}, author = {Gelsinger, DR and Wang, HH}, title = {Toward precision microbiome therapeutics: From black box to blueprint.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {7}, pages = {1157-1161}, doi = {10.1016/j.chom.2026.06.014}, pmid = {42419262}, issn = {1934-6069}, mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/physiology/genetics ; Bacteria/genetics ; Animals ; Gene Editing ; *Precision Medicine/methods ; Microbiota ; }, abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.}, }
@article {pmid42419272, year = {2026}, author = {Crysler, A and de la Fuente-Nunez, C}, title = {Mining the code of life for new antibiotics.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {7}, pages = {1273-1284}, doi = {10.1016/j.chom.2026.06.007}, pmid = {42419272}, issn = {1934-6069}, mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Discovery/methods ; Antimicrobial Peptides/pharmacology ; Humans ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics ; Generative Artificial Intelligence ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) is outpacing antibiotic development, creating an urgent need for discovery strategies that are faster, broader, and more systematic. Here, we review the transition from classical "dirt mining" and phenotypic screening toward digital discovery approaches that treat chemical structures and biological sequences as searchable, engineerable substrates for antibiotic innovation. Modern extensions of conventional screening, including in situ cultivation, co-culture, and microfluidics, have broadened access to previously uncultured microbes. Computer-aided approaches spanning virtual screening, molecular networking, and deep learning have enabled identification of unconventional antibacterial scaffolds from ultra-large chemical libraries. Mining genomes, proteomes, and metagenomes has uncovered antimicrobial peptides, encrypted peptides, and biosynthetic gene clusters encoding novel small-molecule antibiotics. Generative AI now enables design of peptides and small molecules under multiobjective constraints, including potency, toxicity, stability, and resistance risk. Together, these advances point toward discovery platforms that improve novelty, hit rates, and long-term durability in the face of AMR.}, }
@article {pmid42419418, year = {2026}, author = {Lin, YR and Tseng, HY and Lai, ZL and Hsueh, PR}, title = {Metagenomic next-generation sequencing facilitates the diagnosis of disseminated Mycobacterium tuberculosis infection in a patient with complex sepsis.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107918}, doi = {10.1016/j.ijantimicag.2026.107918}, pmid = {42419418}, issn = {1872-7913}, }
@article {pmid42419508, year = {2026}, author = {Hering-Peter, C and Schulz, R}, title = {Physiological responses of floc-forming microalgae-bacteria consortia to environmental perturbations.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135341}, doi = {10.1016/j.biortech.2026.135341}, pmid = {42419508}, issn = {1873-2976}, abstract = {Fast-sedimenting microalgae-bacteria consortia (MBC) offer a cost-efficient pathway for biomass harvesting while remediating polluted water bodies in chemostatic photobioreactors. Understanding how abiotic parameters affect floc morphology, sinking properties and metagenomic species composition remains critical for optimization of these specific bioreactors. This study investigated whether fast-sedimenting MBC maintain structural resilience under moderate stress but lose stability beyond critical physiological tipping points. By investigating the physiological boundaries of five environmental factors, we identified clear operational thresholds. Moderate perturbations including light intensities up to 1500 µmol m[-2] s[-1], salinities from 0 to 35 PSU and low antibiotic concentrations showed no statistically significant impact on settling efficiency. In contrast, extreme pH at 12 and temperatures at 45 °C reduced recovery rates by more than 50 % compared to controls maintaining above 87 % efficiency. The surface charge decreased from -27.94 mV to -4.83 mV under acidic conditions at pH 3, indicating electrostatic destabilization of the floc matrix. Dominance of the cyanobacterium Thermoleptolyngbya spp. persisted above 70 % abundance across all treatments. These findings define a safe operating envelope between pH 6-9 and temperatures from 15 to 35 °C necessary to maintain gravity-driven sedimentation. This work provides quantitative boundaries where biological buffering fails, enabling predictive reactor design that avoids biomass washout in continuous cultivation systems.}, }
@article {pmid42419510, year = {2026}, author = {He, J and Liu, Y and Zhao, Y and Wei, T and Gong, Z and Wu, Y and Kang, X and Zhang, W and Ma, J and Chu, Z and Wang, R}, title = {Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135349}, doi = {10.1016/j.biortech.2026.135349}, pmid = {42419510}, issn = {1873-2976}, abstract = {Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900 °C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2 % compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5 %), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55 %. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.}, }
@article {pmid42419591, year = {2026}, author = {Kim, S and Seo, H and Jo, S and Rahim, MA and Hossain, MS and Shuvo, MSH and Jeong, SY and Lee, MY and Kim, KH and Lee, N and Won, JH and Song, HY and Yoon, SY}, title = {Oral Sodium Butyrate Supplementation, Gut Microbiome Modulation, and Reduced Acute Graft-versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.07.006}, pmid = {42419591}, issn = {2666-6367}, abstract = {BACKGROUND: Acute graft-versus-host disease (aGVHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Disruption of the gut microbiome during transplantation has been implicated in the pathogenesis of aGVHD, yet clinically applicable strategies to modulate the microbiome in immunocompromised patients remain limited.<br><br>OBJECTIVES: To evaluate the association between oral sodium butyrate supplementation and the incidence and severity of aGVHD, and to investigate its impact on gut microbiome recovery following allo-HSCT.<br><br>STUDY DESIGN: In this prospective, single-center study, 39 consecutive patients undergoing allo-HSCT received oral sodium butyrate (1,200 mg/day) from neutrophil engraftment to day +100. Outcomes were compared with 18 historical controls treated at the same institution without butyrate supplementation. The primary endpoint was the cumulative incidence of grade II-IV aGVHD by day +100. Secondary endpoints included lower gastrointestinal aGVHD and microbiome characteristics assessed using shotgun metagenomic sequencing. Competing risk analyses were performed to account for death as a competing event.<br><br>RESULTS: Butyrate supplementation was associated with a lower incidence of grade II-IV aGVHD (30% vs 53%, p=0.028) and grade III-IV aGVHD (5% vs 34%, p=0.002). Lower gastrointestinal aGVHD occurred in 5% of the butyrate group compared with 40% of historical controls (p<0.001). In multivariable competing risk analysis, butyrate supplementation remained independently associated with reduced grade II-IV aGVHD (adjusted HR 0.31, 95% CI 0.11-0.89; p=0.029) and lower gastrointestinal aGVHD (adjusted HR 0.07, 95% CI 0.02-0.30; p<0.001). Microbiome analysis demonstrated improved recovery of gut microbial diversity at day +100 in the butyrate group, with enrichment of commensal taxa and restoration of fecal butyrate levels.<br><br>CONCLUSIONS: Oral sodium butyrate supplementation was associated with reduced incidence and severity of aGVHD, particularly involving the gastrointestinal tract, along with improved microbiome recovery. These findings suggest a potential role for postbiotic-based microbiome modulation in GVHD prevention and warrant validation in randomized controlled trials.}, }
@article {pmid42410232, year = {2026}, author = {Li, Y and Li, J and Wang, H and Fan, J and Tang, K and Yan, G and Dong, W and Lan, T}, title = {Ischial tuberculosis: MRI and mNGS enable early diagnosis in the largest reported case series of twenty two patients.}, journal = {International orthopaedics}, volume = {}, number = {}, pages = {}, pmid = {42410232}, issn = {1432-5195}, support = {PYZ24154//The Scientific Research Cultivation Fund of Capital Medical University/ ; SKLSIM-2024108//The 2024 Youth Project of the Open Research Fund of the State Key Laboratory of Neurology and Oncology Drug Development/ ; }, abstract = {PURPOSE: To analyze the clinical features, diagnosis, treatment, and prognosis of ischial tuberculosis (IT), and to evaluate the diagnostic value of MRI and mNGS in the largest reported case series to date.<br><br>METHODS: Data from 22 patients with confirmed IT treated between January 2013 and January 2023 were retrospectively reviewed. Diagnosis was based on histopathology, microbiology, and molecular tests.<br><br>RESULTS: The mean age was 31.6&#xa0;years (11 to 67). Common symptoms included gluteal pain (100.0%), sitting-induced pain (81.8%), and local swelling (59.1%). Computed tomography (CT) revealed lesions in 86.4% of patients, while magnetic resonance imaging (MRI) showed abnormalities in all 18 patients examined. The ischial tuberosity was the most common site of involvement (63.6%). The T-cell spot test for tuberculosis infection (T-SPOT.TB), Xpert Mycobacterium tuberculosis/rifampicin resistance assay (Xpert MTB/RIF), and metagenomic next-generation sequencing (mNGS) showed positivity rates of 83.3%, 83.3%, and 100%, respectively. Histopathological granulomas were observed in 77.3%. Overall, 68.2% underwent surgical debridement. All patients achieved clinical cure with no recurrence at a mean follow-up of 34.7&#xa0;months.<br><br>CONCLUSION: IT has an insidious onset. MRI (100% sensitivity) is valuable for early diagnosis, and molecular tests, particularly mNGS (100% detection rate), enhance pathogen detection. Surgical debridement combined with standard chemotherapy achieved clinical cure in all patients, but comparative studies are needed to confirm its superiority over conservative treatment.}, }
@article {pmid42410336, year = {2026}, author = {Xie, Y and Cidan, Y and Sun, F and Renqing, C and Cisang, Z and Wang, D and Cideng, D and Basang, W and Zhu, Y}, title = {Bacillus-based probiotic supplementation reshapes rumen bacterial and fungal communities and enhances carbohydrate-degrading functional capacity in weaned yaks.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05372-2}, pmid = {42410336}, issn = {1471-2180}, support = {XZ202401YD0012//Central Government-Guided Local Science and Technology Development Project, Mining and Application of Functional Microorganisms and Enzyme Resources for Efficient Cellulose Degradation in Yaks/ ; CARS-37//Modern Agricultural Industry Technology System for Beef and Yak/ ; QYXTZX-LS2020-01//Breeding and Efficient Propagation of Yaks in Gesangtang of Linzhou County/ ; }, abstract = {This study evaluated the effects of dietary supplementation with Bacillus-based probiotics on growth performance, nutrient digestibility, rumen fermentation, and microbial functional capacity in weaned yaks. Twenty animals were randomly assigned to a basal diet (control group, CON) or the same diet supplemented with Bacillus subtilis and Bacillus licheniformis (probiotic group, PRO) for 90 days. Probiotic supplementation increased average daily gain (P < 0.05) and tended to increase dry matter intake (P = 0.059). In addition, neutral detergent fibre and acid detergent fibre digestibility were improved (P < 0.05), suggesting improved degradation of structural carbohydrates. Rumen fermentation was altered, with increased concentrations of butyrate and isovalerate and reduced ammonia nitrogen, suggesting improved fermentation efficiency and nitrogen metabolism. Microbial analysis showed that probiotics reshaped both bacterial and fungal community structures without affecting α-diversity, indicating selective modulation of key microbial taxa. Notably, the relative abundance of carbohydrate-degrading genera, including Xylanibacter, was increased. Metagenomic analysis further demonstrated changes in microbial functional capacity, as evidenced by increased abundance of carbohydrate-active enzymes and genes associated with cellulose, hemicellulose, chitin, lignin, and starch degradation. These results indicate that Bacillus-based probiotics were associated with improved growth performance and enhanced rumen microbial functional potential related to carbohydrate degradation.}, }
@article {pmid42410398, year = {2026}, author = {Xiang, X and Zhu, Y and Wang, T and Cheng, K and Ming, Y}, title = {Association between salivary microbiota-related amino acid metabolic dysregulation and tacrolimus-induced gingival overgrowth following kidney transplantation.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-09004-z}, pmid = {42410398}, issn = {1472-6831}, support = {81771722//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Kidney transplant (KT) recipients require lifelong immunosuppressive therapy to prevent allograft rejection. Drug-induced gingival overgrowth (DIGO) is a notable adverse effect of tacrolimus, for which effective preventive or therapeutic strategies are lacking. Dysbiosis of the oral microbiota has been implicated as a major risk factor for DIGO. However, its mechanistic role remains poorly understood.<br><br>RESULTS: Twenty KT recipients with newly diagnosed DIGO while receiving tacrolimus were enrolled, along with 20 matched controls with stable graft function. Salivary samples were collected and subjected to metagenomic and untargeted metabolomic profiling. Taxonomic analysis revealed greater microbial heterogeneity in DIGO patients compared to more interconnected communities observed in controls. Periodontitis-associated taxon, including Porphyromonas gingivalis, were enriched in the DIGO group. Multiple differentially expressed microbial genes and metabolites were identified, predominantly enriched in disordered amino acid metabolic pathways. Key metabolites-such as L-proline, carnosine, choline, 5-aminolevulinic acid, and spermidine-showed strong associations with DIGO-related taxon.<br><br>CONCLUSION: A strong association was observed between salivary microbial composition, metabolic profiles, and DIGO. The identified microbiota and metabolite alterations suggest a potential link between amino acid metabolic dysregulation and gingival fibroblast-related pathways in DIGO. These findings provide new insights into the biological features of DIGO and offer a foundation for future mechanistic and therapeutic studies.}, }
@article {pmid42410808, year = {2026}, author = {Wang, Y and Yang, X and Wang, Q and Shen, T and Wang, W and Qiu, J}, title = {Microbial flora and antimicrobial resistance in dental unit waterlines of Chongqing: An observational cross-sectional laboratory study.}, journal = {Medicine}, volume = {105}, number = {27}, pages = {e49461}, doi = {10.1097/MD.0000000000049461}, pmid = {42410808}, issn = {1536-5964}, mesh = {China ; *Water Microbiology ; Cross-Sectional Studies ; *Dental Equipment/microbiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/isolation &amp; purification/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; }, abstract = {To identify pathogenic bacteria in dental water systems and assess microbial diversity and resistance genes, we collected water samples from 35 dental facilities in Chongqing, China. Using the VITEK 2 COMPACT system, we identified 26 strains and 13 species of opportunistic pathogens in 23 samples exceeding the standard limits. In addition, metagenomic sequencing was performed to investigate microbial diversity and resistance genes. Among the 170 collected samples, 78.2% qualified, with no significant variation across samples. However, there was a statistically significant difference in qualifying rates between hospitals of different levels (χ2 = 7.696, P = .021). Most bacteria (80.8%) were Gram-negative and non-Enterobacteriaceae, with only 1 type belonging to the Enterobacteriaceae family. Notably abundant resistance genes included bacA, adeC, mexT, mdfA, adeJ, mdtK, emrB, and mdtB, predominantly associated with multidrug resistance (relative abundance: 71.42%). The contamination of dental unit waterlines is a concern that cannot be overlooked.}, }
@article {pmid42411404, year = {2026}, author = {Bouras, G and Grigson, SR and Durr, L and Papudeshi, B and Mallawaarachchi, V and Vreugde, S and Edwards, RA}, title = {Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.}, journal = {Current protocols}, volume = {6}, number = {7}, pages = {e70405}, doi = {10.1002/cpz1.70405}, pmid = {42411404}, issn = {2691-1299}, support = {//Australian Research Council/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; *Metagenome ; Molecular Sequence Annotation/methods ; *Software ; Bacteriophages/genetics ; Viral Proteins/genetics ; }, abstract = {Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential of prokaryotic viral metagenomes is extremely challenging. Pharokka, Phold, and Phynteny are complementary open-source prokaryotic viral genome annotation tools that utilize a variety of bioinformatics approaches to maximally annotate viral metagenomes. This article describes a protocol for installing and running these tools on a viral metagenomic dataset, followed by visualization of annotations using our client-side Phold Plot web assembly application. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Prokaryotic viral metagenome annotation with Pharokka Basic Protocol 2: Enhanced prokaryotic viral metagenome protein annotation using protein structures with Phold Basic Protocol 3: Further prokaryotic viral metagenome protein annotation using genome synteny and protein language models with Phynteny Basic Protocol 4: Visualization of prokaryotic viral metagenome annotations with Phold Plot web assembly application.}, }
@article {pmid42402588, year = {2026}, author = {Jin, Y and Cui, J and Liu, R and Ma, H and Xu, X and Wu, S and Gan, F and Lu, ZJ and Xu, ZZ}, title = {Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02454-1}, pmid = {42402588}, issn = {2049-2618}, abstract = {BACKGROUND: Bacterial transcription termination is a critical yet underexplored layer of gene regulation in microbial ecosystems. Existing computational tools, however, primarily focus on predicting transcript 3' ends generated by Rho-independent terminators (RITs) in a few model species, leaving gaps in understanding those generated by Rho-dependent terminators (RDTs) and their diversity across Bacteria.<br><br>RESULTS: We developed BATTER (Bacteria Transcript Three Prime End Recognizer), a deep learning-based framework for predicting bacterial transcript 3' termini. BATTER leverages the observation that conserved stem-loop structures are frequently associated with 3' ends of primary transcripts terminated by both RIT and RDT mechanisms across diverse bacterial clades. Compared with existing approaches, BATTER demonstrated superior performance and scalability, enabling a comprehensive analysis of 42,905 representative bacterial genomes. This large-scale application revealed that stem-loop structures exhibit clade-specific properties with greater variations between species than between gene families. Notably, BATTER uncovered that certain Cyanobacteria lineages, despite lacking rho homologs, harbor Rho utilization (RUT)-like sequences near 3' ends, and preliminary experimental validation in E. coli supports their partial functionality in transcription termination. Additionally, BATTER systematically identified pervasive premature termination events in antimicrobial resistance (AMR) genes.<br><br>CONCLUSIONS: BATTER enables large-scale comparative genomic analyses of transcription termination, providing a powerful framework to investigate termination-associated transcriptional regulation in microbial communities. The BATTER tool is available at https://github.com/xu-research-lab/BATTER. Video Abstract.}, }
@article {pmid42402612, year = {2026}, author = {Cao, L and Zhang, G and Zhang, G and Zhang, F and Li, W and Song, Q and He, J and Zhao, J and Zhang, Z}, title = {Cichorium intybus L. polysaccharide improves growth performance and colonic barrier function in weaned piglets via the microbiota-HDCA-TGR5-Akt-NF-κB signaling axis: validation by FMT and in vitro models.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42402612}, issn = {1674-9782}, support = {32302766//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Weaning stress predisposes piglets to intestinal barrier disruption and gut dysbiosis, which contribute to post-weaning diarrhea and poor feed efficiency. Chicory (Cichorium intybus L.) polysaccharide (CLP) is a fructan-rich prebiotic candidate; however, how CLP reshapes the microbiota-metabolite network to protect the colon remains unclear.<br><br>METHODS: In Exp. 1, 96 weaned piglets [Duroc&#x2009;&#xd7;&#x2009;(Landrace&#x2009;&#xd7;&#x2009;Yorkshire), 28&#xa0;days old, 8.03&#x2009;&#xb1;&#x2009;0.2&#xa0;kg] were fed a basal diet (CON group) or a 0.5% CLP supplemented diet (CLP group). In Exp. 2, fecal microbiota from piglets were transplanted into dextran sulfate sodium (DSS)-induced mice to confirm the causal role of the CLP-remodeled microbiota. Metagenomic and untargeted metabolomic analyses were employed to identify key microbial species and functional metabolites. In Exp. 3, Caco-2 cells were treated with varying concentrations of hyodeoxycholic acid (HDCA) for 24&#xa0;h to functionally validate the regulatory effects on TGR5&#xa0;and FXR&#xa0;expression levels.<br><br>RESULTS: The results showed that dietary CLP significantly decreased the feed to gain ratio, diarrhea rate and histology index (P&#x2009;<&#x2009;0.05), but increased goblet cell numbers (P&#x2009;<&#x2009;0.05). Metagenomic sequencing revealed that CLP significantly increased microbial &#x3b1;-diversity and remodeled the community structure, specifically enriching beneficial microbes, such as Blautia sp., Eubacterium sp., and Ruminococcus sp. To test microbiota causality, fecal microbiota from CON or CLP piglets was transplanted into antibiotic treated mice followed by DSS challenge. The CLP modified microbiota alleviates DSS induced colitis, upregulated Occludin and ZO-1 expression, and reduced colonic IL-1&#x3b2; and TNF-&#x3b1; levels. Mechanistically, the CLP remodeled microbiota promoted the accumulation of HDCA, which functioned as a signaling ligand to activate the colonic TGR5 receptor. This activation subsequently suppressed the phosphorylation of Akt (P&#x2009;<&#x2009;0.05), leading to the inhibition of the NF-&#x3ba;B signaling pathway through the reduced phosphorylation of I&#x3ba;B&#x3b1; and the p65 subunit (P&#x2009;<&#x2009;0.05), thereby effectively abrogating the inflammatory response.<br><br>CONCLUSION: Dietary CLP supplementation mitigates weaning induced intestinal injury and inflammation by remodeling the colonic microbiota, specifically enriching HDCA-producing species. The subsequent activation of the HDCA-TGR5-Akt signaling axis inhibits the NF-&#x3ba;B pathway, thereby improving host immune responses and intestinal barrier function.}, }
@article {pmid42402715, year = {2026}, author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD}, title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70698}, pmid = {42402715}, issn = {1365-3040}, support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; }, abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.}, }
@article {pmid42402854, year = {2026}, author = {Cai, Y and Yan, H and Qin, J and Qiang, Y and Lin, GQ and Wang, H and He, QL and Zhao, Q}, title = {Heterologous Expression of an Abandoned Termite Mound Fungus Gene Cluster Reveals a Protective Aldehyde-Alcohol Cycle and a Candidate Termiticidal Metabolite.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.6c00101}, pmid = {42402854}, issn = {2161-5063}, abstract = {The medicinal fungus Wulingshen, comprising multiple Xylaria species, inhabits deserted termite mounds as sclerotia. To explore the molecular basis of its niche adaptation, we employed a synthetic biology-driven approach. Metagenomic and transcriptomic mining of wild specimens identified a conserved biosynthetic gene cluster. Its heterologous reconstruction in the fungal host Aspergillus oryzae enabled the characterization of a family of α-pyrone metabolites and, crucially, the elucidation of a spatially separated aldehyde-alcohol cycle. In this self-protection system, an extracellular oxidase (WlsA) converts an alcohol precursor to a reactive aldehyde, while an intracellular reductase (WlsE) catalyzes the reverse reaction. The aldehyde product exhibits potent toxicity against termites in vitro, suggesting a potential role in ecological interactions. This work establishes a functional genomics platform that decodes cryptic ecological metabolism by integrating multiomics with heterologous pathway expression, providing a generalizable strategy for discovering and mechanistically understanding niche-specific natural products.}, }
@article {pmid42402985, year = {2026}, author = {Asato, Y and Kubo, T and Hashimoto, M and Wakatsuki, T and Sakamoto, H and Tanigawa, T and Kitamura, S and Kadokawa, H}, title = {Bifidobacterium longum BB536 supplementation is associated with increased circulating choline plasmalogen concentrations in non-pregnant, non-lactating dairy cows.}, journal = {Reproduction, fertility, and development}, volume = {38}, number = {10}, pages = {}, doi = {10.1071/RD26107}, pmid = {42402985}, issn = {1448-5990}, mesh = {Animals ; Female ; Cattle ; *Plasmalogens/blood ; Pregnancy ; *Probiotics/administration &amp; dosage ; Dietary Supplements ; Lactation ; *Bifidobacterium ; Animal Feed ; }, abstract = {CONTEXT: Plasmalogens are ether phospholipids implicated in neuroendocrine regulation, including reproductive function. Recent studies have suggested that circulating plasmalogen concentrations are associated with reproductive performance in dairy cows; however, practical strategies to increase these concentrations remain limited.<br><br>AIMS: We hypothesised that supplementation with Bifidobacterium longum increases circulating choline plasmalogen concentrations and that this response depends on physiological state.<br><br>METHODS: Commercial probiotic products were screened using liquid chromatography-mass spectrometry and metagenomics to identify candidates containing plasmalogen-producing bacteria. A product containing the characterised strain B. longum BB536 and products containing other B. longum strains were selected for in vivo evaluation. Selected products were administered to Holstein cattle, and circulating choline plasmalogen concentrations were measured using an enzyme-based fluorometric assay.<br><br>KEY RESULTS: In long-term non-pregnant, non-lactating dairy cows, supplementation with B. longum BB536 significantly increased circulating choline plasmalogen concentrations, with a detectable rise approximately 1 week after the start of treatment and peak concentrations during Days 8-14 (P&#xa0;<&#xa0;0.05). In contrast, no consistent increase was observed in pregnant, lactating dairy cows. Cross-sectional analysis across pregnancy stages showed significant variation in circulating choline plasmalogen concentrations, with lower concentrations during mid- to late gestation. No adverse effects were observed in ruminal pH, blood lactate concentrations, or bodyweight.<br><br>CONCLUSION: These findings suggest that supplementation with B. longum BB536 increases circulating choline plasmalogen concentrations in a state-dependent manner.<br><br>IMPLICATIONS: This study has provided new insight into the regulation of plasmalogens in cattle and suggests a potential nutritional approach for modulating reproductive function.}, }
@article {pmid42403142, year = {2026}, author = {Zheng, Y and Ruan, P and Chen, H}, title = {Severe &lt;em&gt;Pneumocystis Jirovecii &lt;/em&gt;Pneumonia in a Non-HIV Infant: The Diagnostic Value of Metagenomic Next-&lt;br /&gt; Generation Sequencing.}, journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP}, volume = {36}, number = {7}, pages = {961-962}, doi = {10.29271/jcpsp.2026.07.961}, pmid = {42403142}, issn = {1681-7168}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; *Pneumocystis carinii/genetics/isolation &amp; purification ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Infant ; }, abstract = {Null.}, }
@article {pmid42403487, year = {2026}, author = {Calvanese, CM and Valentino, V and Sequino, G and De Vivo, A and Buzzanca, D and Prencipe, S and Demarinis, C and Perri, G and Pontonio, E and Ferrocino, I and Ercolini, D and De Filippis, F}, title = {Lactobacilli, best allies of mental health: a probiogenomic approach to identify potential psychobiotic strains.}, journal = {Current research in food science}, volume = {13}, number = {}, pages = {101490}, pmid = {42403487}, issn = {2665-9271}, abstract = {Targeted dietary strategies and supplements represent a promising approach for the treatment of cognitive problems. Multi-omic approaches may facilitate and accelerate the discovery of new psychobiotic strains and their applications. In this work, we applied metagenomics and comparative genomics to guide the isolation and screening of novel psychobiotic strains from fermented foods. Metagenomes of 1185 fermented food were screened, revealing the occurrence of genes coding for the biosynthesis of neuroactive molecules, supporting the isolation of 73 novel Lactic Acid Bacteria (LAB) strains. Comparative genomic analysis highlighted species-specific patterns, identifying Levilactobacillus brevis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum as potential psychobiotics. In vitro functional screening for the production of neuroactive metabolites confirmed four strains, Lactiplantibacillus plantarum TUCC00000144, Limosilactobacillus fermentum TUCC00000777, Levilactobacillus brevis TO10, Lentilactobacillus diolivorans B92, as the most promising candidates for the development of dietary supplements or innovative fermented food products aimed at supporting mental health.}, }
@article {pmid42403498, year = {2026}, author = {Leprohon, H and Tannir, B and Jolicoeur, G and Domingo, MC and Dufresne, PJ and Morency-Potvin, P and Benoit, P and Grandjean Lapierre, S}, title = {Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study.}, journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada}, volume = {11}, number = {2}, pages = {141-154}, pmid = {42403498}, issn = {2371-0888}, abstract = {BACKGROUND: The analytical performance of bacterial targeted sequencing (BTS), fungal targeted/panfungal sequencing (FTS), and metagenomic next-generation sequencing (mNGS) assays has been previously evaluated and their clinical use is increasing. Limited evidence is available on their true clinical impact on infectious disease diagnosis and treatment.<br><br>METHODS: We conducted a 3-year retrospective cohort study including all patients for whom broad-range sequencing assays were performed directly from clinical samples for the detection of bacterial and fungal pathogens. The operational characteristics, diagnostic and therapeutic impacts of the assays were assessed by reviewing patient clinical files and laboratory information system charts.<br><br>RESULTS: A total of 279 samples from 185 patients were included. The positivity rates for BTS, FTS, and mNGS were respectively 20.5% (47/229), 20% (9/45), and 20% (1/5). Of these 279 samples, 40 (14.3%) had an impact on patient management. The test results helped to establish a diagnosis in 26 (9.3%) cases and led to treatment modifications in 14 (5%). FTS achieved higher impact rates (26.7%) than both BTS (12.2%) and mNGS (0%). Short turnaround times increase impact rates, and the most impactful tests were those performed on bone and intervertebral disc samples, or in patients with negative culture results due to prior antibiotic administration.<br><br>CONCLUSIONS: In this study, the overall diagnostic impact of BTS and FTS was high. Both the diagnostic and treatment impact of those assays can be increased if prescribed in well-selected clinical syndromes and performed on well-selected clinical samples.}, }
@article {pmid42404619, year = {2026}, author = {Ramani, RR and Baskaran, S and Arun, KV and Alamelu, S and Arumugamnainar, D}, title = {Salivary metagenomic profiling of Neisseria , Dialister , and Filifactor species in periodontal health and disease using next-generation sequencing.}, journal = {Journal of oral biology and craniofacial research}, volume = {16}, number = {4}, pages = {101482}, pmid = {42404619}, issn = {2212-4268}, abstract = {BACKGROUND: Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria, Dialister, and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria, Dialister, and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS).<br><br>METHODS: Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3-V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p&#xa0;<&#xa0;0.05.<br><br>RESULTS: Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p&#xa0;=&#xa0;0.001), N. elongata(p&#xa0;=&#xa0;0.015), and N. polysaccharea (p&#xa0;=&#xa0;0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p&#xa0;=&#xa0;0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p&#xa0;=&#xa0;0.011), suggesting its strong association with disease states.<br><br>CONCLUSION: The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.}, }
@article {pmid42404879, year = {2026}, author = {Dai, P and Feng, J and Cao, J and Fan, D}, title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1828633}, pmid = {42404879}, issn = {1664-3224}, mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.<br><br>METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.<br><br>RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-&#x3ba;B, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).<br><br>CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.}, }
@article {pmid42405192, year = {2026}, author = {Scott, CJR and Caccia, S}, title = {metaLoc: protein localisation prediction workflow.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag169}, pmid = {42405192}, issn = {2635-0041}, abstract = {SUMMARY: metaLoc combines existing tools for signal peptide, localisation, and transmembrane helices prediction from protein sequences into a workflow for rapid evaluation of protein datasets. By accepting both protein and nucleotide sequences, the workflow is especially suitable for in silico screening of the growing volumes of sequencing data. With a single command, metaLoc provides a simple, accessible, and user-friendly tool for the bioinformatic investigation of proteomic or metagenomic datasets.<br><br>metaLoc is freely available on the GitHub platform (https://github.com/scottc-bio/metaLoc). The metaLoc workflow is implemented in Nextflow with a modular design utilizing isolated Conda environments for reproducibility. An archived version of this release is permanently available at Zenodo (https://doi.org/10.5281/zenodo.18936772).}, }
@article {pmid42405317, year = {2026}, author = {Wang, Y and Cai, Y and Peng, Z and Hou, F and Jia, Z}, title = {Molecular insights into atmospheric methane-oxidizing USCγ from desert grassland soil based on metagenome-assembled genome analysis.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag151}, pmid = {42405317}, issn = {2730-6151}, abstract = {Upland Soil Cluster Gamma (USCγ) is a key high-affinity aerobic methanotroph driving atmospheric methane oxidation in grassland soils; however, it has never been obtained in pure culture, and its metabolic processes remain largely unknown. Here, we reconstructed a USCγ metagenome-assembled genome (MAG) containing the complete pmoA gene from desert grassland soil in northwestern China, designated USC_AKS. At the site, USCγ accounted for 9.83% of the microbial community in the 10-20 cm layer. BLASTn of its 16S rRNA gene against the NCBI database (excluding uncultured/environmental sequences) showed 93.03% similarity to the non-methanotroph Thioalkalivibrio sulfidiphilus HL-EbGr7 (order Chromatiales). The closest match among named species was an uncultured bacterium (JN672117) at 97.86% similarity. Its pmoA shares 96.18% similarity with the original USCγ-defining sequence. Phylogenomic analysis placed USC_AKS and seven other USCγ MAGs into a monophyletic group of three subclades, distantly related to culturable Type I methanotrophs. Their genomic average nucleotide identity values are all below 95%, confirming eight distinct species. Like other USCγ MAGs, USC_AKS encodes a complete pmoCAB operon, an XoxF-type methanol dehydrogenase, and enzymes for formaldehyde oxidation to CO2. However, it lacks key ribulose monophosphate (RuMP) cycle genes encoding 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexulose isomerase (phi). The serine cycle also appears incomplete, as these MAGs lack hpr, the gene encoding hydroxypyruvate reductase. Moreover, none encode Rubisco, ruling out the Calvin-Benson-Bassham CO2-fixation pathway. Consequently, the metabolic characteristics of USCγ-particularly its carbon assimilation pathway-remain enigmatic, and obtaining pure cultures or enriched consortia is likely the only route to resolving this mystery.}, }
@article {pmid42405318, year = {2026}, author = {Modolon, F and Capo, E and Wardle, DA}, title = {Long-term ecosystem development and retrogression drive microbial specialization for complex organic matter degradation.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag157}, pmid = {42405318}, issn = {2730-6151}, abstract = {Long-term ecosystem development includes a build-up phase followed by a decline (retrogressive) phase characterized by reduced plant productivity and belowground process rates due to reduced nutrient availability. In boreal forests, retrogression is accompanied by soil organic matter (SOM) accumulation, especially in the prolonged absence of fire. However, the role of bacterial communities in SOM dynamics during ecosystem retrogression has been little explored. Using a 5000-year post-fire boreal forest chronosequence, we investigated how long-term succession and retrogression shapes soil bacterial community structure and functional specialization. While the Actinomycetota phylum dominated communities across all chronosequence stages, a significant family-level shift within this phylum occurred in the later (retrogressive) phase, characterized by a transition from Mycobacteriaceae to Streptosporangiaceae. The recovery of metagenome-assembled genomes (MAGs) revealed distinct life-history trade-offs between these families. Streptosporangiaceae MAGs were significantly enriched in genes for degrading phenolics, cellulose, and lignin, and exhibited potential for chitin, lipid and peptide degradation. This positions them as potential decomposers of the primary constituents of stored soil carbon, including plant-derived complex carbohydrates and fungal necromass, during retrogression when fungal activity declines. In contrast, Mycobacteriaceae MAGs are likely to prioritize inorganic phosphate (P i) uptake-by pstS gene enrichment, reflecting adaptation to P availability changes during ecosystem development. Collectively, our results demonstrate that long-term ecosystem retrogression drives shifts in the bacterial communities and functions within the Actinomycetota. These shifts may indicate possible divergent strategies, i.e. recalcitrant carbon turnover versus nutrient scavenging, which could explain shifts in the microbial community as the ecosystem transitions toward retrogressive, nutrient-limited states.}, }
@article {pmid42405543, year = {2026}, author = {Anggraini, D and Yovi, I and Elliyanti, A and Safari, D and Syah, NA and Jati, AP and Sarassari, R and Simatupang, ETM}, title = {Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture Techniques.}, journal = {Infection &amp; chemotherapy}, volume = {58}, number = {2}, pages = {214-223}, doi = {10.3947/ic.2025.0159}, pmid = {42405543}, issn = {2093-2340}, abstract = {BACKGROUND: This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.<br><br>MATERIALS AND METHODS: This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.<br><br>RESULTS: Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).<br><br>CONCLUSION: Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.}, }
@article {pmid42405768, year = {2026}, author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH}, title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0038626}, doi = {10.1128/msphere.00386-26}, pmid = {42405768}, issn = {2379-5042}, abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.}, }
@article {pmid42406122, year = {2026}, author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B}, title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02817-z}, pmid = {42406122}, issn = {1432-184X}, support = {REIG-FPS-2025/038//UCSI University/ ; }, abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.}, }
@article {pmid42407310, year = {2026}, author = {Jiang, ZQ and Xing, RK and Peng, D and Ren, YH and Wei, TY and Guo, WB and Shen, ZM and Wang, CN and Zhang, FL and Yuan, T}, title = {Compartment-specific host association and mobility shape ARG risk in aquaculture systems.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142895}, doi = {10.1016/j.jhazmat.2026.142895}, pmid = {42407310}, issn = {1873-3336}, abstract = {Antimicrobial resistance in aquaculture threatens environmental and public health, but the risk of ARGs cannot be inferred from abundance alone; host context and mobility potential are essential. Here, we investigated how ecological compartments shape ARG host background, mobility, and risk in aquaculture systems. We analyzed 437 metagenomes from water and sediment in freshwater and marine aquaculture across China using resistome profiling, host assignment, genetic localization, ARG-MGE co-occurrence, a four-tier risk framework, and machine learning. We detected 1413 nonredundant ARG subtypes (28 classes). Water had higher ARG diversity, stronger associations with opportunistic pathogens, and stronger mobility-related signals than sediment. High-risk ARGs were concentrated in water: Rank I ARGs were exclusive to water, and water-specific Rank II ARGs accounted for 7.2% (freshwater) and 6.9% (marine) of total ARG diversity, versus 4.2% (freshwater sediment) and 2.9% (marine sediment). The LightGBM model identified salinity, temperature, and pH as key mobility predictors. Together, these results show that ARG risk in aquaculture is jointly shaped by the ecological compartment, host association, and mobility potential, with water acting as the principal high-risk interface. This risk-oriented analytical framework provides a transferable basis for prioritizing surveillance and intervention in aquaculture environments.}, }
@article {pmid42407426, year = {2026}, author = {Dong, F and Hou, A and Hu, X and Wei, L and Sun, F and Xiao, X and Su, X}, title = {Process-dependent niches of rpf-harboring microorganisms regulate nitrogen and carbon functional networks in full-scale activated sludge.}, journal = {Environmental research}, volume = {306}, number = {Pt 2}, pages = {125198}, doi = {10.1016/j.envres.2026.125198}, pmid = {42407426}, issn = {1096-0953}, abstract = {Resuscitating viable but non-culturable (VBNC) microorganisms offers a strategy to unlock hidden metabolic capabilities, enhancing pollutant degradation and system stability in wastewater bioreactors. However, the ecological mechanisms underlying VBNC resuscitation in activated sludge, particularly the role of resuscitation-promoting factor (Rpf) gene-harboring microbial consortia, remain elusive. Here, metagenomic profiling of full-scale anaerobic/anoxic/oxic (A[2]/O) and oxidation ditch processes demonstrates the widespread distribution of rpf-harboring microorganisms in wastewater treatment plants (WWTPs). A[2]/O systems enriched for taxa associated with denitrification and ammonification, while oxidation ditches showed higher abundance of microorganisms involved in nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The two processes configuration harbored distinct sets of rpf-carrying taxa, with Chloroflexota dominating in A[2]/O systems and Nitrospira and Kouleothrix in oxidation ditches. Network analysis further reveals that rpf-harboring taxa may act as ecological connectors between dormant and metabolically active populations, thereby enhancing community cohesion and resilience under fluctuating operational conditions. These findings uncover process-dependent resuscitation ecology shaping activated sludge communities and nutrient transformation pathways, providing a mechanistic foundation for engineering Rpf-mediated microbial interactions to improve biological wastewater treatment.}, }
@article {pmid42409195, year = {2026}, author = {Yan, M and Yang, C and Huang, J and Qi, P and Tang, L and Lu, H}, title = {Reactor performance and microbial responses of sulfate-reducing bacteria sludge under stepwise polyvinyl chloride microplastic exposure.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135334}, doi = {10.1016/j.biortech.2026.135334}, pmid = {42409195}, issn = {1873-2976}, abstract = {Plastic pollution, particularly microplastic contamination, poses potential risks to biological wastewater treatment processes. However, the response of sulfate-reducing bacteria (SRB) sludge systems to polyvinyl chloride (PVC) microplastics remains poorly understood. In this study, a laboratory-scale sulfate-reducing up-flow sludge bed (SRUSB) reactor was operated under stepwise PVC microplastic exposure at 0, 20, 100, and 500 particles/L. COD removal and sulfate reduction showed limited changes at 20 and 100 particles/L, whereas 500 particles/L caused transient inhibition followed by gradual recovery within the same reactor. PVC exposure increased intracellular reactive oxygen species (ROS) levels and lactate dehydrogenase (LDH) release, while live/dead staining indicated no marked increase in cell mortality across the operational stages. Stepwise PVC exposure was also accompanied by enrichment of protein-rich loosely bound extracellular polymeric substances (LB-EPS) and accumulation of PVC-derived additives, including BPA and ATBC. Microbial community analysis showed that the relative abundance of SRB-related genera increased from 8.7% to 24.9%, mainly involving increased abundances of Desulfobacter, Desulfococcus, and Desulforhabdus. Metagenomic annotation further revealed genes associated with EPS precursor supply, polysaccharide assembly/export, protein secretion, antioxidant response, aromatic metabolism, ester-bond hydrolysis, and dissimilatory sulfate reduction. Overall, this study provides a longitudinal characterization of reactor performance and associated physiological, chemical, microbial, and community-level genetic responses of SRB sludge under stepwise PVC microplastic exposure, offering useful insights for evaluating sulfate-reducing saline wastewater treatment systems facing microplastic contamination.}, }
@article {pmid42409199, year = {2026}, author = {Agostini, F and Baruzzo, V and Fernandez, FR and Satta, A and Raga, R and Penzo, D and Modesti, M and Valerin, MC and Campanaro, S and Treu, L and Zampieri, G}, title = {Discovering hidden candidate plastic-degrading enzymes: Combined multi-omics and machine learning strategy.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135332}, doi = {10.1016/j.biortech.2026.135332}, pmid = {42409199}, issn = {1873-2976}, abstract = {Plastic pollution poses a major threat to the stability of natural ecosystems as well as human health. Microbial enzymes have long been considered a potential resource for targeted biodegradation but, except for a few successful cases, the discovery of efficient enzymes has proved challenging. Aiming to accelerate the process, we propose an approach combining metagenomics, metatranscriptomics and semi-supervised learning that selects promising plastic-degrading candidate enzymes from the proteome of relevant microorganisms. Tested on a dataset of over 10,000 microbial proteins, ranking models consistently prioritize known plastic-degrading enzymes, achieving an area under the cumulative distribution function curve above 0.96, with leave-one-family-out cross-validation indicating that performance is largely retained across protein families. As a case study, this work focuses on mixed microbial cultures exposed for extended periods to polyethylene, polyethylene terephthalate, and polyurethane substrates. The prevalent species after selective enrichment were functionally characterized, finding Rhodococcus aetherivorans as the most relevant species in two of the five cultures under investigation. Among the top-ranked proteins, several have high structural similarity with known enzymes despite not being identified by sequence similarity search. Moreover, according to metatranscriptomics results, several of these enzymes were found to be expressed at the same level or above that of annotated enzymes, suggesting that they may have functional relevance. Overall, this work highlights the potential of integrating multi-omics with data-driven methods for enzyme discovery and for accelerating the development of biotechnological solutions to plastic pollution.}, }
@article {pmid42409336, year = {2026}, author = {Wu, J and Lin, M and Fan, Y}, title = {An Unusual Cause of Chronic Hematochezia.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.06.025}, pmid = {42409336}, issn = {1528-0012}, }
@article {pmid42409355, year = {2026}, author = {Nguyen, HT and Bez, C and Tran, MQ and Tran, LT and Pham, VT and Bertani, I and Venturi, V and Dinh, HT}, title = {Rhizospheric Fungal Communities and Their Role in Biocontrol of Fusarium in Robusta Coffee (Coffea canephora) in Vietnam.}, journal = {The plant pathology journal}, volume = {}, number = {}, pages = {}, doi = {10.5423/PPJ.OA.12.2025.0186}, pmid = {42409355}, issn = {1598-2254}, abstract = {Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS ampliconbased metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2-10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.}, }
@article {pmid42409501, year = {2026}, author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D}, title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {240}, number = {}, pages = {119678}, doi = {10.1016/j.foodres.2026.119678}, pmid = {42409501}, issn = {1873-7145}, abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.}, }
@article {pmid42409516, year = {2026}, author = {Moon, SH and Yang, X and Kim, J and Leighton, E and Jun, SR and DiCaprio, E and Gale, C and Chen, S and Li, X and Huang, E}, title = {Comprehensive analyses of carbapenem-resistant and ESBL-producing bacteria in fresh vegetables and their resistome in the United States.}, journal = {Food research international (Ottawa, Ont.)}, volume = {240}, number = {}, pages = {119552}, doi = {10.1016/j.foodres.2026.119552}, pmid = {42409516}, issn = {1873-7145}, abstract = {Carbapenem-resistant and extended-spectrum beta-lactamase (ESBL)-producing bacteria, once largely confined to healthcare settings, are increasingly detected in community environments. Food and the environment may act as important reservoirs for clinically relevant antibiotic-resistant bacteria. A large-scale surveillance study was conducted from 2022 to 2023 to assess antibiotic resistance in retail fresh vegetables across three U.S. regions: the Midsouth, Midwest, and West Coast. A total of 1218 samples representing five vegetable categories (carrots, lettuce, spinach, sprouts/microgreens, and salads) were analyzed for carbapenem-resistant bacteria and ESBL-producing Enterobacterales. Culture-based methods included selective isolation on CHROMagar, antibiotic susceptibility testing, phenotypic evaluation of ESBL and carbapenem resistance, and carbapenemase detection and typing. Whole-genome sequencing of phenotypically resistant isolates was used to identify beta-lactamase genes. Overall, 62 carbapenem-resistant isolates (5.09%) and 70 ESBL-producing Enterobacterales isolates (5.74%) were recovered. Carbapenemase-producing Enterobacterales included 30 Enterobacter strains and one Kluyvera strain, with carbapenem-resistant Enterobacter most frequently isolated from sprouts and microgreens. ESBL-producing strains included 39 Serratia, 20 Enterobacter, 6 Klebsiella, 3 Raoultella, and 2 Rahnella isolates. Comparative genomic analyses showed close similarity between vegetable isolates and human clinical strains. Notably, the carbapenemase gene blaIMI-6 identified in Enterobacter asburiae from microgreens was transferable to Escherichia coli by conjugation. Shotgun metagenomics of 40 samples further confirmed diverse resistance genes. These findings highlight vegetables as potential reservoirs of clinically important antibiotic resistance and emphasize the need for ongoing surveillance in both vegetable products and their production environments.}, }
@article {pmid42409884, year = {2026}, author = {Studer Silva Gutierrez, FAO and Morandi, SC and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC}, title = {Influence of smoking on the human ocular surface microbiome and tear proteome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60743-z}, pmid = {42409884}, issn = {2045-2322}, abstract = {The ocular surface hosts microbes of low abundance and their genomes, collectively called the ocular surface microbiome (OSM). The OSM is involved in maintaining health and protecting the eye from infection. Although disruption of this microbial balance has been linked to various eye diseases, the effect of smoking, a known risk factor for ocular conditions, on the OSM remains unclear. We analysed ocular samples from smokers (n = 17) and non-smokers (n = 24) using metagenomic sequencing and proteomics approaches to assess both microbial composition and functions, as well as the host protein profiles. Microbial DNA was examined for bacterial, fungal, and viral taxa, with contaminants removed using microDecon. Statistical analyses showed no significant differences in microbial diversity or tear proteins between groups, apart from one bacterial gene. No bacterial, fungal, or viral species were uniquely associated with smoking status. While no clear smoking-related effects were observed in microbial communities or tear proteome composition, the overall stability of tear proteins may reflect intrinsic resilience dynamics that maintain low microbial abundance on the ocular surface.}, }
@article {pmid42401772, year = {2026}, author = {Afonso, AC and Lema, JM and Trueba-Santiso, A}, title = {Metaproteomics for Water Biotechnology: Considerations and Study Cases.}, journal = {Advances in experimental medicine and biology}, volume = {1510}, number = {}, pages = {21-44}, pmid = {42401772}, issn = {0065-2598}, mesh = {*Proteomics/methods ; *Biotechnology/methods ; Multiomics ; *Water Purification/methods ; Water Microbiology ; Wastewater/microbiology ; Biofilms ; }, abstract = {This chapter summarizes the current knowledge on the practical, methodological, and interpretative aspects of applying metaproteomics in water biotechnology. We outline the full metaproteomic workflow-from sampling and protein extraction to LC-MS/MS acquisition, database construction, quantitative analysis, and bioinformatic interpretation-and emphasize critical considerations specific to complex matrices such as EPS-rich biofilms, granular sludge, and low-biomass drinking water. Case studies illustrate how metaproteomics can clarify mechanisms of micropollutant degradation, nitrogen-transforming pathways, biofilm functional architecture, and microbial resilience under operational stress. Recent advances in data-independent acquisition, metagenome-informed databases, and integrative multi-omics are shown to substantially improve depth, reproducibility, and functional resolution. Finally, we discuss emerging applications in wastewater-based epidemiology, where metaproteomics complement nucleic-acid-based surveillance by enabling the detection of large biomolecule biomarkers of population health and industrial activity. Although metaproteomics is already being applied across a wide range of water cycle contexts and is producing promising, robust results, several challenges, including limitations in analytical chemistry, database completeness, and bioinformatics workflows, continue to hinder its broader implementation. Continued technical research and innovation are therefore essential to fully unlock its potential in water biotechnology.}, }
@article {pmid42401776, year = {2026}, author = {Zapata-Peñasco, I and Herrera-Díaz, J}, title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.}, journal = {Advances in experimental medicine and biology}, volume = {1510}, number = {}, pages = {121-145}, pmid = {42401776}, issn = {0065-2598}, mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth &amp; development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; }, abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.}, }
@article {pmid42401984, year = {2026}, author = {Pangga, GM and Richmond, A and Hughes, C and Psifidi, A and Xia, D and Blake, D and Ijaz, UZ and Gundogdu, O}, title = {Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00596-z}, pmid = {42401984}, issn = {2524-4671}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.<br><br>RESULTS: We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p&#x2009;>&#x2009;0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n&#x2009;=&#x2009;271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.<br><br>CONCLUSION: Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.}, }
@article {pmid42402030, year = {2026}, author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W}, title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0084825}, doi = {10.1128/msphere.00848-25}, pmid = {42402030}, issn = {2379-5042}, abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.}, }
@article {pmid42402034, year = {2026}, author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q}, title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0388925}, doi = {10.1128/spectrum.03889-25}, pmid = {42402034}, issn = {2165-0497}, abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.<br><br>IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.}, }
@article {pmid42402279, year = {2026}, author = {Jiang, C and Wang, Z and Xie, B and Huang, H and Zhan, M and Kim, Y and El-Kady, AA and Su, Y}, title = {Fructose-Induced bioenergetic surplus Unlocks fatty acid biosynthesis pathway dominance over reverse β-Oxidation: Mechanistic insights into High-Caproate production from food waste.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135298}, doi = {10.1016/j.biortech.2026.135298}, pmid = {42402279}, issn = {1873-2976}, abstract = {Chain elongation (CE) is an effective strategy for converting organic wastes into value-added medium-chain fatty acids (MCFAs), wherein electron donors (EDs) dictate process efficiency. However, beyond substrate toxicity and limited reducing power, conventional EDs such as ethanol and lactate impose a chronic bioenergetic constraint: their minimal net ATP yield thermodynamically restricts CE strictly to the energy-neutral reverse β-oxidation (RBO) pathway. To overcome this bioenergetic bottleneck, this study investigated fructose as a high-energy-yielding multidimensional ED to drive n-caproate production from food waste in a mixed-culture system. Herein, the results demonstrated a dose-dependent enhancement of n-caproate, peaking at 12.38 g/L with a remarkable selectivity of 63.0 % (50 g/L fructose dosage). Mechanistically, fructose fermentation established an in-situ synergistic multi-ED microenvironment (fructose, ethanol, and lactate) that buffered toxicity and sustained robust reducing power. More critically, intensive glycolytic flux induced a hyper-energetic intracellular state characterized by abundant ATP and elevated NADH/NAD[+] ratio. Meanwhile, the activities of key enzymes (e.g., phosphofructokinase and butyrate kinase) were significantly stimulated, redirecting carbon flow toward butyrate and n-caproate. This favorable energetic and metabolic environment further selectively enriched Limosilactobacillus spp., which glycolyzed fructose into essential carbon intermediates for CE. Finally, metagenomic profiling revealed that the fructose-induced ATP surplus profoundly enriched genes associated with the ATP-dependent fatty acid biosynthesis (FAB), while suppressing RBO-related genes. This uncovers a paradigm shift from the RBO-dominated route to a FAB-driven mechanism. These findings unravel how a targeted carbohydrate structurally rewires the thermodynamic hierarchy of CE pathways, providing novel mechanistic blueprints for upgrading complex organic wastes into high-value biochemicals.}, }
@article {pmid42402284, year = {2026}, author = {Dar, RA and Tsui, TH and Du, Z and Zhang, L and Smoliński, A and Xiang, G and Liu, R}, title = {Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135326}, doi = {10.1016/j.biortech.2026.135326}, pmid = {42402284}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.}, }
@article {pmid42402338, year = {2026}, author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandón, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR}, title = {Pre-treatment Gut Microbiome Diversity and Function Linked to Cytotoxic and Natural Killer Cell Immune Responses after N-803 Treatment in People with HIV.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag369}, pmid = {42402338}, issn = {1537-6591}, abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.<br><br>METHODS: In this exploratory longitudinal metagenomic study, we analyzed fecal microbiomes from 10 ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.<br><br>RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were nominally enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii showed a nominal increase after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further identified potentially important associations between short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.<br><br>CONCLUSIONS: These findings in a limited Phase 1B clinical study suggest that gut microbiome diversity prior to immunotherapy may influence host response. These results provide a basis for further investigation into microbiome-based strategies to improve efforts to cure HIV.}, }
@article {pmid42399687, year = {2026}, author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y}, title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10434-2}, pmid = {42399687}, issn = {2399-3642}, abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.}, }
@article {pmid42399871, year = {2026}, author = {Du, W and Pan, F and Lan, P and Xie, L and Zheng, C and Wu, H}, title = {Metagenomic next-generation sequencing-guided management of descending mediastinitis and empyema caused by Segatella baroniae: a case report.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04465-y}, pmid = {42399871}, issn = {1471-2466}, abstract = {BACKGROUND: Deep neck infections can rapidly progress to descending mediastinitis and empyema, both of which are associated with high morbidity and mortality. Early diagnosis and timely intervention are essential but can be challenging, particularly in infections caused by rare anaerobic pathogens.<br><br>CASE PRESENTATION: We report a case of a 63-year-old man presenting with fever and neck pain. Computed tomography revealed extensive cervical emphysema and pneumomediastinum with a large right-sided empyema. The patient developed respiratory failure requiring endotracheal intubation. Endoscopic examination identified a retropharyngeal fistula, and thoracoscopic exploration confirmed communication between the mediastinum and pleural cavity. Combined cervical, mediastinal, and thoracic drainage was performed. Metagenomic next-generation sequencing identified Segatella baroniae as the predominant pathogen, guiding targeted antimicrobial therapy. The patient showed gradual clinical and radiological improvement and was discharged in good condition.<br><br>CONCLUSION: This case highlights the importance of early recognition and aggressive surgical management in deep neck infections complicated by descending mediastinitis. Metagenomic next-generation sequencing may facilitate rapid pathogen identification and guide targeted therapy in complex anaerobic infections.}, }
@article {pmid42399943, year = {2026}, author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W}, title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42399943}, issn = {1743-422X}, support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; }, abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.}, }
@article {pmid42400043, year = {2026}, author = {Wang, Y and Xue, X and Usyk, M and Sharma, A and Anastos, K and Post, WS and Hodis, HN and Wang, Z and Witt, MD and Rinaldo, CR and Brown, TT and Palella, FJ and Gange, S and Kuniholm, MH and Sha, BE and Caron, P and Gerszten, RE and Clish, CB and Guillemette, C and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB and Peters, BA}, title = {Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01709-8}, pmid = {42400043}, issn = {1756-994X}, support = {R01HL095129/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; R01HL148094/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; K01HL137557/HL/NHLBI NIH HHS/United States ; K01HL160146/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Sex hormones and HIV infection both influence cardiovascular health. However, the association between sex hormones and subclinical atherosclerosis is not fully understood, especially in the context of HIV.<br><br>METHODS: Among 321 men (65% with HIV) from the MACS/WIHS Combined Cohort Study, we measured 14 serum sex hormones and sex hormone-binding globulin (SHBG), assessed carotid artery plaque (IMT&#x2009;>&#x2009;1.5&#xa0;mm) using high-resolution B-mode ultrasound, and performed metagenomic sequencing on stool samples. In 312 men, we measured 986 plasma metabolites via liquid chromatography-tandem mass spectrometry and 2883 plasma proteins using the Olink Explore 3072 platform. In stratified analyses of men with (MWH) and without HIV (MWOH) and adjusting for covariates and multiple testing, we (1) examined associations of sex hormones with plaque; (2) characterized multi-omics profiles related to sex hormones; and (3) generated sex hormone-related omics scores via linear combination of related species, metabolites, and proteins, respectively, to explore whether these sex hormone-related multi-omics profiles were associated with plaque.<br><br>RESULTS: Median age of participants was 62&#xa0;years (interquartile range: 58-68), and 31.5% had carotid artery plaque. Sex hormones were differentially associated with plaque in MWH and MWOH. In MWH, an inverse association was observed between SHBG and plaque (OR&#x2009;=&#x2009;0.60 per 1-SD increase, 95% CI: 0.41, 0.90). Furthermore, higher SHBG levels were associated with overall gut microbial composition, lower abundance of species from genera Prevotella, Fibrobacter and Coprococcus, higher levels of certain metabolites (primarily lipid and carnitine metabolites) and proteins enriched in the cell-cell adhesion pathway. Some SHBG-related species (e.g., Mediterranea massiliensis), metabolites (e.g., phosphatidylcholine-based lipids) and proteins (e.g., enriched in immune response pathway) were also associated with plaque in MWH. All three SHBG-related omics scores were inter-correlated and inversely associated with plaque in MWH. In MWOH, estrone-sulfate was positively associated with plaque (OR&#x2009;=&#x2009;3.80, 95% CI: 1.41, 10.22) but not with any species, metabolites or proteins.<br><br>CONCLUSIONS: Higher SHBG, and related microbial species, circulating metabolites, and proteins, were inversely associated with carotid artery plaque. These findings suggested that SHBG may play a protective role in subclinical atherosclerosis in MWH.}, }
@article {pmid42400260, year = {2026}, author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S}, title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2695485}, doi = {10.1080/19490976.2026.2695485}, pmid = {42400260}, issn = {1949-0984}, mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; }, abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.}, }
@article {pmid42400618, year = {2026}, author = {Yu, J and Jiang, C and Sakai, Y and Mino, S and Sawabe, T}, title = {The Sea Cucumber Holobiont and Probiotics: Recent Progress on Apostichopus japonicus.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42400618}, issn = {1432-0991}, support = {JP19K22262//MEXT Kaken/ ; }, mesh = {Animals ; *Symbiosis ; *Probiotics ; *Stichopus/microbiology/physiology/genetics ; *Sea Cucumbers/microbiology/physiology ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {After the first definition of the term "Holobiont" by Margulis in the introduction of symbiosis as "Association throughout a significant portion of the life history" in 1991 [1], the understanding of holobiont has become an important goal in modern biology today [2]. Recent advances in microbial collection, genome/metagenome/transcriptome sequencings, and bioassays for host-microbes interactions push us towards a fuller understanding of holobiont in various aspects of life on Earth. Historically, holobiont and related hologenome concepts have been tested and expanded through research on marine organisms such as coral, fish, sea cucumber, sponge, and squid. In particular, the sea cucumber Apostichopus japonicus is a physiologically and ecologically unique marine invertebrate in which the holobiont can be studied with its significant capability of organ regeneration, presence of microbes in coelomic fluid, their mysterious nutrition connected to slow growth, and improvements in seed production for the bio-conservation of endangered and essential fisheries resources. The animals are also important in evolutionary terms on a branch of the Deuterostomia clade sharing ancestry with humans, so we can also compare to and learn from knowledge on the human-microbes interactions. In this review, recent progress in the sea cucumber A. japonicus holobiont studies, and the discovery of probiotics candidates among its pioneer microbiomes are described. By understanding this recent progress, we expect to stimulate new and further perspectives on basic biology, bio-conservation, and sustainable aquaculture of sea cucumber.}, }
@article {pmid42400712, year = {2026}, author = {Song, Y and Mao, C and Liu, P and Yang, G and Kang, L and Li, Z and Zhou, W and Liu, X and Yao, S and Yang, Y}, title = {Microbial community structure and function and their linkages with methane production in sediments of thermokarst lakes on the Tibetan Plateau.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42400712}, issn = {1869-1889}, abstract = {Thermokarst lakes represent a critical source of atmospheric methane (CH4), owing to large amounts of microbially generated CH4 in sediments. However, the structure and function of lake sediment microbiota, as well as their roles in mediating CH4 production, remain poorly understood across broad geographic scales. Here, we combined high-throughput sequencing, a 224-d anaerobic incubation, and stable isotopic analyses to investigate sediment microbiota and CH4 production across 30 thermokarst lakes along a 1,100 km permafrost transect on the Tibetan Plateau. Our results revealed that lake characteristics (i.e., lake depth and salinity-alkalinity) shaped sediment microbial composition and function. Deeper lakes exhibited enriched methanogenic taxa and pathways. In contrast, shallower lakes with higher salinity-alkalinity were dominated by microbial consortia that suppress net CH4 production via methanotrophs consuming CH4 and sulfate reducers competing with acetoclastic and hydrogenotrophic methanogens. Accordingly, cumulative CH4 production decreased by one order of magnitude from deeper lakes (2.5 log10CH4-C µg/g) to shallow and alkaline lakes (1.3 log10CH4-C µg/g) or salinity-alkalinity lakes (1.1 log10CH4-C µg/g). This variation was modulated by both key microbial consortia and sediment organic carbon and nitrogen supply. Overall, these results disentangled how lake characteristics restructured microbial dynamics to alter sediment CH4 production, and identified critical microbial consortia that could predict spatial variations in sediment CH4 production across thermokarst lakes.}, }
@article {pmid42401057, year = {2026}, author = {Zheng, Y and Wang, C and Niu, X and Han, C and Zhang, Z and Yang, H and Zhang, S and Ye, X and Li, L and Lv, J and Ma, Z and Liu, H and Ma, Y and Su, X}, title = {Coupled geochemical profiling and metagenomics reveal controls on phosphine preservation and emission in a eutrophic Estuary.}, journal = {Water research}, volume = {304}, number = {}, pages = {126393}, doi = {10.1016/j.watres.2026.126393}, pmid = {42401057}, issn = {1879-2448}, abstract = {Matrix-bound phosphine (MBP) represents a critical yet poorly constrained component of aquatic phosphorus cycling, and the controls governing its preservation and emission in eutrophic estuarine systems remain incompletely resolved. The spatial controls on MBP preservation and atmospheric phosphine emission across the Pearl River Estuary (PRE) were investigated by integrating sediment phosphorus fractionation, sub-millimeter diffusive gradients in thin films (DGT) profiling, and metagenomic sequencing. Sedimentary MBP was detected at all sites and varied markedly along the estuarine gradient, ranging from 2.38 to 36.85 ng kg[-1] ww, with significant positive correlations with Org-P and TP (p < 0.05). The PRE acted as a net atmospheric source of PH3 during summer, with air-water interface (AWI) fluxes ranging from -5.35 ± 0.63 to 28.90 ± 4.67 ng m[-2] h[-1] and highest emissions concentrated at inner-estuarine nearshore sites. DGT-derived labile P-Fe-S coupling patterns and systematic shifts in microbial metabolic functional potential (e.g., dsrA, mcrA, and ptxD genes) were broadly consistent with the spatial distribution of MBP, suggesting that microscale redox conditions and microbial community function may collectively contribute to reduced-P preservation. The accumulation of Org-P and OM in nearshore depositional zones, driven by terrestrial inputs and local hydrological conditions, may progressively shift sedimentary phosphorus cycling toward pathways that favor reduced-P preservation and sustained atmospheric PH3 emissions. Collectively, these findings offer new insights into the spatial controls on MBP preservation and atmospheric PH3 emission in eutrophic estuarine systems, which are essential to understanding the complex biogeochemical processes that regulate nutrient cycling in these fragile ecosystems.}, }
@article {pmid42401342, year = {2026}, author = {Zeng, Y and Zhang, L and Zou, Y and Liu, L and Chen, B}, title = {Enhancing catalytic efficiency of a deep-sea alkaline lipase through integrated engineering of lid-associated dynamics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135300}, doi = {10.1016/j.biortech.2026.135300}, pmid = {42401342}, issn = {1873-2976}, abstract = {A deep-sea alkaline lipase, MyLip2, fromMoritella yayanosiiwas identified from a metagenomic library of 1,048,576 genes. The wild-type enzyme preferred medium- to long-chain p-nitrophenyl esters, with optimal activity at pH 10.5 and 40 °C, but its specific activity was only 2.93 U/mg toward p-nitrophenyl palmitate. To improve performance, we used a structure- and sequence-guided strategy targeting noncatalytic residues around the catalytic center and lid region. Combinatorial engineering produced triple A271F/V250L/L231P and quadruple A271F/V250L/L231P/T300K (4 M), with comparable specific activities of 743.4 and 745.4 U/mg; 4 M was chosen for its high activity and improved thermal tolerance. This variant showed ∼ 196-fold higher catalytic efficiency (kcat/Km) toward p-nitrophenyl palmitate, with increasedVmax and kcat. Molecular docking, kinetics, and simulations indicated that the substitutions support a more open and catalytically accessible lid conformation, facilitating substrate access and turnover. Comparison with reported lipases indicated that MyLip2 and 4 M combine alkaline preference, medium- to long-chain activity, and improved performance. This work provides a high-performance deep-sea alkaline lipase and suggests that catalytic efficiency can be improved by tuning noncatalytic residues that influence the catalytic-center microenvironment and lid dynamics, without mutating the catalytic triad or redesigning the lid.}, }
@article {pmid42401346, year = {2026}, author = {Ping, Q and Chen, X and Jin, Y and Chen, Y and Zheng, M and Wang, L and Li, Y}, title = {Deciphering the structural and stoichiometric regulation of anaerobic digestion: A cross-scale perspective from molecular thermodynamics to methanogenic pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135314}, doi = {10.1016/j.biortech.2026.135314}, pmid = {42401346}, issn = {1873-2976}, abstract = {Proteins and polysaccharides are the predominant organic fractions of waste activated sludge (WAS). However, the regulation mechanisms of their distinct molecular structures and compositional ratios on the efficiency of anaerobic digestion (AD) remain unclear. This study comprehensively investigates their impacts on AD performance, focusing on molecular thermodynamics and functional gene regulation involved in electron transfer, energy conversion, and methanogenic pathways. The results demonstrate that molecular structure is a key factor determining substrate bioavailability. The protein with a mainly β-structure (xylanase) and randomly coiled polysaccharide (pullulan) exhibited superior hydrolysis, acidification, and methanogenic efficiency due to increased enzyme binding affinity. Conversely, α-helical protein and triple-helix polysaccharide displayed restricted enzymatic accessibility. Further studies revealed the combination of xylanase and pullulan at the optimal C/N ratio (35) effectively balanced nutrition, thereby achieving the highest cumulative methane yield. Metagenomic and metatranscriptomic analyses revealed that the optimal structures and C/N stoichiometry not only enriched GH13 enzymes, but also shifted the metabolic pathway from acetoclastic to hydrogenotrophic methanogenesis. Moreover, it enhanced interspecies electron transfer and energy conversion efficiency by promoting NADH dehydrogenases, formate dehydrogenase and heterodisulfide reductase, thereby establishing a highly efficient and stable metabolic network in AD system. These findings provide novel insights into the microbial and biochemical regulation driven by substrate structure and stoichiometry from cross-scale perspective, thereby offering a theoretical basis and regulatory strategy for the efficient resource recovery of waste activated sludge.}, }
@article {pmid42401622, year = {2026}, author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH}, title = {The mouse gut microbiota responds to predator odor and predicts host behavior.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01028-1}, pmid = {42401622}, issn = {2055-5008}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, abstract = {Chronic stressors can alter the mammalian gut microbiota in ways that mediate host stress responses, but the impacts of acute stressors on these interactions are less well understood. Here, we show that brief exposure of wild-derived mice to predator odor altered gut-microbiota composition, which in turn predicted host behavior. We investigated the individual and combined effects of 15-minute exposures to synthetic fox fecal odor and 30 days of chronic social isolation, an established chronic stressor. Using ethological assays, visceral adipose tissue transcriptomics, and genome-resolved metagenomics, we found that predator-odor exposure significantly affected mouse behavior, gene expression, and gut microbiota. Predator odor-responsive bacteria were associated with the expression of genes involved in anti-microbial defense, and host behavioral responses were predicted by random forest models trained on gut-microbiota profiles. These findings indicate interactions between the gut microbiota and wild-mouse responses to the threat of predation, an ecologically relevant acute stressor.}, }
@article {pmid42401690, year = {2026}, author = {Ribero, MN and Schiaffino, MR and Filloy, J}, title = {Grassland afforestation more than forestry intensification shapes soil multifunctionality via microbial compositional change under abiotic constraints.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60845-8}, pmid = {42401690}, issn = {2045-2322}, support = {UBACyT 2018//Universidad de Buenos Aires/ ; }, abstract = {Soil ecosystem multifunctionality (EMF) is driven by the interplay of abiotic and biological factors, yet how these interactions respond to anthropogenic pressures remains poorly understood. Here, we evaluated how grassland afforestation and its intensification shape soil edaphic conditions, microbial diversity, and EMF along a 200 km grassland-eucalypt plantation transect in Argentina. EMF was estimated, accounting for six ecosystem functions related to nutrient provisioning, organic matter cycling, and pathogen control. Microbial diversity was studied through the taxonomic, functional, and phylogenetic dimensions of prokaryotes, mycorrhizae, and fungal saprotrophs. Abiotic and biotic drivers of individual ecosystem functions and EMF were assessed using correlations, linear mixed models, structural equation models, and Multiple Regressions on distance Matrices. Individual ecosystem functions responded differentially to environmental drivers: functions linked to soil physicochemical processes were primarily associated with edaphic conditions, whereas biologically mediated functions were more closely linked to climate and grassland afforestation. Soil multifunctionality, however, was driven by edaphic and climatic conditions, particularly soil sand percentage and precipitation, with no direct association with microbial alpha diversity or afforestation. In contrast, similarity in fungal composition explained similarity in EMF, suggesting a coupling between microbial composition and soil conditions associated with grassland afforestation. Grassland conversion to commercial forest, rather than forestry intensification, altered individual soil functions and microbial functional composition without further reducing EMF. Overall, our findings indicate that afforestation influences soil EMF through changes in microbial composition, but that these effects are constrained by abiotic drivers.}, }
@article {pmid41738567, year = {2026}, author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D}, title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.}, journal = {Journal of fish diseases}, volume = {49}, number = {8}, pages = {e70143}, doi = {10.1111/jfd.70143}, pmid = {41738567}, issn = {1365-2761}, support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; }, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; }, abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.}, }
@article {pmid42392820, year = {2026}, author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY}, title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {51}, number = {9}, pages = {2652-2664}, doi = {10.19540/j.cnki.cjcmm.20260107.707}, pmid = {42392820}, issn = {1001-5302}, mesh = {Animals ; *Drugs, Chinese Herbal/administration &amp; dosage ; *Reperfusion Injury/metabolism/prevention &amp; control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; }, abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.}, }
@article {pmid42393176, year = {2026}, author = {Gordon, LM and Sevigny, JL and Buck, CB and Murray, MJ and Sidor, IF and Newton, AL and Palisoul, SM and Kelly, M and Nigatu, AS and Simpson, SD and Popov, VL and Waltzek, TB and Tsongalis, GJ and Frasca, S and Thomas, WK}, title = {A novel adomavirus from proliferative skin lesions of a broadnose sevengill shark (Notorynchus cepedianus).}, journal = {Npj viruses}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44298-026-00210-8}, pmid = {42393176}, issn = {2948-1767}, support = {P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; }, abstract = {In May of 2022, an aquarium-maintained broadnose sevengill shark (Notorynchus cepedianus) developed proliferative skin lesions that prompted pathologic and molecular investigation. Histopathologic examination revealed epidermal hyperplasia consisting of proliferation of spinous epithelial cells with mild dysplasia. Metagenomic sequencing identified a novel adomavirus with an 18,834 base pair circular double-stranded DNA genome. The virus, provisionally named broadnose sevengill shark adomavirus (7AdoV), contains two bidirectionally expressed protein-coding gene sets. Genomic annotation and structural predictions of proteins were used to contextualize 7AdoV phylogenetically and functionally. Transcriptomic analysis showed that expression of the structural late gene set was higher than the replicative early gene set at the time of diagnostic sampling. In situ hybridization using RNAscope technology localized transcripts of the adomavirus Wasp gene to epithelial cells of the hyperplastic epidermis. Infection by this novel adomavirus was associated with superficial and proliferative lesions that were self-limiting and resolved in this shark.}, }
@article {pmid42393215, year = {2026}, author = {Nthuku, S and Mordecai, J and Babajide, AA and Makoko, D and Sawadogo, Y and Awe, OI}, title = {The Kenyan Human Gut Virome Catalogue reveals extensive viral diversity and age-dependent community structure.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60183-9}, pmid = {42393215}, issn = {2045-2322}, abstract = {The human gut virome is a critical yet understudied component of the microbiome that shapes microbial community structure and host-microbe interactions. However, most existing human gut virome reference databases have been constructed predominantly from populations in high-income countries, resulting in the substantial underrepresentation of African populations. To help address this disparity, we developed the Kenyan Human Gut Virome Catalogue (KHGVC), the first comprehensive human gut virome resource for Kenya and the first country-specific human gut virome catalogue from Africa. Using a standardized viromics pipeline applied to 626 fecal metagenomes spanning infants and adults across three Kenyan counties, we reconstructed 116,968 viral operational taxonomic units (vOTUs). Cross-catalogue comparisons revealed extensive novelty where 65.6% of KHGVC's vOTUs larger than 10 kb lacked matches in five major human gut virome databases, and 95% remained unique relative to the Unified Human Gut Virome (UHGV). Temperate bacteriophages accounted for ~ 70% of vOTUs, supporting a major role for lysogeny in gut ecosystem stability. Functional annotation assigned putative roles to ~ 27% of predicted viral proteins, primarily structural and replication-associated functions. Application of KHGVC revealed pronounced age-dependent virome structuring in which infant viromes were less diverse and enriched in Bifidobacterium-infecting phages, including Bifidobacterium longum, whereas adult viromes exhibited greater diversity and expansion of Prevotella-associated phages. Together, the KHGVC substantially expands known human gut viral diversity and provides a foundational reference for Kenyan and African virome research. The KHGVC can be accessed freely through a publicly available interactive web interface (https://igmr.org/software/kenyavirocat).}, }
@article {pmid42394019, year = {2026}, author = {Dicko, A and Barro, SG and Sombie, S and Séré, R and Bonkoungou, I}, title = {Applications of Metagenomics and Artificial Intelligence in Characterizing Antimicrobial Resistance in Livestock: A Systematic Review.}, journal = {Studies in health technology and informatics}, volume = {338}, number = {}, pages = {328-332}, doi = {10.3233/SHTI260857}, pmid = {42394019}, issn = {1879-8365}, mesh = {Animals ; *Metagenomics/methods ; *Livestock/microbiology/genetics ; *Artificial Intelligence ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Humans ; One Health ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) is an urgent global health threat, intensified by the widespread use of antimicrobials in livestock production. This study synthesizes the current landscape of combining metagenomic sequencing with artificial intelligence (machine learning and deep learning) to characterize, surveil, and predict AMR within the One Health framework. A comprehensive multi-database literature search was conducted, and, following PRISMA guidelines, 10 peer-reviewed studies meeting the inclusion criteria were selected for full synthesis. Metagenomic shotgun sequencing significantly surpasses conventional culture-based methods by directly capturing antimicrobial resistance genes (ARGs) from complex biological communities. AI algorithms substantially outperform traditional bioinformatic tools, achieving high predictive accuracy (AUC-ROC > 0.90) and revealing consistent ARG transfer pathways that link livestock, human, and environmental compartments. Integrating metagenomics with AI delivers a paradigm shift for proactive AMR surveillance. However, standardization, interpretability, and technological adaptation to resource-limited settings-especially in sub-Saharan Africa-remain urgent priorities to inform effective public health policy.}, }
@article {pmid42394335, year = {2026}, author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X}, title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {55}, number = {3}, pages = {491-498}, doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019}, pmid = {42394335}, issn = {1000-8020}, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; }, abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.<br><br>METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1&#x2236;1&#x2236;1 ratio) and Mix-B group(same bacterial strains, in a 10&#x2236;1&#x2236;1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 &#xd7; 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.<br><br>RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, &#x3b2;-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.<br><br>CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.}, }
@article {pmid42394341, year = {2026}, author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V}, title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.}, journal = {Journal of environmental quality}, volume = {55}, number = {4}, pages = {e70215}, doi = {10.1002/jeq2.70215}, pmid = {42394341}, issn = {1537-2537}, support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; }, mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; }, abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.}, }
@article {pmid42394361, year = {2026}, author = {Queiroz, VF and Tatara, JM and Jivaji, AM and Given, CJ and Dutra, LAL and Abbas, W and Ricky, Z and Stokke, R and Stensvåg, K and Abrahao, JS and Almeida, GMF}, title = {Isolation of a Cohort of Giant Viruses From Above the Arctic Circle in Northern Norway.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70366}, doi = {10.1111/1462-2920.70366}, pmid = {42394361}, issn = {1462-2920}, support = {311192/A65276//Troms&#xf8; Forskningsstiftelse/ ; 101150485//Horizon 2020 Framework Programme/ ; 101162830/ERC_/European Research Council/International ; 315427//Norges Forskningsr&#xe5;d/ ; TMS2020TMT13//Trond Mohn stiftelse/ ; }, mesh = {*Giant Viruses/isolation &amp; purification/classification/genetics ; Arctic Regions ; Norway ; Phylogeny ; *Acanthamoeba/virology ; Mimiviridae/isolation &amp; purification/classification/genetics ; *Seawater/virology ; Fresh Water/virology ; }, abstract = {Viruses are the most abundant biological entities on Earth. Metagenomic data indicates a higher viral abundance of viruses of unicellular eukaryotes in the polar regions, information still not matched by broad isolation efforts using samples collected in these regions. Here we describe a prospection effort using diverse samples collected above the Arctic circle, including freshwater and marine samples from urban areas, deep-sea hydrothermal vents and sea ice samples from the Nansen Basin. We isolated 10 giant viruses capable of infecting Acanthamoeba spp., five representing the Marseilleviridae family and five representing the Mimiviridae family. These viruses are the northernmost isolates found so far in the Nordic countries and consist of a unique cohort of Arctic viruses that differs geographically and temporarily from a cohort already described from the Siberian permafrost. Despite an apparent viral diversity in the samples, the uniqueness of the samples themselves and the use of additional non-amebozoan strains as hosts, our viruses are still representatives of known viral families. In conclusion, here we show the isolation of giant viruses in Northern Norway and highlight the potential host bias towards Acanthamoeba in giant virus prospection, indicating the need to break this bias to diversify the isolation of environmental viruses.}, }
@article {pmid42394639, year = {2026}, author = {Zhu, H and Yang, P and Tu, Y and Fu, X and Yang, X and An, N}, title = {A Case Report of Meningitis with Possible Coinfection by Listeria monocytogenes and Mycobacterium tuberculosis (Detected by Metagenomic Next-Generation Sequencing) and Literature Review.}, journal = {Case reports in critical care}, volume = {2026}, number = {}, pages = {9615951}, pmid = {42394639}, issn = {2090-6420}, abstract = {RATIONALE: The study is aimed at exploring the complex clinical scenario of a patient with systemic lupus erythematosus who developed a rare coinfection with Listeria monocytogenes and Mycobacterium tuberculosis. The rationale is to highlight the diagnostic and therapeutic challenges in managing such a case, particularly in the context of immunosuppression and the need for effective antimicrobial therapy. This case underscores the importance of advanced diagnostic techniques like metagenomic next-generation sequencing in identifying coinfections and the critical balance required in treating both infections while managing the underlying autoimmune condition.<br><br>PATIENT CONCERNS: This case report presents a 58-year-old female patient who initially manifested thrombocytopenia and was diagnosed with SLE in an external hospital. After treatment, her condition did not improve. On the contrary, she developed a fever and a headache, and her disturbance of consciousness gradually worsened. The patient was admitted to our hospital with a suspected diagnosis of lupus encephalopathy and central nervous system infection.<br><br>DIAGNOSES: MRI plain scan showed linear enhancement shadows in the right temporal pole and bilateral cerebellar hemisphere regions on the fluid-attenuated inversion recovery three-dimensional volumetric fluid-attenuated inversion recovery contrast-enhanced scan. Subsequently, NGS of the cerebrospinal fluid detected L. monocytogenes and M. tuberculosis, suggesting a possible mixed infectious meningitis caused by these two pathogens.<br><br>INTERVENTIONS: The patient underwent a comprehensive treatment regimen including antiListeria and antituberculosis therapies. Unfortunately, this was followed by the development of liver failure and various other complications. In response, we administered interventions such as blood purification and liver support measures. Furthermore, we organized a multidisciplinary consultation to address the complex medical needs of the patient.<br><br>OUTCOMES: Despite aggressive medical interventions, the patient's condition deteriorated. She developed multiorgan failure, which significantly impacted her prognosis. The patient's family elected to withdraw life-sustaining treatment, and the patient passed away within 24&#x2009;h after discharge.<br><br>LESSONS: This case underscores the importance of early and accurate diagnosis, particularly for immunocompromised patients with complex clinical presentations. Identifying mixed infections is crucial, and it also poses a significant challenge in selecting appropriate antimicrobial agents and conducting relevant tests.}, }
@article {pmid42394779, year = {2026}, author = {Wishahi, M and Badawy, M}, title = {Letter to the Editor: Urinary infection in European guidelines 2025 vs microbiology culture results in the management of urinary infection.}, journal = {World journal of experimental medicine}, volume = {16}, number = {2}, pages = {115894}, pmid = {42394779}, issn = {2220-315X}, abstract = {We read with great interest the study by Yadav et al published in the World Journal of Experimental Medicine, which postulated a nomogram including patient's critical factors, other than urine sample. European Association of Urology (EAU) published the guidelines on urological infection 2025. The EAU guidelines 2025 of urinary infections (UIs) has classified in two distanced categories: Localized UTs and systemic UTs according to specific patient's symptoms and clinical signs, this new practical classification replaced previous concept of non-complicated urinary tract infection (UTI) against complicated UTI. The new EAU classification categorizes UIs as either localized or systemic, according to the presence of specific clinical signs and symptoms, this new practical classification replaced previous concept of non-complicated UTI against complicated UTI, irrespective of the results of bacteriological findings. In the new classification of UIs, the classification is based on clinical set-up on which the practitioner or urologist will manage the patient. Management of UIs is crucial to consider the urinary and gut microbiota. It was established recently that antibiotic use affects microbiota homeostasis in the gut and urinary tract that will initiate dysbiosis.}, }
@article {pmid42394824, year = {2026}, author = {Wu, Y and Cai, H and Wu, Q and Wu, J and Hu, J and Huang, E and Li, Z and Liang, S and Hu, X and Dai, J and Liao, R}, title = {The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1873187}, pmid = {42394824}, issn = {2235-2988}, mesh = {Animals ; *CRISPR-Cas Systems ; Humans ; *Mosquito-Borne Diseases/virology ; *Epidemiological Monitoring ; *Culicidae/virology ; *Mosquito Vectors/virology ; *Viruses/genetics/isolation &amp; purification/classification ; *Virus Diseases/virology/transmission/diagnosis ; }, abstract = {Mosquito-borne virus surveillance increasingly requires rapid, distributed detection of co-circulating pathogens, serotypes, and lineages across clinical and vector-sampling sites. CRISPR-Cas platforms offer a programmable toolkit for this purpose, but their readiness differs substantially across surveillance functions. Here, we review CRISPR-Cas methods for mosquito-borne virus surveillance across detection, tracing, and discovery-supporting targeted screening. Detection is the most advanced application: selected Cas12- and Cas13-based assays for dengue, Zika, chikungunya, West Nile, Japanese encephalitis, and related mosquito-associated viruses report sub-hour workflows, portable readouts, and targeted serotype- or lineage-marker discrimination. However, performance remains assay-, target-, and sample-matrix-dependent, and validation in pooled mosquito samples and field settings is still limited. Tracing currently relies mainly on validated portable amplicon-sequencing workflows, whereas CRISPR-aided sample-preparation methods such as DASH, FLASH, RAPID-DASH, and Cas9-targeted enrichment remain transferable opportunities for host depletion or target enrichment rather than established mosquito-borne virus genomic-surveillance workflows. For discovery-oriented surveillance, multiplex CRISPR-Cas systems such as CARMEN can support targeted screening of known or near-neighbor viruses represented by predesigned crRNAs, while metagenomic next-generation sequencing remains necessary for divergent or previously unknown viruses. Across these functions, CRISPR-Cas programmability may accelerate parts of assay redesign, but practical retargeting still requires compatible amplification primers, effector-specific target constraints, cross-reactivity assessment, and analytical revalidation. Routine surveillance use will require integrated demonstrations with clinical and pooled-vector samples, comparison against established molecular and sequencing methods, cost validation, and regulatory evidence.}, }
@article {pmid42394849, year = {2026}, author = {Ding, J and Liu, F and Zhao, Y and He, Z and Shi, Y and Shu, L}, title = {Protists show high resilience and thrive under multiple chemical stressors.}, journal = {mLife}, volume = {5}, number = {3}, pages = {388-392}, pmid = {42394849}, issn = {2770-100X}, abstract = {Protists are an underexplored but functionally important component of aerobic-activated granular sludge under pollution stress. Using metagenomics, we profiled protistan responses to ciprofloxacin, triclosan, and Cu[2+] (alone or in combination). Protists remained a stable 6.35%-7.88% of the bacterial community, and the consumers were the most abundant groups. Ciprofloxacin showed little effect on protist abundance, while Cu[2+] increased protist abundance, especially consumers. Stress conditions also strengthened predominantly positive protist-bacteria associations, suggesting cross-domain interactions that may enhance community resilience. These results demonstrate that protists are key determinants in stabilizing microbial communities under multiple stressors.}, }
@article {pmid42395046, year = {2026}, author = {Kumar, A and Ghosh, D}, title = {Letter to the Editor: Dengue virus as an underrecognized cause of encephalitis in tropical Asia - Bridging diagnostic and surveillance gaps.}, journal = {World journal of virology}, volume = {15}, number = {2}, pages = {118082}, pmid = {42395046}, issn = {2220-3249}, abstract = {Arboviral encephalitis remains a major public health concern in tropical Asia, where the etiology of a substantial proportion of central nervous system infections remains undetermined despite endemic circulation of dengue virus (DENV) and Japanese encephalitis virus. Laboratory confirmation is frequently absent in clinically suspected encephalitis. Perera et al recently published a study in World Journal of Virology, highlight this diagnostic gap by identifying DENV infection in 6.06% of encephalitis cases, including molecular evidence of DENV-3 neuroinvasion. These findings add to the growing evidence that DENV can cause encephalitis and meningoencephalitis across age groups. However, encephalitis in endemic settings is etiologically heterogeneous, and dengue represents only one of several infectious and immune-mediated contributors. Neurological dengue is likely under-recognized due to overlapping clinical presentations and limited diagnostic capacity. The identification of DENV-3 is noteworthy given its recurrent association with neurological disease. Limited concordance between reverse transcription polymerase chain reaction and immunoglobulin M assays reflects challenges related to viral kinetics, timing of specimen collection, and flaviviral serological cross-reactivity. Strengthening surveillance through integrated molecular and serological diagnostic strategies, including multiplex polymerase chain reaction and metagenomic next-generation sequencing, is essential to reduce undiagnosed encephalitis and improve clinical management and public health preparedness in tropical Asia.}, }
@article {pmid42395425, year = {2026}, author = {Shih, JB and Zhao, C and Pollard, KS and Lind, AL}, title = {Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.24.734308}, pmid = {42395425}, issn = {2692-8205}, abstract = {Microbial eukaryotes are prevalent members of host-associated and free-living microbial communities, but are routinely excluded from studies of these communities. Existing methods for eukaryote detection from whole metagenome sequencing are limited by contamination of eukaryotic reference genomes and incomplete taxonomic coverage. Our previously published tool EukDetect addressed these challenges using a curated database of universal BUSCO marker genes, but lacked validated quantitative abundance metrics and was built from a limited number of genomes. Here we present EukDetect2, incorporating a database containing 6,948 microbial eukaryotic genomes representing 6,594 unique species, 2,339 of which are newly added since EukDetect version 1, alongside quantitative metrics for estimating absolute and relative abundance of microbial eukaryotes. Using simulated data, we demonstrate accurate abundance estimation, no false positives from bacterial or host-derived reads, and equivalent or greater sensitivity and specificity than alternative taxonomic profiling tools across a range of microbial abundances and community compositions. Applying EukDetect2 across globally distributed human gut microbiome cohorts, we find that Blastocystis spp. and Dientamoeba fragilis are the most prevalent gut eukaryotes across cohorts, while host-associated fungi are consistently less prevalent than commensal protists. Blastocystis abundance is positively associated with a gut microbial community enriched for fiber-fermenting microbes and depleted for pro-inflammatory and industrialization-associated taxa. EukDetect2 provides sensitive, accurate, and quantitative metrics for investigating microbial eukaryotes from metagenomic samples.}, }
@article {pmid42395547, year = {2026}, author = {Kokroko, N and Jayanti, R and Sapoval, N and Nute, MG and Nakhleh, L and Treangen, TJ}, title = {Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.22.733643}, pmid = {42395547}, issn = {2692-8205}, abstract = {MOTIVATION: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challenge due to fragmented metagenomic assemblies, reference bias, reliance on gene boundaries, and limited ability to model structural mosaicism and patterns across genomes.<br><br>METHODS: We present Kente, a novel pangenome graph-based framework designed for HGT detection that aligns metagenomic assembly contigs to a curated database of >600 genus-level bacterial pangenome graphs constructed using minigraph. Kente infers local taxonomic composition along contigs using alignment evidence and classifies candidate transfers using structured clade-transition topologies (e.g., A-B-A sandwich, open tips, and mosaic patterns). A complementary intra-genus module detects inter-species transfers within a single genus graph using segment-level clade annotations.<br><br>RESULTS: Across simulated intra- and inter-genus transfer scenarios, Kente achieves higher precision and comparable recall relative to existing gene-centric microbiome HGT detection approaches while reducing false positives from fragmented assemblies. Application to real human gut metagenomes (HMP2, n = 26) demonstrates Kente's ability to detect candidate cross-lineage transfer regions in complex microbial communities. Runtime profiling shows near-linear scaling with input size, enabling efficient analysis of large metagenomic assemblies.<br><br>https://github.com/treangenlab/Kente.}, }
@article {pmid42395643, year = {2026}, author = {Yang, S and Yu, Q and Zeng, Y and Lu, Y and Xia, C and Cheng, F and Liu, Y and Liu, M and Chen, Y}, title = {Direct viral invasion and tumor-like pulmonary nodules: A fatal case of mpox in a patient with advanced HIV disease.}, journal = {Biosafety and health}, volume = {8}, number = {3}, pages = {228-233}, pmid = {42395643}, issn = {2590-0536}, abstract = {While mpox is typically a self-limiting zoonosis, individuals with advanced human immunodeficiency virus type 1 (HIV-1) infection are at increased risk for severe visceral complications and high mortality. We report a fatal case of fulminant mpox pneumonia in a 38-year-old male with advanced HIV-1 Infection and severe immunosuppression (CD4[+] T-cell count <100 cells/µL). The patient initially presented with characteristic cutaneous lesions but rapidly progressed to dyspnea and respiratory failure. Serial chest imaging revealed diffuse, solid perivascular nodules and patchy consolidations were highly suggestive of pulmonary malignancy. While initial microbiological cultures and clinical presentation (Day 4) suggested bacterial and fungal superinfections, metagenomic next-generation sequencing (mNGS) of lung tissue biopsy identified an overwhelming burden of mpox virus (MPXV; 260,840 sequence reads), cytomegalovirus (CMV) and Epstein-Barr virus (EBV), confirming direct viral invasion of the pulmonary parenchyma. Despite comprehensive treatment with antibiotics, antifungals, CMV-targeted therapy, and mechanical ventilation (specific anti-orthopoxvirus agents were unavailable), the patient succumbed to progressive respiratory failure on Day 31. This case highlights that mpox can manifest as severe necrotizing pneumonia with tumor-like radiological features in patients with acquired immunodeficiency syndrome (AIDS). It underscores the necessity of early pulmonary imaging and molecular testing in high-risk populations to differentiate mpox pneumonia from malignancy or opportunistic infections.}, }
@article {pmid42395675, year = {2026}, author = {Almuhanna, AA and Vatte, C and Guo, Q and Elsalamouni, TS and Al-Muhanna, FA and Aboalrihy, AM and Alhabib, HA and Almomen, MF and Alali, RA and Habara, AH and Alrubaish, MA and Alfalah, KM and Cyrus, C and Abdul-Rahman, IS and Keating, BJ and Al-Ali, AK and Wang, C}, title = {Gut microbiota in a Saudi population with chronic kidney disease.}, journal = {World journal of nephrology}, volume = {15}, number = {2}, pages = {118343}, pmid = {42395675}, issn = {2220-6124}, abstract = {BACKGROUND: The gut microbiota (GM) plays an important role in chronic kidney disease (CKD) progression, and dialysis modalities can differentially impact the GM composition and function. There is also limited information on the GM in Arab populations.<br><br>AIM: To investigate the distinct microbial profiles and functional alterations associated with hemodialysis (HD) and peritoneal dialysis (PD) in a Saudi Arabian cohort.<br><br>METHODS: We performed whole-genome metagenomic sequencing on fecal samples from 189 participants (controls and CKD, HD, and PD patients).<br><br>RESULTS: We detected distinct microbial profiles across all patient groups compared with that of the controls. Microbial risk scores derived from differentially abundant taxa accurately distinguished CKD, PD, and HD patients from controls, with area under the curves exceeding 0.9. Compared with HD patients, PD patients exhibited reduced species richness, an increased abundance of opportunistic pathogens (particularly Proteobacteria), and increased virulence. Functional analysis revealed suppressed energy metabolism and activated proinflammatory pathways in PD patients. Cooccurrence network analysis demonstrated decreased microbial community resilience in PD patients, with increased Proteobacteria interactions. Conversely, the HD group showed partial recovery of microbial balance and beneficial metabolic functions, including increased short-chain fatty acid metabolism and reduced lipopolysaccharide biosynthesis.<br><br>CONCLUSION: The findings of this study highlight the potential of the microbial profile as a robust biomarker for CKD classification and underscore the differential impacts of different dialysis modalities.}, }
@article {pmid42395905, year = {2026}, author = {Li, H and Li, N and Wang, C and Yang, J and Dong, Z and Cai, Z and Li, J and Chen, Y and Zheng, J and Zhu, J}, title = {Dysbiosis and unsustainable delayed gut microbiota development as non-invasive biomarkers for predicting autism spectrum disorder in Chinese children.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753665}, pmid = {42395905}, issn = {1664-302X}, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social impairment, restricted interest, repetitive behavior, and stereotypical behavioral patterns. Diagnosing ASD presents considerable challenges; a previous large-sample study in children linked ASD and intestinal flora imbalances.<br><br>METHODS: To explore the composition and functional changes of the gut microbiota in children with ASD, shotgun metagenomic sequencing was used to evaluate the gut microbiota of 78 Chinese children (34 with ASD and 44 with typical development [TD] children).<br><br>RESULTS: We observed differences in the gut microbiota composition and richness between children with ASD and TD in this cohort. The &#x3b1;-diversity of the gut microbiota in the ASD group fluctuated more with age than that in the TD group, based on cross-sectional data. Age-related dynamic changes in the gut bacteria of TD children were not clearly observed in children with ASD. Gut microbiota of children with ASD showed a higher number of antibiotic resistance genes compared to TD. Additionally, the functional gene pathways related to carbohydrate-active enzymes and amino acid metabolism and synthesis appeared reduced in the ASD group.<br><br>DISCUSSION: This exploratory study describes key compositional and functional characteristics of the gut microbiota in Chinese children with ASD. Our preliminary findings identify differential bacterial taxa that may be considered as potential candidates for further investigation as fecal markers, and suggest differences in age-related gut microbiota patterns between ASD and TD children. However, due to the modest sample size, cross-sectional design, and lack of external validation, these results should be regarded as a preliminary exploration and require confirmation in larger, independent cohorts.}, }
@article {pmid42396176, year = {2026}, author = {Deb, D and Liguori, F and Shuster, BM and Huang, R and Shoreibah, S and Wang, S and Rojas Ocampo, NE and Murray, KP and Danino, T}, title = {Toward development of soil-derived Bacillus isolates as lung cancer cytotoxic agents.}, journal = {Biodesign research}, volume = {8}, number = {2}, pages = {100074}, pmid = {42396176}, issn = {2693-1257}, abstract = {The wide-ranging impact of the human microbiome on health and disease has sparked growing interest in employing bacteria as live therapeutics. Natural properties of bacteria have been enhanced using synthetic biology to treat diverse diseases, from infections to inflammation and cancer. However, a major obstacle in this area is identifying specific bacterial hosts and molecular payloads that are both safe and effective for specific diseases or cancers. In this study, we explored environmental microbial diversity as a promising source of new therapeutic agents that could be engineered for bacterial drug delivery systems. We collected and characterized soil bacteria from 25 urban public parks, then evaluated their secreted metabolites for anti-cancer activity using both monolayer and three-dimensional spheroid models of lung cancer. Metagenomic analysis, toxicity profiling, and co-culture assays revealed that several Bacillus species isolated from Manhattan park soils produced compounds with strong, dose-dependent cytotoxic effects on lung cancer cells. Furthermore, we demonstrated that Bacillus subtilis-a well-characterized, gram-positive model organism-was capable of colonizing lung tumor spheroids, suggesting its potential as a safe and effective chassis for bacterial cancer therapy. Complementing these experiments, we developed a mechanistic ordinary differential equation (ODE) model of the bacteria-spheroid co-culture that is consistent with our bacterial and spheroid growth data. Overall, our findings highlight a discovery platform for the screening of environmental microbes as chassis or payload sources for microbial cancer therapies.}, }
@article {pmid42396177, year = {2026}, author = {Ross, DAN and Lauzon, J and Makarenkov, V and Kembel, SW}, title = {Metagenome-assembled genomes from the temperate forest phyllosphere in Eastern Canada.}, journal = {Access microbiology}, volume = {8}, number = {7}, pages = {}, pmid = {42396177}, issn = {2516-8290}, abstract = {The phyllosphere is host to diverse microbial communities surviving in dynamic environmental conditions and which form important relationships with their hosts. Here, we constructed metagenome-assembled genomes (MAGs) from 25 temperate forest phyllosphere samples collected in Eastern Canada. We found 423 dereplicated MAGs with completeness ≥50% and contamination ≤10%, using a combination of co-assembly strategies. The MAGs were predominantly classified into the bacterial phyla Pseudomonadota (n=197), Actinomycetota (n=88) and Acidobacteriota (n=50) and included two archaeal MAGs in the phylum Thermoproteota. These genomes can help to improve reference database entries of phyllosphere-affiliated microbes, increasing our understanding of phyllosphere microbial phylogenomic and community dynamics and the ecological roles of phyllosphere microbiomes.}, }
@article {pmid42396572, year = {2026}, author = {Campos, PE and Collins, PC and Ruane, A and Carlsson, JE and Carlsson, J}, title = {Instance of a Heteroplasmic Mitogenome in Alvinocaridid Shrimp Mirocaris fortunata (Martin &amp; Christiansen 1995) Found at the Moytirra Deep-Sea High-Temperature Hydrothermal Vent Field.}, journal = {Ecology and evolution}, volume = {16}, number = {7}, pages = {e73956}, pmid = {42396572}, issn = {2045-7758}, abstract = {In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The 15,923-bp-long sequence displays 98.72% pairwise identity with its closest relative, Mirocaris indica. A significant proportion of the mitochondrial genome (0.63%) corresponds to heteroplasmic sites that were found on 14 of the 37 genes, including cox1, though all such sites induce synonymous mutations. This level of heteroplasmy may serve as the first step for recombination of the mitogenome by paternal leakage and/or a less effective purifying selection in somatic tissues. We also take advantage of the shotgun deep sequencing strategy to assess the metagenomic composition of the sample and are able to detect other deep-sea hydrothermal vent species present at the vent system.}, }
@article {pmid42397430, year = {2026}, author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H}, title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42397430}, issn = {1436-6215}, mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.<br><br>METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.<br><br>RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.<br><br>CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.}, }
@article {pmid42397535, year = {2026}, author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK}, title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42397535}, issn = {1614-7499}, abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.}, }
@article {pmid42397700, year = {2026}, author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D}, title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001778}, pmid = {42397700}, issn = {2057-5858}, mesh = {Humans ; *Enterococcus faecium/genetics/isolation &amp; purification/classification ; *Vancomycin-Resistant Enterococci/genetics/isolation &amp; purification/classification ; *Metagenomics/methods ; *Gram-Positive Bacterial Infections/microbiology/transmission ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Metagenome ; }, abstract = {Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity and can miss transmission involving low-abundance and co-colonizing strains. Here, we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures obtained between 2020 and 2025 at a single hospital. GI tract populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters including 6 clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.}, }
@article {pmid42397950, year = {2026}, author = {Karthik, Y and Nanjareddy, K and Arthikala, MK}, title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2693436}, doi = {10.1080/15592324.2026.2693436}, pmid = {42397950}, issn = {1559-2324}, mesh = {*Glycine max/microbiology/growth &amp; development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF &amp; PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.}, }
@article {pmid42397959, year = {2026}, author = {Umezawa, K and Tsuji, JM and Tani, Y and Nohara, S and Amann, RI and Fukui, M}, title = {Isolation of Allocrenothrix methanica reveals distinct ecophysiologies of filamentous methanotrophs and adaptations to O2 limitation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag178}, pmid = {42397959}, issn = {1751-7370}, abstract = {Ferdinand Cohn observed abundant filamentous bacteria in drinking water wells in 1870 that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular methanotrophs, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotrophic strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their unique cell biology and ecology. We demonstrate that the strains are microaerobic and grow as filaments of cells, which are connected by unidirectionally oriented structures. The strains have broad genomic repertoires for addressing O2 limitation that are uniquely associated with lacustrine Crenothrix compared to related clades based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we also detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to O2 limitation, and we propose that the strains uniquely store or share metabolic intermediates between cells in filaments to thrive under such conditions. Our cultivation-based findings for these strains, which we name Allocrenothrix methanica, provide new insights into the diversity, evolution, and ecology of filamentous methanotrophs, connecting over 150 years of microbiology research and opening vast new opportunities to investigate bacteria contributing to the global methane cycle under O2 limitation.}, }
@article {pmid42398003, year = {2026}, author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG}, title = {Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.}, journal = {Genome biology and evolution}, volume = {18}, number = {7}, pages = {}, doi = {10.1093/gbe/evag152}, pmid = {42398003}, issn = {1759-6653}, support = {//Costco/Project Apis m/ ; 2005306//NSF IOS Collaborative Research/ ; 2022049//NSF DBI Biology Integration Institutes/ ; //Bill and Melinda Gates Foundation to Phase Genomics/ ; }, mesh = {Animals ; Bees/virology/microbiology ; *Bacteriophages/genetics ; *Host Specificity/genetics ; Genetic Variation ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Selection, Genetic ; Metagenome ; }, abstract = {Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.}, }
@article {pmid42398208, year = {2026}, author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z}, title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {159}, number = {}, pages = {158533}, doi = {10.1016/j.phymed.2026.158533}, pmid = {42398208}, issn = {1618-095X}, abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.<br><br>PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.<br><br>METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-&#x3b2;) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-&#x3b2;, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).<br><br>RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of&#x2192;4)-&#x3b1;-D-Glcp-(1&#x2192;,&#x2192;4)-&#x3b2;-D-Galp-(1&#x2192;, and &#x2192;4,6)-&#x3b1;-D-Glcp-(1&#x2192; linkages and &#x3b1;-D-Glcp-(1&#x2192; branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-&#x3b2; antiviral pathway via microbial-derived acetate.<br><br>CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-&#x3b2; antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-&#x3b2; homeostasis, highlighting its potential for influenza prevention.}, }
@article {pmid42398246, year = {2026}, author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X}, title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130396}, doi = {10.1016/j.jenvman.2026.130396}, pmid = {42398246}, issn = {1095-8630}, abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.}, }
@article {pmid42398311, year = {2026}, author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V}, title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128605}, doi = {10.1016/j.micres.2026.128605}, pmid = {42398311}, issn = {1618-0623}, abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.}, }
@article {pmid42398436, year = {2026}, author = {Funk, T and Zaheer, R and Wobeser, B and Conrad, C and McLeod, L and Gow, S and Otto, SJG and Waldner, CL and McAllister, T}, title = {Evaluating detection of Histophilus somni immunoglobulin-binding protein A DR2 Fic: A species-specific gene target for recombinase polymerase amplification relative to long-read sequencing of respiratory samples from feedlot calves.}, journal = {Research in veterinary science}, volume = {210}, number = {}, pages = {106315}, doi = {10.1016/j.rvsc.2026.106315}, pmid = {42398436}, issn = {1532-2661}, abstract = {Histophilosis is an important cause of morbidity and mortality as well as antimicrobial use in feedlot cattle across North America. Detection of Histophilus somni by culture is challenging, and there is no standardized tool for distinguishing isolates that carry virulence factors most likely to contribute to disease. The DR2 repeat of H. somni-associated virulence factor 'immunoglobulin-binding protein A' (ibpA DR2) harbors a Fic domain that mediates host cell cytotoxicity and is essential for histophilosis. For rapid detection of ibpA DR2 in extracted DNA, we developed a real-time recombinase polymerase amplification (RPA) assay with a runtime of 24 min at 39 °C. DNA from H. somni-RPA-positive respiratory swabs (n = 73) was screened for ibpA DR2 using the novel RPA assay and long-read metagenomic sequencing, as well as nanopore whole-genome sequencing (WGS) of H. somni isolated from the same samples. IbpA DR2 was identified in 71% and 70% of tested samples using RPA and WGS, respectively, and in ≤41% of samples using metagenomic sequencing. The likelihood of detection by RPA did not differ (OR 1.1, 95% CI (0.42, 2.9), P > 0.99) from WGS; however, agreement between these assays was only fair (κ = 0.31). Conversely, RPA (OR 3.4, 95% CI (1.6, 8.2)) and WGS (OR 8.0, 95% CI (2.4, 42)) were more likely (P < 0.001) to detect ibpA DR2 than metagenomic sequencing, likely reflecting limited coverage of H. somni by metagenomics. This study demonstrated that RPA and long-read WGS detected ibpA DR2 with similar frequencies in extracted DNA and H. somni isolates, respectively. Further testing of non-target isolates confirmed the analytical specificity of ibpA DR2 to H. somni. Further investigation of the diagnostic validity for RPA-based ibpA DR2 detection is required in a larger cohort of field samples, as a rapid screening tool for H. somni most likely to contribute to disease.}, }
@article {pmid42398457, year = {2026}, author = {Fonseca, A and Kenney, S and Bierly, S and Boney, J and Ganda, E}, title = {Assessing the impact of dietary interventions on the resistomes of broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107343}, doi = {10.1016/j.psj.2026.107343}, pmid = {42398457}, issn = {1525-3171}, abstract = {Antimicrobial resistance (AMR) is a major One Health concern, and while natural feed additives such as probiotics and phytotherapeutics are increasingly used as alternatives to antimicrobial growth promoters (AGPs) in poultry production, their potential effects on the selection of antibiotic resistance genes remain poorly understood. Therefore, our objective was to characterize the effects of a probiotic and an essential oils blend on the broiler resistome. Cobb 500 1-day-old chicks (N=320) were randomly allocated in 32 cages, with eight replicates of ten broilers per cage per treatment and were raised until day 21. Treatments consisted of four diets: a basal diet (negative control), a basal diet with Bacitracin Methylene Disalicylate (BMD) at 50 g/ton, a basal diet with an essential oil blend at 100 g/ton, and a basal diet with a probiotic (Bacillus subtilis) at 226.8 g/ton. Excreta samples were collected at three-time points (1, 10, and 21 days) to characterize broilers' resistome. The DNA extracted from these samples was sequenced using shotgun metagenomics on the NovaSeq platform and statistical analyses were done using Kruskal-Wallis and PERMANOVA to assess gene diversity. Across all samples, 823 unique ARGs were identified. These genes spanned a broad spectrum of classes, including multi-compound, metals, drugs, and biocides resistance. No significant differences in alpha diversity of these genes (P = 0.51) were observed between treatment groups; however, AMR gene diversity varied by age (P < 0.001). A statistically significant difference was observed in beta diversity across ages (P = 0.001), but not between treatments (P = 0.95). While age impacted AMR gene diversity, under our experimental conditions, antibiotics or other in-feed additives did not significantly alter broiler resistomes. This study advances poultry AMR surveillance by demonstrating that resistome diversity and composition in broiler chickens are predominantly shaped by age-dependent microbial succession, while neither in-feed antibiotics nor non-antibiotic feed additives induced persistent or treatment-specific alterations in ARG profiles under the conditions tested.}, }
@article {pmid42398478, year = {2026}, author = {Gao, Q and Hou, J and Ding, W and Qi, C and Xu, D and Zhou, C and You, G}, title = {Carbon-to-nitrogen stoichiometry shapes divergent intracellular and extracellular antibiotic resistance gene fates through a dissolved organic matter-extracellular polymeric substance-mobile genetic element cascade in cyanobacteria-bacteria co-cultures.}, journal = {Water research}, volume = {304}, number = {}, pages = {126390}, doi = {10.1016/j.watres.2026.126390}, pmid = {42398478}, issn = {1879-2448}, abstract = {The carbon-to-nitrogen (C:N) ratio constrains microbial metabolism, yet whether nutrient stoichiometry controls the differential fates of intracellular (iARGs) versus extracellular antibiotic resistance genes (eARGs) remains unknown. This study aimed to test whether C:N ratios approaching the bacterial threshold elemental ratio (TER) would maximize iARG enrichment through a dissolved organic matter (DOM)-extracellular polymeric substance (EPS)-mobile genetic element (MGE) cascade, while eARG dynamics would be governed by physicochemical processes. Cyanobacteria-bacteria co-cultures at four C:N ratios (5:1, 10:1, 20:1, 40:1) were analyzed using shotgun metagenomics, FTICR-MS, 3D-EEM, untargeted metabolomics, and EPS fractionation. C:N = 10:1 produced the highest iARG abundance (65.1 ± 17.4 TPM, mean ± SD) and a 17-fold iARG/eARG ratio, while eARG showed no significant treatment effect (Kruskal-Wallis p = 0.082, treating triplicate subsamples as observations). FTICR-MS revealed the lowest intensity-weighted O/C (0.334), most negative NOSC (-0.67), and highest molecular diversity (8029 formulas) at C:N = 10:1, indicating a uniquely reduced, aliphatic-enriched DOM pool. (Note: FTICR-MS samples were pooled from triplicate subsamples per treatment, yielding one composite per C:N level; these results are therefore descriptive and unreplicated.) EPS polysaccharide/protein ratios peaked at 2.8, correlating with iARG across treatments (ρ=0.91, p < 0.001) but inversely with eARG (ρ=-0.59, p = 0.044). Guanosine (ppGpp precursor) peaked at C:N = 10:1 (ρ=0.75 with iARG) while UDP-glucose was depleted, confirming active EPS biosynthesis. Piecewise structural equation modeling identified a pathway from C:N through DOM, EPS, and MGE to iARG (R[2]=0.78, Fisher's C p = 0.31), whereas eARG depended on eDNA physicochemical trapping (R[2]=0.41). These findings provide evidence that nutrient stoichiometry acts as a selective control on ARG partitioning, suggesting that C:N monitoring could be incorporated into eutrophic water ARG risk assessment.}, }
@article {pmid42398553, year = {2026}, author = {Xu, J and Zhang, X and Sun, W and Zhang, X and Wu, P and Wang, A}, title = {Hydroxylamine steers nitrogen metabolism toward dissimilatory nitrate reduction to ammonium by suppressing competitive denitrification.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135307}, doi = {10.1016/j.biortech.2026.135307}, pmid = {42398553}, issn = {1873-2976}, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is important for nitrogen conservation and resource recovery in wastewater treatment, but its efficiency is often limited by competition for electrons and substrates from denitrifiers. Although hydroxylamine (NH2OH) has been shown to modulate various nitrogen transformation processes, its long-term effects on DNRA systems and the underlying microbial ecological responses remain unclear. In this study, the nitrogen transformation performance, electron transfer characteristics, and microbial community succession in DNRA systems were comprehensively investigated under prolonged exposure to 0-5 mg/L NH2OH. The results demonstrated that, with increasing NH2OH concentrations, the system consistently achieved near-complete nitrate removal without nitrite accumulation, and the effluent NH4[+]-N reached up to 51.5 mg/L, indicating a substantial enhancement of DNRA ammonium production. Functional activity analyses and apparent electron-equivalent balance suggested an increased contribution of DNRA to nitrate-reduction-associated electron consumption. Metagenomic analyses further showed that NH2OH could decrease the relative abundances of denitrification-related genes, including nirS, norB, and nosZ, while increasing those of narG and the nrf gene cluster. Building upon the existing DNRA functionality, NH2OH selectively enriched a tolerant DNRA population, exemplified by Ignavibacteriota, and facilitated cross-feeding interactions and electron transfer network remodeling involving fermentative bacteria. Collectively, these findings suggest that NH2OH can weaken denitrification competition and increase the apparent contribution of DNRA to nitrate-reduction-associated electron consumption, thereby enhancing ammonium production. Moreover, these findings may provide a theoretical basis for the future development of DNRA-Anammox coupled processes for high-level nitrogen removal.}, }
@article {pmid42398606, year = {2026}, author = {Liu, J and Liu, Y and Zheng, Y and Wang, H and Wang, J and Zhang, Y and Wang, K}, title = {Intestinal metabolic characteristics of Smilax china L. pectic polysaccharide and prediction of its gut microbiota-mediated mechanism.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153348}, doi = {10.1016/j.ijbiomac.2026.153348}, pmid = {42398606}, issn = {1879-0003}, abstract = {This study aimed to investigate the intestinal metabolic characteristics and mechanisms of the pectic polysaccharide isolated from the medicinal plant Smilax china L. (SCLP). Firstly, in vitro simulated digestion confirmed that SCLP remained stable in simulated digestive fluids. Subsequently, in vivo real-time tracking of intestinal metabolism based on fluorescent labeling revealed that SCLP maintained its prototype in the small intestine and began to be degraded into fragments (Mw < 4000 Da) upon reaching the cecum and colon, where it was retained for prolonged periods. Pseudo-sterile mouse experiments indicated the mediating role of gut microbiota in SCLP metabolism. Furthermore, metagenomic sequencing suggested that SCLP increased the proportion of polysaccharide utilization loci (PULs) from Phocaeicola vulgatus and Bacteroides uniformis, elevated the gene numbers of carbohydrate-active enzymes (CAZymes) including GHs, GTs and CBMs, and activated pathways of carbohydrate metabolism. Finally, in vitro bacterial culture study verified the degradation and utilization of SCLP by Phocaeicola vulgatus and Bacteroides uniformis. In summary, this work elucidates the intestinal metabolic profile of SCLP, providing valuable insights for its further development and utilization.}, }
@article {pmid42398615, year = {2026}, author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J}, title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153356}, doi = {10.1016/j.ijbiomac.2026.153356}, pmid = {42398615}, issn = {1879-0003}, abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.}, }
@article {pmid42399247, year = {2026}, author = {Liao, H and Cui, HX and Chen, LX and Duan, CS and Li, J and Zhao, S and Zhu, YG and Su, JQ}, title = {Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75234-y}, pmid = {42399247}, issn = {2041-1723}, abstract = {Glacier forelands undergo a transition from oligotrophic to eutrophic conditions during primary succession. Reduced sulfur compounds may serve as an energy source for early microbial colonizers, yet the sulfur oxidation potential and key taxa remain largely unknown. Here, we perform a multi‑omics survey across a 130‑year chronosequence on the Tibetan Plateau. Glacial retreat profoundly reshapes both viral communities (61,394 viral operational taxonomic units, vOTUs) and microbial communities (404 metagenome‑assembled genomes, MAGs). Notably, Oxidative Dissimilatory sulfite reductase (Dsr) operon‑encoding Sulfur‑Oxidizing Bacteria (ODSOB) were specifically enriched within the first 1-5 years after retreat. Their associated viruses predominantly follow a "piggyback‑the‑winner" strategy, influencing host cold shock protein evolution and potentially modulating sulfur oxidation via iron‑sulfur (Fe‑S) cluster assembly. Metatranscriptomics reveals elevated expression of the oxidative Dsr operon and Form‑I ribulose‑1,5‑bisphosphate carboxylase/oxygenase (RubisCO) in early stages, coinciding with higher sulfate, sulfite, sulfide, and dissolved inorganic carbon (DIC)‑to‑dissolved carbon ratios compared to later stages. These findings indicate that ODSOB support DIC fixation and sulfide detoxification during early ecosystem development. Collectively, this study uncovers the eco‑evolutionary dynamics between viruses and microbes in developing ecosystems and provides genomic and functional evidence for ODSOB as key drivers of soil formation and primary succession in glacial forelands.}, }
@article {pmid42399252, year = {2026}, author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J}, title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01079-4}, pmid = {42399252}, issn = {2055-5008}, support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.}, }
@article {pmid42399304, year = {2026}, author = {Sun, Y and Cheng, X and Zhou, J and Li, R and Wei, Y and Li, H and Qin, Y and Bao, J and Ren, X and Qu, S and Liu, W}, title = {Bio-stimulants improve tomato growth by regulating the rhizosphere microbiome involved in phosphorus and nitrogen cycling.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59808-w}, pmid = {42399304}, issn = {2045-2322}, support = {2024CXPT056//the Key R&amp;D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; }, abstract = {Bio-stimulants are promising environment friendly alternatives to support sustainable agricultural development, capable of boosting crop growth and yield while cutting down excessive dependence on chemical synthetic fertilizers. Nevertheless, the explicit regulatory mechanisms by which bio-stimulants exert the role of growth-promoting functions still remain largely unclear and require further systematic clarification. In this study, we explored the influences of bio-stimulants (rich in humic acid) on tomato growth performance and rhizosphere microbial community assembly via greenhouse trials, and comparatively analyzed the functional differences between foliar spraying and root irrigation application modes. The results demonstrated that bio-stimulants treatment markedly improved tomato aboveground biomass, plant nitrogen and phosphorus accumulation by 17.1%, 27.4% and 22.7%, respectively. Meanwhile, bio-stimulants application effectively raised soil available nitrogen and soil organic matter levels, and further facilitated phosphorus assimilation in tomato plants. Metagenomic sequencing confirmed that bio-stimulants substantially reshaped the overall structure and composition of tomato rhizosphere microbiome. Specifically, they dramatically enriched the relative abundance of core microbial taxa responsible for soil nitrogen fixation and phosphorus solubilization. Collectively, these results clearly elaborate the underlying action mechanism: bio-stimulants optimize rhizosphere micro-ecological environment, enrich functional nutrient-solubilizing microorganisms, improve soil nutrient availability, and ultimately promote nutrient absorption and vegetative growth of tomato plants. This study confirms that bio-stimulants can serve as efficient and reliable regulators to advance green and sustainable crop production.}, }
@article {pmid42342250, year = {2026}, author = {Baghbanzadeh, M and Mann, BT and Crandall, KA and Rahnavard, A}, title = {seqLens: Optimizing Language Models for Genomic Predictions.}, journal = {Molecular biology and evolution}, volume = {43}, number = {7}, pages = {}, doi = {10.1093/molbev/msag139}, pmid = {42342250}, issn = {1537-1719}, support = {2109688//National Science Foundation/ ; }, mesh = {*Genomics/methods ; *Models, Genetic ; Large Language Models ; Evolution, Molecular ; Genome ; }, abstract = {Understanding evolutionary variation in genomic sequences through the lens of language modeling has the potential to revolutionize biological research. Yet to maximize the utility of language modeling in genomics, we must overcome computational challenges in tokenization and model architecture adapted to diverse genomic features across evolutionary timescales. In this study, we investigated key elements in genomic language modeling (gLM), including tokenization, pretraining datasets, fine-tuning approaches, pooling methods, and domain adaptation, and applied the language models to diverse genomic data. We gathered two evolutionarily distinct pretraining datasets: one consisting of 19,551 reference genomes, including over 18,000 prokaryotic genomes (115 B nucleotides) and the remainder eukaryotic genomes, and another more balanced dataset with 1,354 genomes, including 1,166 prokaryotic and 188 eukaryotic reference genomes (180 B nucleotides). We trained five byte-pair encoding tokenizers and pretrained 52 gLMs, systematically comparing different architectures, hyperparameters, and classification heads. We introduce seqLens, a family of models based on disentangled attention with relative positional encoding, which outperforms relatively similar-sized models in 13 of 19 benchmarking phenotypic predictions. We further explore continual pretraining, domain adaptation, and parameter-efficient fine-tuning methods to assess trade-offs between computational efficiency and accuracy. Our findings demonstrate that relevant pretraining data significantly boost performance, alternative pooling techniques can enhance classification, tokenizers with larger vocabulary sizes negatively impact generalization, and gLMs are capable of understanding evolutionary relationships. These insights provide a foundation for optimizing genomic language models for identifying diverse evolutionary genomic features and improving genome annotations.}, }
@article {pmid42386120, year = {2026}, author = {Nancy, N and Sharma, M and Singh, K and Singh, B and Sharma, PK}, title = {Mutation T71R enhanced the structural stability and functional activity of wild type superoxide dismutase cloned from soil metagenome.}, journal = {Gene}, volume = {}, number = {}, pages = {150294}, doi = {10.1016/j.gene.2026.150294}, pmid = {42386120}, issn = {1879-0038}, abstract = {In this study, we report engineering of three mutations m1, m2, and m3 respectively in the wild type SOD, cloned form soil metagenome. Expressed proteins from wild type and mutants were purified to homogeneity using Ni-NTA affinity chromatography. Biochemical characterization of mutants demonstrated enhanced functional activity at varying pH and temperature compared to wild type and other mutant proteins. Additionally, it also showed increased specific activity of 185 ± 0.75 U/mg compared to 150 ± 0.042 U/mg and 168 ± 0.25 U/mg respectively for mutant m1, m2 and m3. Altogether, it was observed that the relative enzyme activity of mutant m1, m2 and m3 enhanced ∼ 30 %, 10 % and 17 % respectively compared to wild type. Biophysical investigation carried out employing circular dichroism and intrinsic tryptophan fluorescence also demonstrated conformational stability in the secondary and tertiary structure of mutant m1 compared to the wild type at varying pH and temperature. Interestingly, in silico molecular simulation dynamics studies carried out at 300 ns demonstrated structural stability, reduced flexibility and attainment of stable conformation in this mutant form. Molecular simulation analysis revealed that mutation T71R in m1 tends to introduce β-sheet like secondary structure at protein surface, which might enhance residue-residue interactions within this protein, leading to allover enhancement in the stability and activity of this mutant.}, }
@article {pmid42386249, year = {2026}, author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J}, title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {124}, number = {1}, pages = {101323}, doi = {10.1016/j.ajcnut.2026.101323}, pmid = {42386249}, issn = {1938-3207}, mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; }, abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).<br><br>OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.<br><br>METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.<br><br>RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.<br><br>CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.}, }
@article {pmid42387129, year = {2026}, author = {Kumar, A and Kumar, A and Tyagi, A and Singh, R and Charaya, MU}, title = {A review of bloodstream infections-pathogens, pathogenesis, diagnostic strategies, treatment methods-challenges and future aspects.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42387129}, issn = {1435-4373}, abstract = {PURPOSE: Bloodstream infections (BSIs) remain a major cause of morbidity and mortality worldwide and continue to represent a substantial challenge to modern healthcare systems. These infections arise when pathogenic microorganisms gain access to the bloodstream, triggering systemic inflammatory responses that may progress to sepsis, septic shock, multi-organ dysfunction, and death. This review provides a comprehensive overview of the historical development, epidemiology, pathogenesis, diagnosis, treatment, and future perspectives of BSIs. The major bacterial, fungal, viral, and parasitic pathogens associated with BSIs are discussed, with particular emphasis on their virulence attributes, mechanisms of immune evasion, antimicrobial resistance, and clinical significance.<br><br>METHODS: A comprehensive literature review was conducted using peer-reviewed publications, clinical guidelines, surveillance reports, and systematic reviews published between 2010 and mid-2026. Evidence related to bacterial, fungal, viral, and parasitic bloodstream pathogens, host-pathogen interactions, diagnostic modalities, antimicrobial resistance mechanisms, and emerging therapeutic and diagnostic innovations was critically evaluated and integrated.<br><br>RESULTS: BSIs continue to impose a substantial healthcare burden, driven by increasing antimicrobial resistance, delayed diagnosis, and diverse pathogen-specific virulence mechanisms. Bacterial pathogens remain the predominant cause of BSIs, whereas Candida species represent the leading fungal agents. Advances in molecular diagnostics, metagenomic sequencing, biomarker-guided testing, and artificial intelligence-assisted analyses have substantially improved rapid pathogen detection and therapeutic decision-making. Precision medicine, genomic surveillance, and novel antimicrobial agents show considerable promise for enhancing clinical management and addressing multidrug-resistant infections.<br><br>CONCLUSION: Bloodstream infections remain a major global health challenge due to their complex pathogenesis, increasing antimicrobial resistance, and high associated mortality. Improving patient outcomes requires early and accurate pathogen identification, prompt initiation of targeted antimicrobial therapy, effective antimicrobial stewardship, and continuous epidemiological surveillance. The integration of next-generation diagnostics, artificial intelligence-assisted pathogen detection, genomic surveillance, and precision medicine has the potential to transform BSI diagnosis and management by enabling rapid, individualized therapeutic interventions.}, }
@article {pmid42387141, year = {2026}, author = {Zou, P and Wang, X and Zhao, H and Yang, K and Ye, J and Sun, Y and Meng, X and Yi, Z and Xiong, X and Li, W}, title = {Mycobacterium Abscessus Infection after Breast Augmentation: Case Reports and Literature Review.}, journal = {Aesthetic plastic surgery}, volume = {}, number = {}, pages = {}, pmid = {42387141}, issn = {1432-5241}, abstract = {BACKGROUND: Mycobacterium abscessus (M. abscessus) infection following breast augmentation is a rare complication, yet evidence and standardized treatments remain limited. Challenges include diagnostic difficulties and prolonged treatment periods.<br><br>METHODS: We report two cases of M. abscessus infection following breast augmentation and conducted a structured narrative review of PubMed literature to explore prevention, diagnosis, and treatment strategies associated with this condition.<br><br>RESULTS: The two patients underwent different breast augmentation procedures: one received autologous fat transfer, and the other had a prosthetic implant inserted. Following confirmation of M. abscessus infection via metagenomic next-generation sequencing (mNGS), both patients underwent through surgical debridement and drainage with daily amikacin irrigation. Combination antibiotic therapy was administered, including intravenous amikacin and linezolid, plus oral azithromycin. Both patients demonstrated good tolerance to the prescribed antibiotics, achieving effective infection control without recurrence over a 12-month follow-up period. The rigorous debridement and targeted antibiotic therapy significantly enhanced treatment efficacy.<br><br>CONCLUSION: This study reports two rare cases of M. abscessus infection occurring after breast aesthetic surgery. Such infections are difficult to diagnose and are often associated with prolonged treatment courses. We successfully identified the causative pathogen through mNGS and implemented a comprehensive treatment strategy that included multiple surgical debridements, local irrigation, and combination antimicrobial therapy with azithromycin, amikacin, and linezolid, which was associated with favorable clinical outcomes. Rather than establishing a definitive management model, this study provides practical, case-based insights into the diagnosis and management of postoperative M. abscessus infections.<br><br>LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .}, }
@article {pmid42387381, year = {2026}, author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B}, title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42387381}, issn = {1471-2180}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; }, abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.<br><br>RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq.&#xa0;Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.<br><br>CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.}, }
@article {pmid42387416, year = {2026}, author = {Ishio, D and Eguchi, H and Hotta, F and Miyamoto, T}, title = {Blepharoconjunctivitis mimicking conjunctival tumor associated with Streptococcus intermedius sinusitis: case report and literature review.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13910-6}, pmid = {42387416}, issn = {1471-2334}, abstract = {Streptococcus intermedius, a commensal bacterium in the human oral cavity, can occasionally cause severe infections in deep tissues. The patient was referred because of a conjunctival tumor. She had severe nasal cavity and periocular tissue inflammation that persisted for over a year. Microbiological examination of the nasal and ocular specimens identified S. intermedius as the pathogenic strain. The inflammation and the conjunctival mass subsided after systemic and topical administration of a susceptible antibiotic. Smear microscopy of the eye and nasal discharge was useful for the differential diagnosis. 16S metagenomic analysis using MinION as an adjunctive diagnostic tool has contributed to the species identification of the pathogenic strain.}, }
@article {pmid42387479, year = {2026}, author = {Vastolo, A and Tolone, M and Gannuscio, R and Staropoli, A and Giosa, D and Bonomo, A and Vinale, F and Cutrignelli, MI and Todaro, M}, title = {Impact of Opuntia spp. by-product silage on sheep metabolic profile, rumen fermentation and microbial communities.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05646-x}, pmid = {42387479}, issn = {1746-6148}, support = {cod. U-Gov PRJ-1776; CUP: J83C22000830005//National Recovery and Resilience Plan (PNNR) of Italy: project Biometric-Call PNNR a cascata-Universit&#xe0; della TUSCIA/ ; }, abstract = {BACKGROUND: Prickly pear (Opuntia ficus-indica) by-products represent a promising alternative feed resource for improving the sustainability of sheep production systems in Mediterranean areas. This study evaluated the effects of prickly pear by-product (PPB) silages on rumen fermentation, metabolic profile, and rumen microbiome in lactating ewes. Twelve Valle del Belice ewes were assigned to three dietary treatments (control, CTR; prickly pear peel silage, PPP; and pastazzo silage, PPS) in a Latin square design. Blood biochemical parameters, rumen volatile fatty acids (VFA), and metagenomic profiles were analysed.<br><br>RESULTS: PPB inclusion did not induce significant changes in blood biochemical parameters, which remained within physiological ranges. Rumen fermentation parameters were significantly affected, with the PPP diet increasing total VFA concentration and promoting a more glucogenic profile through higher propionate production. The rumen microbiome was dominated by Prevotella, which showed higher relative abundance in the CTR diet. PPB supplementation was associated with shifts in microbial functional profiles, including pathways related to polyphenol degradation, vitamin K2 biosynthesis, and central carbon metabolism, partially consistent with observed changes in rumen fermentation. No significant effects were observed on methanogenesis-related pathways.<br><br>CONCLUSIONS: Prickly pear by-product silages, particularly prickly pear peel, modulate rumen fermentation and microbial functional profiles in lactating ewes without adversely affecting systemic metabolic status.}, }
@article {pmid42387526, year = {2026}, author = {Bing, Y and Yuan, W and Liang, L and Li, J and Chen, Y and Feng, L and Li, X and Li, H and Zhong, J and Wang, L and Tong, Z and Liu, X}, title = {Alterations in the fecal virome and bacteriome-virome interplay in IPAH.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03797-x}, pmid = {42387526}, issn = {1465-993X}, support = {Nos. 82570072, 82170302//Innovative Research Group Project of the National Natural Science Foundation of China/ ; Nos. Ysbz2025004, Ysbz2025005, Ysbz2025006, Ysbz2025007//the Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; }, abstract = {BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening cardiovascular disorder characterized by complex multisystem disturbances. Although alterations in the gut microbiota have been reported in IPAH, how the gut virome interacts with bacterial communities and host metabolism remains unclear.<br><br>METHODS: We enrolled 28 patients with IPAH and 30 age-matched healthy controls (HCs). Fecal viromes and bacteriomes were profiled by metagenomic sequencing, and serum metabolomic data were integrated to construct virus-bacterium-metabolite interaction networks. Random forest models were used to evaluate the diagnostic potential of virome features.<br><br>RESULTS: IPAH patients exhibited markedly reduced gut virome diversity (Shannon, Simpson, and Pielou indices, p&#x2009;<&#x2009;0.05) and distinct community structures from HCs (p&#x2009;<&#x2009;0.01). A total of 499 differential viral operational taxonomic units (vOTUs) were identified, accompanied by extensive reorganization of interaction networks. At the phylum level, Hofneiviricota was enriched and Phixviricota depleted, both correlating with clinical indicators. Virus-bacterium associations were markedly increased in IPAH (44,894 vs. 17,920, r&#x2009;>&#x2009;0.5). Notably, vOTU2967, vOTU1924, and vOTU4522 were elevated and inversely related to Bacteroides, whose depletion was associated with increased lactic acid levels. Mediation analysis confirmed significant indirect virus-bacterium-metabolite effects (p&#x2009;<&#x2009;0.05). Random forest models based on vOTUs or viral families effectively distinguished IPAH patients from controls, highlighting the exploratory potential of gut virome features for mechanistic insights.<br><br>CONCLUSIONS: IPAH is characterized by reduced virome diversity, altered viral taxa, and reorganized virus-bacterium-metabolite networks. These findings suggest that gut viruses may influence disease progression by modulating bacterial metabolism, providing a potential avenue for biomarker discovery and therapeutic intervention.}, }
@article {pmid42387604, year = {2026}, author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY}, title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.}, journal = {Infectious diseases of poverty}, volume = {15}, number = {1}, pages = {}, pmid = {42387604}, issn = {2049-9957}, support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; }, mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; }, abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.<br><br>METHODS: Female BALB/c mice and Sprague Dawley rats (n&#x2009;=&#x2009;10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.<br><br>RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P&#x2009;<&#x2009;0.05) while Bacteroidetes increased (P&#x2009;<&#x2009;0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P&#x2009;<&#x2009;0.05) but decreased in rats (P&#x2009;<&#x2009;0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P&#x2009;<&#x2009;0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.<br><br>CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.}, }
@article {pmid42388191, year = {2026}, author = {Zhang, J and Fu, C and Tan, S and Lyu, B and Shu, G and Shi, L and Wu, Y and Guo, P}, title = {How Host Phylogeny, Diet, and Habitat Affect Gut Microbial Diversity in Wild Snakes.}, journal = {Ecology and evolution}, volume = {16}, number = {7}, pages = {e73902}, pmid = {42388191}, issn = {2045-7758}, abstract = {Gut microbiota plays critical roles in host digestion, immune regulation, neurochemical signaling, and metabolic homeostasis. Based on wild snakes (73 individuals from 23 species) from China, we explored the composition, characteristics, and functions of gut microbes across different groups using fecal metagenomic samples; further we explored the relative contributions of host phylogeny, diet, and habitat to the microbial structure. Among 23 wild snake species, the dominant gut microbial phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with Bacteroides, Salmonella, Citrobacter, and Aeromonas comprising the major genera. Mantel test revealed a significant correlation (r = 0.3173, p = 0.0055) between microbial composition at the genus level and host genetic divergence (p-distance), indicating potential phylogenetic influence on gut microbial profiles. While α-diversity and principal coordinate analysis showed no marked differences across different subgroups. Linear discriminant analysis effect size demonstrated notable differences in the gut microbes of the terrestrial snakes with different diets and vertebrate-feeding snakes with different habitats. Functional annotation of microbial genes indicated enrichment in metabolic processes, as well as environmental and genetic information processing. Carbohydrate-active enzymes were predominantly from GT2, GT4, GT51, and GH23 families. Linear discriminant analysis effect size showed different diets and habitats had distinct differential taxa. Additionally, antibiotic resistance gene profiles varied across groups, with acrB, AcrF, MexB, acrD, and mdtF being most prevalent. Future studies should increase the samples and comprehensively consider different ecological factors to explore the impacts on the composition and functions of snake gut microbes on different evolutionary, which will provide a deeper understanding of the interrelationships between snake gut microbes and their hosts.}, }
@article {pmid42388299, year = {2026}, author = {Maccario, L and Otani, S and Szarvas, J and Mortensen, LH and Elberling, B and Møller, KE and Madsen, CEK and Aarestrup, FM and Priemé, A}, title = {Microbial composition of archaeological middens: tracing human footprints through centuries in Greenland's ancient settlements.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809037}, pmid = {42388299}, issn = {1664-302X}, abstract = {The history of Greenland is marked by different waves of Paleo-Inuit immigration from North America from 2,500 BC to the 12th century and from the 10th to 15th century, Norse settlers immigrated from Northwest Europe and flourished in Southwest Greenland with the introduction of domestic livestock. The different Inuit and Norse cultures created middens by dumping and accumulating domestic waste; a latent source of microbes, including potential pathogens, that might have been preserved due to the general wet and cold conditions in the region. The aim of this study was to evaluate whether ancient Arctic settlements might be possible hot-spots for pathogenic agents that may spread to the surrounding environment because of current climate changes. Using metagenomics, we compared the microbial communities and resistomes of 78 samples from middens from different ages and locations in West and South Greenland (two Paleo-Inuit, four Norse and one early Colonial-time middens) to 143 soil samples from nearby surroundings. We found that the middens harbor a distinctive microbial signature enriched in human-associated bacteria. Those include opportunistic pathogens such as Clostridium perfringens and Paeniclostridium sordellii. In some early colonial midden layers, C. perfringens and Paraclostridium tenue together accounted for up to ~40%-50% of MetaPhlAn-derived relative abundance in individual samples. Antimicrobial resistance genes representing 17 resistance classes were detected across all sites, dominated by β-lactam and tetracycline resistance. Transect analyses across an actively eroding midden showed that midden-derived bacteria were confined to local erosion layers and were rapidly replaced by native marine communities, indicating limited environmental dispersal.}, }
@article {pmid42388302, year = {2026}, author = {Cao, H and Wang, Q and Ren, W and Wang, A and Tian, W and Zhang, D and Chen, J}, title = {Characterization of the gastric mucosal microbiota in tumoral and peritumoral mucosa in patients with advanced gastric cancer from Northwest China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1763714}, pmid = {42388302}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastric microbiota affects tumor development and treatment response, yet the characteristics and interactions of mucosal bacteria and fungi in advanced gastric cancer (AGC) remain unclear.<br><br>METHODS: Here we analyzed 177 mucosal samples (88 peritumoral and 89 tumoral) from 91 AGC patients in Northwest China using shotgun metagenomic sequencing.<br><br>RESULTS: MetaPhlAn4 and Kaiju were used to annotate the gastric mucosal microbial composition. MetaPhlAn4 has identified 12 phyla (no phylum-level differences), 98 genera and 278 species. PERMANOVA revealed age and tumor location significantly influenced microbial composition in tumoral mucosa. Wilcoxon signed-rank test revealed that 10 species including Serratia surfactantfaciens, Pseudomonas protegens, Treponema pectinovorum, Streptococcus anginosus, Bacteroides heparinolyticus, Selenomonas sputigena, and Mogibacterium diversum were significantly enriched in tumoral tissue, whereas five species including Actinomyces graevenitzii, Gemella sanguinis, Porphyromonas pasteri, Helicobacter pylori, and Leptotrichia sp. oral taxon-215 were more abundant in peritumoral mucosa. HUMAnN4 showed tumor-enriched bacteria were involved in metabolic pathways including polysaccharide degradation, biosynthesis of fatty acids, nucleotides, and arginine/histidine/purine/pyrimidine, which were primarily linked to S. surfactantfaciens. Peritumor-enriched bacteria were associated with L-tryptophan biosynthesis, L-arginine degradation, and TCA cycle. Kaiju annotation further revealed 2,429 bacteria, 12 archaea, 74 viruses, 82 fungi, and 63 other eukaryota species, among which the majority of significantly different species were enriched in the tumoral mocusa. Mycobiome analysis revealed eight fungal phyla, 82 genera and 82 species. PERMANOVA revealed that age had a significant effect on fungal composition in peritumoral mucosa, and five species including Saccharomyces cerevisiae, Aspergillus ochraceoroseus, Aspergillus fumigatiaffinis, Mitosporidium daphniae, and Puccinia striiformis were significantly positively correlated with age. Alpha diversity using Shannon index was significantly reduced in peritumoral mucosa at both genus and species levels. Wilcoxon signed-rank test revealed that all the significantly different fungi, including eight phyla, 46 genera, and 42 species were significantly enriched in tumoral mucosa. Correlation analysis indicated tumor-enriched bacteria were positively correlated with tumoral fungi but negatively with peritumoral fungi, suggesting possible synergistic bacteria-fungi interactions.<br><br>DISCUSSION: This study comprehensively characterizes the gastric mucosal bacteriome and mycobiome in AGC, illuminates potential microbiota-mediated carcinogenic mechanisms, identifies candidate biomarkers, and fills a regional research gap.}, }
@article {pmid42388305, year = {2026}, author = {Zhang, H and Ma, L and Jia, L and Li, Y and Wang, Y and Wang, W and Wu, W and Wang, H and Li, H and Zhang, Y and Chen, G and Hou, K and Dong, J}, title = {Multi-omics analysis reveals the potential for fermented Cordyceps militaris mushroom substrate in laying hens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807060}, pmid = {42388305}, issn = {1664-302X}, abstract = {This study examines how varying levels of fermented Cordyceps militaris mushroom substrate (CMMS) in laying hen diets affect production performance, digestive health, immunity, cecal microbiota, metabolites, and quorum-sensing functions. Fermentation reduced CMMS dry matter, NDF, and phosphorus content (p < 0.05). Replacing 30% of the diet with fermented CMMS significantly improved laying rate, egg weight, feed intake, and feed efficiency (p < 0.05), while enhancing yolk color, Haugh units, and lipase activity. A 20% substitution increased nutrient digestibility and immunoglobulin levels (p < 0.05). Metagenomic analysis revealed increased abundance of Phocaeicola, Alistipes, and Parabacteroides (p < 0.05) with enhanced energy metabolism and specific gene families. Metabolomic analysis identified 1,529 differentially expressed metabolites, with carboxylic acids being most prevalent (21.20%), and enhanced taurine/hypotaurine metabolism and GPI-anchor biosynthesis. Parabacteroides showed negative correlations with certain metabolites, while Alistipes correlated positively with PemK/MazF family genes (p < 0.001). CMMS fermented feed proportions influence cecal microbiota, their metabolites, and quorum sensing in laying hens, affecting production, digestibility, immunity, metabolism, and health, demonstrating CMMS potential as alternative poultry nutrition.}, }
@article {pmid42388398, year = {2026}, author = {Yu, L and Chong, Z and Yanchun, L and Yingying, H}, title = {The Diagnosis of Human Neurological Infection Caused by Rabies Virus Using Metagenomic Next-Generation Sequencing: Two Case Reports.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {1910139}, pmid = {42388398}, issn = {2090-6625}, abstract = {The rabies virus (RABV) causes acute progressive and fatal encephalomyelitis. Two case studies of RABV neurological infection identified using metagenomic next-generation sequencing (mNGS) are presented in this paper. A total of 39 RABV sequences were detected using mNGS in the cerebrospinal fluid (CSF) in Case 1. The detected sequences were located in the 0%-35% range of the enriched and amplified region and had a 27 × sequencing depth. A total of 75 RABV sequences were detected using mNGS in the CSF in Case 2. These cases illustrate that mNGS use during the early diagnosis of infectious diseases is critical. They also indicate that RABV can remain latent in the human body for many years. Disease prevention education for people who have experienced bites or scratches by rabid animals is therefore crucial.}, }
@article {pmid42388653, year = {2026}, author = {Zhang, X and Sun, E and Zhao, Z and Li, S and Shen, X and Liu, J and He, Q and Wang, Y and Zhao, F and Zhao, H and Zhang, H}, title = {Intervention With Lacticaseibacillus paracaseiPC-01 Fermented Milk Beverage Ameliorates Functional Dyspepsia and Modulates Gut Microbiome: A Pilot Study.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {7}, pages = {e71928}, pmid = {42388653}, issn = {2048-7177}, abstract = {Functional dyspepsia (FD) is a common chronic gastrointestinal disorder characterized by persistent or recurrent epigastric symptoms in the absence of detectable structural abnormalities. In this pilot study, we explored whether a Lacticaseibacillus paracasei PC-01 (PC-01) fermented milk beverage alleviates FD symptoms. Fifty-five patients with FD were randomized into an experimental group (EP, n = 37) receiving the PC-01 fermented milk beverage (5.0 × 10[8] CFU/mL, 200 mL/day) or a control group (CP, n = 18) receiving the active comparator, an acidified milk beverage (non-fermented, without PC-01) (200 mL/day). The interventions lasted 28 days, with symptom scores on the 7-point Global Overall Symptom Scale (GOSS) and Gastrointestinal Symptom Rating Scale (GSRS), and fecal samples were collected at baseline (day 0), 14, and 28. Consumption of the PC-01 fermented milk beverage in this pilot study was associated with improvements in FD symptoms, and a higher effective response rate was observed in the EP group than in the CP group (p = 0.04). Metagenomic analysis revealed that, compared with the CP group, the EP group exhibited significant enrichment of potentially beneficial bacteria (e.g., Blautia) and a reduction in potentially pathogenic bacteria (e.g., Clostridium paraputrificum), accompanied by significant downregulation of the fatty acid β-oxidation I (FAO-PWY) pathway. We acknowledge that the limitation of this pilot study is that the acidified milk beverage used as the control might also exert certain effects on gastrointestinal symptoms and gut microbiota, which could not be fully avoided due to the lack of a fully inert placebo. Collectively, the findings of this preliminary study indicate that the PC-01 fermented milk beverage may alleviate FD-related symptoms and modulate the gut microbiome and metabolic pathways, highlighting its potential in ameliorating FD-associated symptoms. Further large-sample, multi-center, and long-term clinical studies are warranted to verify these preliminary results and establish the long-term efficacy and safety of FD management.}, }
@article {pmid42388798, year = {2026}, author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH}, title = {Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.06.716669}, pmid = {42388798}, issn = {2692-8205}, abstract = {Microbial communities of geothermal habitats are central to understanding the evolution of life on Earth. Metagenomics has provided insight into the role of viruses in shaping microbial diversity of complex environments. However, identification of novel viruses is constrained by lack of marker genes and low nucleotide similarities between related viral taxa. While microbial and viral diversity have been explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain underexplored. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing steam and volcanic gases such as CO2 and H2S. Comparatively physicochemically dynamic to hot springs, fumarole temperatures and gas emissions rapidly fluctuate with volcanic activity. Here, we describe viruses identified metagenomically from microbial mats hosted near basaltic fumaroles on the Big Island of Hawaìi. To our knowledge, this is the first systematic survey of fumarole viruses. Our utilization of a sensitive profile-based approach for identification reveals high viral diversity in fumaroles, resulting in estimation of two undescribed order-level clades of Caudoviricetes (tailed phages). Viral metabolic genes provide evidence of viral-mediated adaptation of microbes to fumarole conditions. We describe patterns of viral diversity that diverge from the Bank model of viral ecology, hinting at viral dispersal between biofilms and high viral richness and evenness. Lastly, we provide a description of the first terrestrial geothermal environment dominated by Microviridae, previously only described in viral communities of deep ocean hydrothermal vents. This study offers important findings for exploration of viral ecology in extreme environments.}, }
@article {pmid42388836, year = {2026}, author = {Liu, B and Ding, Q and Tang, S and Dong, H and Li, RJ and Gan, M and Wei, J and Zhang, N and Wu, C and Zhang, TH and Yu, HZ and Zheng, Z}, title = {Avian paramyxovirus type 1-associated severe pneumonia in humans: Molecular characterization and zoonotic transmission risk.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101501}, pmid = {42388836}, issn = {2352-7714}, abstract = {BACKGROUND: Avian paramyxovirus serotype 1 (APMV-1, Newcastle disease virus) is a major poultry pathogen. Human infections are rare and typically self-limiting, but its potential to cause severe respiratory disease and the mechanisms underlying cross-species transmission remain understudied.<br><br>METHODS: We analyzed a 65-year-old male with severe pneumonia who had contact with sick backyard feeder chickens. Immunocompetence was evaluated via routine blood tests and serum immunoglobulin levels. mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, suggesting a potential avian-to-human transmission.<br><br>RESULTS: mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, providing molecular clues for zoonotic infection.<br><br>CONCLUSIONS: APMV-1 Class I genotype 1.1.2 1b can cross the species barrier and cause life-threatening pneumonia in immunocompetent humans. Our findings highlight its underrecognized zoonotic potential, emphasizing the need for enhanced surveillance in avian and human populations and research into determinants of cross-species pathogenicity.}, }
@article {pmid42389124, year = {2026}, author = {Zhou, Y and Bian, P and Yang, C and Qu, J and Wang, H and Gao, W}, title = {Differences in carbon sequestration capacity, rhizosphere microorganisms and metabolic functions among different herbaceous plants.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1849153}, pmid = {42389124}, issn = {1664-462X}, abstract = {Mitigating the rapid increase in global CO2 concentrations necessitates a deeper understanding of plant-microbe symbiotic carbon sequestration. While previous research has predominantly focused on woody plants, the carbon sequestration potential and mechanisms of herbaceous plants and their rhizosphere microbiomes remain largely underexplored. To address this gap, this study employed metagenomic technology to systematically investigate the carbon sequestration capacities and metabolic mechanisms of seven plant species and their rhizosphere soil microorganisms. Plant physiological measurements were integrated with microbial functional profiles predicted via PICRUSt2. The results show that the rhizosphere soil microbial communities generally possess functional genes for carbon decomposition and carbon fixation, providing evidence for the coupling of intracellular decomposition and synthesis metabolism in microorganisms. Notably, Spearman correlation analysis established a direct statistical link between plant physiological performance and specific microbial metabolic pathways. These findings demonstrate a functional coupling between plant physiology and rhizosphere microbial carbon metabolism. By linking plant phenotypes to microbial gene pathways, this study reveals that herbaceous plants and their rhizosphere microbiomes form an integrated carbon sequestration system. Therefore, leveraging such plant-soil interactions offers a promising strategy to enhance ecosystem carbon sinks and mitigate rising atmospheric CO2.}, }
@article {pmid42389176, year = {2026}, author = {Ubani, O and Ngole-Jeme, VM}, title = {Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112987}, pmid = {42389176}, issn = {2352-3409}, abstract = {This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically selected sites exposed to distinct anthropogenic pressures, including industrial effluent discharge, sewage overflow, greywater inputs, informal settlement runoff, and landfill leachate to generate a unique microbial genomic data. Environmental DNA was extracted and sequenced using the PacBio Sequel IIe platform, producing high-fidelity long reads suitable for improved assembly contiguity and functional reconstruction. Post-quality control processing yielded 4.9 × 10[4] to 1.6 × 10[5] HiFi reads per sample, corresponding to 0.34-1.02 Gb of high-accuracy sequence data per site. Long-read assemblies generated between 16,080 and 54,670 predicted protein-coding genes per sample. Taxonomic classification using Kaiju assigned 94.1-99.8% of assembled sequences to reference taxa. Domain-level profiles were exclusively bacterial dominated, with few rare or undetected (0.000-0.001%) archaeal, eukaryotic, or viral representation. Phylum-level composition was strongly dominated by Pseudomonadota (83-95%), followed by Bacillota (3-10%) and Bacteroidota (1-14%), with Actinomycetota consistently below 1%. Functional annotation using the DRAM pipeline identified 9390-31,251 KEGG orthologs, 969-3039 MEROPS peptidases, 13,454-45,103 Pfam domains, and 202-776 carbohydrate-active enzyme (CAZy) genes across assemblies. Distilled metabolic modules indicated the presence of near‑complete electron transport chain complexes (I-V), denitrification-associated pathways, sulfur oxidation and dissimilatory reduction genes, and diverse carbohydrate degradation functions; methanogenesis‑associated modules were not detected among the annotated metabolic pathways recovered in this dataset. The dataset provides genomic coverage of urban wetland microbiomes shaped by mixed industrial and municipal stressors and represents one of the few long-read metagenomic resources available for southern African freshwater wetlands. The availability of assembled contigs, gene annotations, metabolic reconstructions, enables reuse for comparative environmental genomics, biogeochemical modelling, bioremediation gene discovery, resistome screening, and microbial ecology investigations. This high-fidelity long-read sequencing resource expands opportunities for structural and functional analyses of anthropogenically influenced wetland ecosystems and supports future research in environmental biotechnology, bioinformatics-driven ecosystem monitoring, and microbial adaptation to urban pollution gradients.}, }
@article {pmid42389349, year = {2026}, author = {Iranzo, J and Wolf, Y and Koonin, E}, title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9816737/v1}, pmid = {42389349}, issn = {2693-5015}, abstract = {Background Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome? Results We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors. Conclusions Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving ground for emerging defense systems, which might eventually become cost-effective once optimized by selection.}, }
@article {pmid42389510, year = {2026}, author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F}, title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1760700}, pmid = {42389510}, issn = {2235-2988}, mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation &amp; purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; }, abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.<br><br>METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).<br><br>KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.<br><br>CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.}, }
@article {pmid42389512, year = {2026}, author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Lázaro-Martínez, JL}, title = {Correction: Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1902309}, doi = {10.3389/fcimb.2026.1902309}, pmid = {42389512}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1729196.].}, }
@article {pmid42389745, year = {2026}, author = {Ota, Y and Nukui, Y and Gu, Y and Saito, R}, title = {Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm.}, journal = {Biofilm}, volume = {12}, number = {}, pages = {100377}, pmid = {42389745}, issn = {2590-2075}, abstract = {Antimicrobial resistance (AMR), particularly among carbapenemase-producing organisms, poses a major global health threat. Although hospital wastewater is considered an AMR hotspot, its functional contribution to resistance dynamics remains poorly defined. We developed in situ biofilms in hospital wastewater and applied integrated metagenomic, metatranscriptomic, and culture-based analyses to characterize community structure and gene expression. Biofilms exhibited greater biomass and higher contamination with extended-spectrum β-lactamase-producing Escherichia coli than planktonic wastewater. Biofilms were enriched in surface-adapted Flavobacteriaceae species and a broader array of carbapenemase genes, whereas wastewater showed higher abundance of gut-associated Bacteroidaceae species and virulence factors. Mobile genetic elements linked multiple AMR genes and showed increased expression in biofilms, including bla IMP family carbapenemases. Culture confirmed bla IMP-1 in four biofilm isolates and one wastewater isolate. These findings indicate that hospital-wastewater biofilms can serve as important reservoirs that promote the persistence and potential dissemination of clinically relevant carbapenem resistance.}, }
@article {pmid42390233, year = {2026}, author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X}, title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0036926}, doi = {10.1128/msphere.00369-26}, pmid = {42390233}, issn = {2379-5042}, abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.}, }
@article {pmid42390270, year = {2026}, author = {Varona, NS and Schellenberg, L and Barnes, W and Scholten, Y and Haas, AF and Silveira, C}, title = {Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0039526}, doi = {10.1128/msystems.00395-26}, pmid = {42390270}, issn = {2379-5077}, abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in carbon cycling within marine environments. In coral reefs, dissolved organic matter (DOM) released by benthic primary producers such as algae fuels heterotrophic microbial growth, which can be detrimental to corals. This microbialization process has been associated with the abundance and replication strategies of bacteriophages, but the direct relationship between reef DOM composition and bacteriophage communities remains unclear. Here, we combine metabolomics, metagenomes, and viromes to demonstrate that phage communities have significant relationships with DOM composition on the reefs of Curaçao, Southern Caribbean. While total viral abundances did not significantly correlate with overall dissolved organic carbon (DOC) concentration on these reefs, co-occurrence networks identified thousands of statistically significant associations between free or cell-associated viruses and organic compounds. Cell-associated phages had significantly more positive associations with compounds that had a reduced nominal oxidative state of carbon (NOSC). Furthermore, temperate phages were more frequently correlated with metabolites exhibiting higher Gibbs energy than putatively lytic phages. Six of the ten viruses with the highest number of positive associations with metabolites were temperate (i.e., encoded an integrase or were identified as a prophage), despite this network consisting of approximately 90% lytic viruses. These temperate viruses were predicted to infect members of the genus Sphingobium. Together, these findings reveal a connection between phage replication strategies and DOM energy availability, with potential implications for coral reef biogeochemistry.IMPORTANCECoral reefs are highly dynamic ecosystems where microbial communities and organic matter cycles are intricately linked. This study provides new insights into how bacteriophages interact with dissolved organic matter (DOM) composition, revealing that cell-associated bacteriophages, particularly temperate phages, are associated with more energy-rich organic compounds. These findings suggest that DOM could affect the lysis-lysogeny decision of temperate phages or that lysogeny may play an underappreciated role in shaping the reef carbon cycle. Energy-rich organic compounds have generally been associated with increased algal abundances and coral decline. By demonstrating significant connections between viral infection strategies and the energy content of DOM, our results highlight the potential for phages to influence coral reef biogeochemistry and health.}, }
@article {pmid42390352, year = {2026}, author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Jingjing, X and Lianyi, H and Wang, B and Li, Y and Roeselers, G and Gong, S}, title = {Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo02082h}, pmid = {42390352}, issn = {2042-650X}, abstract = {The neonatal period is a critical stage of development during which the gut microbiome profoundly influences both short- and long-term health and nutrition. Its maturation from infancy to childhood is shaped by interacting environmental factors, including feeding mode, birth mode, and geographic location. A clinical study of 445 infants and toddlers (aged 0-24 months) from six socioeconomically diverse regions in China investigated age-related trajectories of gut microbiome and metabolomic development, with a particular focus on feeding mode. The study included a breastfed reference group and a formula-fed group that received an open-label formula containing a prebiotic mixture of short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS, 9 : 1). Longitudinal fecal samples were analyzed using shotgun metagenomic and metabolomic approaches. Feeding mode was strongly associated with variations in gut microbiome structure and function, along with birth mode and geographic location. Bifidobacterium and Bacteroides were the dominant taxa in both groups and exhibited dynamic abundance trajectories over time. Increased Bifidobacterium abundance was correlated with gene functions involved in starch and fatty acid metabolism as well as the fructose-6-phosphoketolase pathway (Bifid shunt). Comparative metabolomic analyses of amino acids and bile acids revealed highly similar metabolic profiles between the two groups. These findings highlight the association between feeding mode with the developing gut microbiome and describe age-dependent trajectories in Chinese children.}, }
@article {pmid42390679, year = {2026}, author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F}, title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.}, journal = {Ecotoxicology (London, England)}, volume = {35}, number = {6}, pages = {}, pmid = {42390679}, issn = {1573-3017}, support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; }, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; }, abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.}, }
@article {pmid42390736, year = {2026}, author = {Qi, M and Ye, H and Lei, D and Shao, J and Zhou, W}, title = {Metagenomic next-generation sequencing assists in identifying neurosyphilis: a case series.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {42390736}, issn = {1439-0973}, support = {Y20240739//Wenzhou Science &amp; Technology Bureau/ ; }, abstract = {BACKGROUND: Neurosyphilis is a severe manifestation of syphilis caused by Treponema pallidum and remains challenging to diagnose because of heterogeneous clinical presentations and the limited performance of cerebrospinal fluid (CSF) assays. Here, we report four neurosyphilis cases in which CSF metagenomic next-generation sequencing (mNGS) detected T. pallidum and explore its potential value as an adjunctive diagnostic tool.<br><br>METHODS: We retrospectively reviewed four HIV-negative adults treated at the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University in whom CSF mNGS detected T. pallidum and the overall clinical assessment supported neurosyphilis. Demographic data, presentations, neuroimaging, CSF parameters, serology, antimicrobial therapy, and outcomes were extracted from the medical records.<br><br>RESULTS: All patients had positive syphilis serology and inflammatory CSF profiles with lymphocytic pleocytosis (40-130 cells/&#xb5;L) and elevated CSF protein (0.70-1.26&#xa0;g/L). Brain magnetic resonance imaging (MRI) revealed non-specific chronic structural changes in all patients (including white matter hyperintensities, cerebral atrophy, and ventricular enlargement), with no acute ischemic, hemorrhagic, or neoplastic lesions. Bacterial cultures remained negative after 48&#xa0;h. CSF mNGS detected T. pallidum in all cases (unique reads 8-135; standardized mapped reads number (SMRN) 1-53; genome coverage 0.0260-0.4945%), including three patients whose predominant presentations were neuropsychiatric. Following anti-treponemal therapy with ceftriaxone or penicillin, all patients showed clinical improvement.<br><br>CONCLUSIONS: In this case series, CSF mNGS provided direct detection of T. pallidum and supported the diagnosis of neurosyphilis in patients with diverse, often neuropsychiatric presentations when conventional microbiology was non-diagnostic. CSF mNGS may serve as a useful adjunct in selected patients, but results should be interpreted alongside clinical features and CSF inflammation rather than in isolation.}, }
@article {pmid42391470, year = {2026}, author = {Plominsky, AM and Peoples, LM and Norenberg, M and Ramirez-Flandes, S and Podell, S and Mullane, KK and Casagrande, D and Roman, C and Pockalny, R and Smith, DC and Belser, C and Poulain, J and Allen, EE and Glud, RN and Ulloa, O and Barber, N and D'Hondt, S and Bartlett, DH}, title = {Minimising decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag064}, pmid = {42391470}, issn = {1751-7370}, abstract = {The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimising pressure and temperature effects. When compared to samples collected under pressurised conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a > 20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurised (e.g., members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g., Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.}, }
@article {pmid42391838, year = {2026}, author = {Yu, YH and Marín Arancibia, M}, title = {Mesorhizobium bavaricum sp. nov. and Mesorhizobium monacense sp. nov., two novel Lotus-associated species harbouring symbiotic plasmids.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {5}, pages = {126739}, doi = {10.1016/j.syapm.2026.126739}, pmid = {42391838}, issn = {1618-0984}, abstract = {Legumes establish a mutualistic interaction with nitrogen-fixing rhizobia. Lotus japonicus is a model for studying this symbiosis; however, only a limited number of rhizobial species nodulating this host have been taxonomically described. Here, we characterise four Mesorhizobium strains (DC-1.1[T], Qj1B1, DC-1.5[T], and Qj2B2) isolated from root nodules of Lotus japonicus and Lotus burttii. Multi-locus phylogeny and phylogenomic analyses resolved these isolates into two well-supported monophyletic clades. Genome-based comparisons supported their classification as distinct taxa, with strains DC-1.1[T] and Qj1B1 showing 95.2% average nucleotide identity (ANI) and 62.9-63.5% digital DNA-DNA hybridisation (dDDH) values relative to Mesorhizobium newzealandense ICMP 19545[T], whereas DC-1.5[T] and Qj2B2 exhibited 92.5-92.8% ANI and 49.9-50.5% dDDH compared with Mesorhizobium waimense ICMP 19557[T]. Together with chemotaxonomic and physiological traits, these data support the proposal of two novel species, Mesorhizobium bavaricum sp. nov. (DC-1.1[T] and Qj1B1) and Mesorhizobium monacense sp. nov. (DC-1.5[T] and Qj2B2). Metagenomic analyses predicted high environmental prevalence for these novel taxa, particularly within soil habitats. Isolates DC-1.1[T], Qj1B1, and DC-1.5[T] effectively nodulated Lotus burttii and significantly promoted plant growth, whereas Qj2B2 neither nodulated nor enhanced growth. Comparative genomic analysis revealed that the nodulating isolates harbour symbiotic genes (nod, fix, and nif) on symbiotic plasmids, a rare feature in Mesorhizobium strains, whereas Qj2B2 lacks essential nod and nif genes. Consistent with these genomic features, symbiotaxonomic analysis assigned the nodulating isolates to symbiovar loti. These results highlight the potential of these isolates as models for comparative analyses of symbiotic plasmid evolution and horizontal gene transfer.}, }
@article {pmid42391940, year = {2026}, author = {Wang, J and Guo, C and Pu, X}, title = {Metabolic filtering as a putative mechanism linking soil metabolome and microbial community assembly along a lake expansion gradient.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128601}, doi = {10.1016/j.micres.2026.128601}, pmid = {42391940}, issn = {1618-0623}, abstract = {Climate-driven lake expansion across the Qinghai-Tibet Plateau induces profound edaphic shifts, but how these abiotic changes shape soil microbial assembly remains unclear. Soil metagenomics and metabolomics were integrated along a 0-10 km spatial gradient at Gahai. Redundancy analysis (RDA) identified moisture (NDWI) and salinity (SI) as primary ecosystem drivers. Structural equation modeling (SEM) provided exploratory evidence consistent with a mediation pathway (P = 0.64, CFI = 1, RMSEA = 0), in which environmental factors potentially influenced microbial community structure indirectly, via reshaping the soil metabolome rather than through a direct path. Moisture availability exerted a strong negative effect on soil metabolic profiles (λ = -0.93), leading to a pronounced negative correlation between the metabolome and microbial community (λ= -0.97). Multi-omics integration attributed this pattern to stress-induced accumulation of defensive metabolites, including Feruloylputrescine and 3-Methylthiopropyl-desulfoglucosinolate. These compounds showed significant negative correlations with dominant genera (e.g., Candidatus Kryptobacter). This "metabolic filtering" is hypothesized to selectively limit the presence of non-adapted taxa based solely on correlational SEM and network analyses, supporting our tentative hypothesis that increasing environmental stress may promote a transition from competitive interactions toward patterns consistent with stronger deterministic filtering. Our exploratory findings suggest that the soil metabolome acts as a functional interface mediating microbial adaptation and strategic resource allocation to lake expansion in this high-altitude saline-alkali system. However, due to regional heterogeneity, these patterns provide a theoretical baseline for plateau lake ecosystems and should be applied with caution to broader geographic areas.}, }
@article {pmid42391942, year = {2026}, author = {Castellano-Hinojosa, A and de Freitas, J and de Carvalho, DU and Monus, BD and González-López, J and Strauss, SL and Albrecht, U}, title = {Compartmental and functional responses of the citrus microbiome and resistome to the systemic delivery of oxytetracycline by trunk injection.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128613}, doi = {10.1016/j.micres.2026.128613}, pmid = {42391942}, issn = {1618-0623}, abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely limits citrus production worldwide. We investigated how oxytetracycline (OTC) trunk injection affects the citrus holobiont, examining its ability to suppress CLas and improve tree performance while assessing compartment-specific responses of the microbiome and resistome. A field experiment was conducted in CLas-infected sweet orange trees, integrating qPCR pathogen quantification, fruit yield and juice quality measurements, functional pathway analysis, and genome-resolved profiling across leaves, bark, fibrous roots, and the rhizosphere at three time points after injection. OTC reduced CLas abundance in leaves and improved fruit yield and juice quality without altering microbial diversity. No clear OTC-associated shifts in microbial functional pathways were observed in aboveground compartments, and resistome profiles were strongly compartment-dependent but showed no detectable response to OTC treatment. However, pronounced functional shifts were detected in belowground compartments, with consistent reductions in carbon-, nitrogen-, and phosphorus-related pathways and declines in several taxa and metagenome-assembled genomes associated with nutrient turnover. In contrast, stress-tolerance and xenobiotic-responsive microorganisms were enriched. In addition, these belowground responses were associated with low-abundance, rare taxa rather than by changes in alpha diversity or the dominant community, revealing a hidden functional reconfiguration that was concentrated in the root and rhizosphere compartments most relevant to nutrient cycling and long-term soil health. These findings demonstrate that systemically delivered OTC induces targeted, compartment-specific reorganization of microbiome functions rather than broad disruption. By linking physiological improvement with functional and genome-resolved microbial responses, this study highlights the broader ecological consequences of antibiotic interventions in perennial crops.}, }
@article {pmid42392368, year = {2026}, author = {Cheng, M and Qin, X and Han, Y and Tan, F and She, M and Zhu, X and Yuan, L and Teng, M and Ou, X and Luo, S and Xiang, P and Chen, L and Yang, F}, title = {Genomic and biosynthetic landscape of high-temperature Daqu microbiome.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135297}, doi = {10.1016/j.biortech.2026.135297}, pmid = {42392368}, issn = {1873-2976}, abstract = {As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82% of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3% are novel, and 17,031 biosynthetic gene clusters, of which 62.63% are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.}, }
@article {pmid42392373, year = {2026}, author = {Long, Y and Zhu, C and Wu, X and Hou, J and Zeng, J and Wu, SL}, title = {Magnetite-driven food waste conversion toward high-value medium-chain fatty acids production through promoted biological processes and electrochemical environment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135299}, doi = {10.1016/j.biortech.2026.135299}, pmid = {42392373}, issn = {1873-2976}, abstract = {Achieving high-value valorization of food waste (FW) into medium-chain fatty acids (MCFAs) is vital for alleviating environmental pressure and advancing carbon neutrality. However, the inherent electron transfer and metabolic bottlenecks in FW bioconversion process restrains the conversion efficiency of MCFAs. Herein, the performance and comprehensive mechanisms of Fe3O4-enhanced MCFA production were comprehensively studied through integrated batch fermentation tests, bio-electrochemical characterizations, and metagenomic analysis. Results revealed that the optimal dosage of 8 g/L Fe3O4 enhanced caproate production to 3409.32 mg COD/L (a 3.7-fold increase over the control group). Notably, this dosage drove the further elongation of carbon chains, yielding high-energy-density heptanoate (C7) and caprylate (C8), thereby elevating MCFA selectivity from 5.5 % to 38.6 %. Further analysis indicated that Fe3O4 promoted all biological processes (solubilization, hydrolysis, acidogenesis, and chain elongation). Mechanically, Fe3O4 optimized the electrochemical microenvironment, enhancing conductivity and electron transport system (ETS) activity by 32.5 % and 69.1 %, respectively. The correlation-based network analysis confirmed a strong correlation (r > 0.4) between product distribution, iron cycling (Fe[2+] concentration), and conductivity. Metagenomic analysis elucidated that by enriching core functional genera like Clostridium and Sphaerochaeta and associated functional microbial genes, Fe3O4 synergistically promoted the efficient bioconversion of FW into MCFAs. This study offers new mechanistic insights into enhancing MCFA production via magnetite-regulated electron transfer, providing a robust strategy for efficient resource recovery from complex organic wastes.}, }
@article {pmid42392375, year = {2026}, author = {Hou, K and Yang, B and Zhao, R and Zhang, J and Duan, Y}, title = {Dose-dependent effects of biochar on low-temperature anammox: reactor performance, community variation, and functional potential.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135296}, doi = {10.1016/j.biortech.2026.135296}, pmid = {42392375}, issn = {1873-2976}, abstract = {Low temperature is a major constraint on the practical application of anaerobic ammonium oxidation (anammox). Although biochar has been reported to improve low-temperature anammox, the effect of dosage remains insufficiently understood. In this study, mature anammox sludge was amended with 0, 3, 7, and 9 g/L bamboo-derived biochar and operated under a stepwise temperature decrease from 35 to 15°C, followed by low-temperature operation for 70 d. Reactor performance, extracellular polymeric substances (EPS), microbial community composition, and metagenomic functional potential were analyzed to clarify the dose effect of biochar. Among the tested dosages, 7 g/L biochar achieved the highest nitrogen removal efficiency (48.6%) at 15°C, which was 12.8 percentage points higher than the control value of 35.8%. Biochar-amended reactors also showed higher EPS contents than the control, and the 7 g/L group better maintained the PN/PS ratio under low-temperature stress. Community analysis indicated a higher relative abundance of Candidatus Brocadia in the biochar-amended groups, especially at 7 g/L. Metagenomic analysis further showed higher abundance of genes associated with nitrogen metabolism, carbon metabolism, and EPS-related precursor synthesis in the 7 g/L group. These results suggest that an appropriate biochar dosage can improve low-temperature anammox performance and is associated with EPS stabilization, enrichment of key functional taxa, and enhanced functional potential. This study provides guidance for biochar dosage optimization in low-temperature anammox systems.}, }
@article {pmid42392574, year = {2026}, author = {Vita, AA and Brown, J and Norby-Adams, L and Ghanem, N and Weir, TL and Goldenberg, JZ}, title = {Microbial-derived polyphenol metabolites and the gut microbiota: A scoping review of clinical studies.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101700}, doi = {10.1016/j.tjnut.2026.101700}, pmid = {42392574}, issn = {1541-6100}, abstract = {BACKGROUND: Dietary (poly)phenols are widely recognized for their health-promoting properties, yet their bioactivity is largely contingent upon gut microbial metabolism. Individual differences in microbiome composition lead to variable production of microbial-derived (poly)phenol metabolites (MPMs) and thus contribute to divergent health outcomes.<br><br>OBJECTIVE: This scoping review aimed to systematically map the scope of clinical evidence reporting relationships between MPMs and gut microbiota composition and function, highlighting research gaps to guide future investigations.<br><br>METHODS: Using pre-defined search criteria, two reviewers identified human clinical studies reporting relationships between metabolite levels and microbiome outcomes.<br><br>RESULTS: Fifty-six studies were included. Evidence was frequently focused on phenolic acids (n=20), phytoestrogens (n=18), and urolithins (n=17), with relationships between microbiota and other MPMs only being reported in 1-2 studies. The majority of studies across MPM categories used 16S rRNA gene sequencing for identification of gut microbiota (n=42), among other methods, with only six studies using metagenomic shotgun sequencing, thus limiting taxonomic resolution and functional inference. Findings revealed recurrent associations between specific microbes and MPMs; while some reflected known producer taxa (e.g., Gordonibacter and urolithins), others may represent broader community-level interactions (e.g., Alistipes and equol). However, these results varied across (poly)phenol class, intervention type, and host-specific context.<br><br>CONCLUSION: This scoping review identified recurrent microbiota-MPM associations alongside major evidence gaps, including limited functional microbiome characterization and sparse investigation of several MPM classes/subclasses (e.g., resveratrol-, flavanone-, and flavan-3-ol-related MPMs). Future research using standardized, high-resolution multi-omics approaches is needed to improve identification of reproducible microbial signatures and mechanisms underlying (poly)phenol metabolism, and to link these features with functional health outcomes.}, }
@article {pmid42379395, year = {2026}, author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, P and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM}, title = {Oat-rich low-gluten diet modulates plasma short-chain fatty acids without significant changes in fecal microbiome or inflammatory markers - a randomized clinical trial in people with cardiometabolic risk.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101690}, doi = {10.1016/j.tjnut.2026.101690}, pmid = {42379395}, issn = {1541-6100}, abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.<br><br>OBJECTIVE: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers during a 6-week oat- or rice-rich LGD in individuals with increased cardiometabolic risk.<br><br>METHODS: The participants (n=69) were allocated into two parallel groups following a 6-week LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (Novaseq X Plus) and characterized using MetaPhlAn4. Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by UHPLC-MS, and inflammatory markers were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with linear mixed-effects model.<br><br>RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. Particularly, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (ptimeXgroup=0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (ptimeXgroup=0.025), and more changes in the microbiome. This is possibly due to more substantial dietary changes from a low rice consumption compared to the habitual diet in the baseline. No significant differences between or changes within the groups in inflammatory markers were observed.<br><br>CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and inflammatory markers in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome towards potentially unfavorable direction.<br><br>NCT05526092, https://clinicaltrials.gov/study/NCT05526092.}, }
@article {pmid42379815, year = {2026}, author = {Patel, I and Mammel, M and Gangiredla, J and Mukherjee, A}, title = {Targeted amplicon sequencing for enhanced detection of spiked Shiga toxin-producing Escherichia coli in ready-to-eat romaine lettuce: a proof-of-concept study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0102226}, doi = {10.1128/spectrum.01022-26}, pmid = {42379815}, issn = {2165-0497}, abstract = {The early and accurate detection of low-level pathogenic and indicator organisms in fresh produce is critical for preventing widespread foodborne outbreaks. Contamination of leafy greens with foodborne pathogens, such as Shiga toxin-producing Escherichia coli (STEC), is a significant public health issue, making rapid and sensitive detection methods critical for mitigating outbreaks. Although next-generation sequencing (NGS) is a powerful tool for pathogen identification, challenges remain in detecting low contamination levels in food products. Here, we demonstrate the use of a custom targeted amplicon sequencing (TAS) primer panel targeting species with food safety concerns, including known human foodborne pathogens, opportunistic pathogens, and indicator organisms related to food spoilage. Using a quasi-metagenomics approach, this proof-of-concept study demonstrates that, compared to whole-metagenomic sequencing (WMS), TAS is a rapid and sensitive NGS-based method for detecting low levels of pathogens. Ready-to-eat romaine lettuce was spiked with STEC and incubated in enrichment medium. DNA was isolated at 0.5, 5, and 6 h, and libraries were prepared for both WMS and TAS. The results indicated that TAS was more sensitive than WMS not only at detecting the pathogen at the species level but also at identifying key virulence markers stx1 and stx2. Overall, our targeted sequencing approach provides a rapid and sensitive molecular method to detect and identify foodborne pathogenic bacteria, demonstrating its potential for application in food safety.IMPORTANCEDetecting low-level pathogenic and indicator organisms is critical to prevent foodborne outbreaks. Conventional methods lack speed and sensitivity. While next-generation sequencing methods, such as whole-metagenomic sequencing (WMS), offer a broad microbial landscape view, detecting pathogens at low concentrations within complex food matrices remains challenging. To address this, a targeted amplicon sequencing (TAS) panel was designed to identify species of food safety concern and key indicator organisms. This study demonstrates that TAS is more sensitive than WMS. The application of this TAS assay provides an important bridge between qPCR and WMS by detecting and characterizing pathogens that might be present in low numbers and otherwise missed in an enrichment. TAS allows multiplexing and overcomes the critical limitation of sensitivity in complex samples, providing a robust tool for food safety surveillance. Our findings demonstrate the potential use of targeted next-generation sequencing (NGS)-based methods to mitigate the risk of foodborne illnesses.}, }
@article {pmid42379825, year = {2026}, author = {Wang, S and Chen, M and Jiao, D}, title = {ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0410125}, doi = {10.1128/spectrum.04101-25}, pmid = {42379825}, issn = {2165-0497}, abstract = {UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes.<br><br>IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.}, }
@article {pmid42380482, year = {2026}, author = {Kang, X and He, P and Zhang, H and Lü, F}, title = {Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10568-3}, pmid = {42380482}, issn = {2399-3642}, abstract = {Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.}, }
@article {pmid42381037, year = {2026}, author = {Garcia-Castillo, L and Ferrero, G and Blaževitš, O and Francescato, G and Eliass, AT and Cortez, NE and Beltrà, M and Tarallo, S and Pardini, B and Costelli, P and Naccarati, A and Longo, VD and Penna, F}, title = {Fasting-mimicking diet counteracts gut microbial dysbiosis in experimental lynch syndrome.}, journal = {Cancer &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40170-026-00446-1}, pmid = {42381037}, issn = {2049-3002}, abstract = {The development of colorectal cancer (CRC) is largely influenced by hereditary factors, with up to one-third of cases linked to genetic predisposition. In parallel, environmental factors such as diet and intestinal microbiota play a significant role. Lynch syndrome (LS), the most common form of hereditary CRC, is due to mutations in DNA mismatch repair genes. Diet interventions such as calorie restriction (CR) can modify the course of the disease, altering nutrient supply and promoting beneficial microbial populations. Fasting-mimicking diets (FMD) are plant-based CR regimens that showed promise in modulating the gut microbiota and suppressing CRC progression in pre-clinical ectopic cancer models. In this study, Villin-Cre/Msh2-floxed (VCM) mice, modelling LS, were subjected to periodic FMD cycles for 10 months. FMD regimen influenced animal weight in a sexually dimorphic manner, stably reducing animal body weight only in males. Moreover, shotgun metagenomic sequencing revealed that FMD mitigated the dysbiotic longitudinal changes associated with cancer onset, preserving beneficial species, such as Lactobacillus johnsonii, and reducing adverse species, such as Escherichia coli. Metabolic pathway analysis also showed significant differences, with FMD preventing the upregulation of pathways involved in amino acid and nucleotide synthesis, potentially promoting tumour growth. Overall, the findings suggest that periodic FMD may result useful in a multimodal approach for LS management, counteracting gut microbiota alterations.}, }
@article {pmid42381048, year = {2026}, author = {Porcel Sanchis, D and Pola, M and Engelberts, JP and Guerra-Font, O and Messer, L and Alberola-Mora, I and Escobar Sáez, L and Pérez Gómez, N and Portolés Campo, &#xc1; and Valero-Tebar, J and Naya Garmendia, LM and Preciado Barahona, JC and Gil García, R and Arnau, V and McIlroy, SJ and Džunková, M}, title = {Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02456-z}, pmid = {42381048}, issn = {2049-2618}, abstract = {BACKGROUND: Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.<br><br>RESULTS: Using ethanol-preserved specimens archived for up to 30&#xa0;years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.<br><br>CONCLUSIONS: Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.}, }
@article {pmid42381185, year = {2026}, author = {Mouanes-Abelin, J and Pomares, C and Montoya, JG and Pondrom, M and Maria, L and Zimmer, AJ and Gomez, CA}, title = {Toxoplasmosis Beyond Transplantation: Diagnostic and Prevention Challenges in a Patient Receiving Targeted Immunomodulators.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {}, number = {}, pages = {e70263}, doi = {10.1111/tid.70263}, pmid = {42381185}, issn = {1399-3062}, abstract = {Toxoplasmosis has long been recognized as a serious complication in immunocompromised host, particularly those with advanced HIV/AIDS, hematopoietic stem-cell transplantation (HSCT), solid-organ transplant (SOT), and hematological malignancies. The rapid expansion of targeted immunomodulators, including chimeric antigen receptor T-cell (CAR-T) therapies, monoclonal antibodies, and small-molecule inhibitors, is creating new at-risk populations beyond traditional transplant settings. We present a 9-year-old boy with high-risk B-cell acute lymphoblastic leukemia (B-ALL), who developed prolonged fever and macrophage activation syndrome (MAS). After an extensive unrevealing workup, disseminated acute toxoplasmosis was identified incidentally on bone marrow aspirate via morphologic identification of tachyzoites and confirmed by Toxoplasma gondii PCR. This case exemplifies the emerging threat of toxoplasmosis in non-transplant immunomodulated hosts and supports three core mitigation strategies. First, baseline Toxoplasma IgG and IgM serology should be obtained in all patients initiating targeted immunotherapy, recognizing that B-cell depletion or hypogammaglobulinemia may render IgG unreliable, and that IgM may be falsely negative, delayed, or persistently positive in immunocompromised individuals. Second, targeted PCR from clinically relevant compartments or metagenomic next-generation sequencing when conventional diagnostics is unrevealing should be applied early. Third, prevention requires a bundled approach: baseline screening, patient education for seronegative individuals, and trimethoprim-sulfamethoxazole prophylaxis with or without serial qPCR monitoring for seropositive patients. Toxoplasmosis is no longer a transplant-exclusive concern. As targeted immunomodulators reshape practice across rheumatology, oncology, neurology, and autoimmune disease, infectious diseases specialists must lead efforts to raise cross-specialty awareness, establish guidelines, and build registries to define the true burden of toxoplasmosis in these growing populations.}, }
@article {pmid42381379, year = {2026}, author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA}, title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690687}, doi = {10.1080/19490976.2026.2690687}, pmid = {42381379}, issn = {1949-0984}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.}, }
@article {pmid42381607, year = {2026}, author = {Lv, JL and Zhu, MQ and Gao, T and Pan, Y and Yu, HQ and Min, D and Xiong, YJ and Liu, DF}, title = {Profiling Active Low-Abundance Microbes in As/Sb-Contaminated Soils via d-Amino Acid-Based In Situ Labeling.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c07045}, pmid = {42381607}, issn = {1520-5851}, abstract = {Soil microbial communities play a pivotal ecological role in contaminated environments. However, conventional metagenomic approaches struggle to distinguish between "potential function holders" and "in situ metabolically active executors". Here, we employed a method combining fluorescent d-amino acid labeling, fluorescence-activated cell sorting, and metagenomics (FDAA-FACS-Metagenomics) to capture and profile active microbes in complex soils. The secondary addition of As(V) and Sb(V) enhanced the community's reductive activity toward these metalloids, reshaping the active assemblages. Clostridium was markedly enriched, and several low-abundance members were activated as true executors of the reduction process. MAGs recovered via FDAA-FACS revealed an active core community with functional partitioning: some taxa participated directly in As(V)/Sb(V) reduction, while others contributed to community stability through tolerance and metabolic support. Notably, a Desulfitobacteriaceae genome (MAG29) harbored both arrAB and anrAB gene clusters, a complete Wood-Ljungdahl carbon fixation pathway, and nitrogen fixation genes. These genomic features suggest the potential for a multifunctional metabolic lifestyle involving metalloid reduction, carbon fixation, and nitrogen transformation. Such metabolic versatility may enable MAG29 to contribute to coupled carbon-nitrogen cycling and metalloid transformation under contaminated environmental conditions. These findings emphasize the important ecological roles of rare, metabolically active microbes in metalloid transformation and soil ecosystem functioning.}, }
@article {pmid42381665, year = {2026}, author = {Flach, CF and Berglund, F and Osena, G and Huijbers, PMC and Larsson, DGJ}, title = {Sewage surveillance for assessing clinical antibiotic resistance prevalence: Combining metagenomic and phenotypic data.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101485}, pmid = {42381665}, issn = {2352-7714}, abstract = {Surveillance of antibiotic resistance in clinical isolates is a cornerstone for the management of bacterial infections but is limited in large parts of the world, often due to lack of resources. Sewage surveillance has been proposed as a promising, resource-efficient complement to the traditional surveillance approach based on samples from many individual patients. Both phenotypic data on resistance in sewage isolates and abundance of antibiotic resistance genes in sewage have been shown to correlate with resistance prevalence in clinical isolates. Here, we aimed to directly compare and combine an isolate-based and a gene-based sewage surveillance approach to evaluate what best can reflect clinical resistance rates. The two approaches, based on susceptibility testing of collected E. coli isolates and metagenomic sequencing, respectively, were applied to municipal sewage samples collected in ten European countries. The data generated was related to available data on resistance to aminopenicillins, fluoroquinolones, third generation cephalosporins and aminoglycosides prevalence in clinical E. coli isolates using beta regression models. None of the tested individual predictors were superior across all four investigated classes of antibiotics. For modelling of aminopenicillin resistance, a clearly higher R[2] value was obtained when isolate-based and gene-based data was combined as predictors, also after adjusting for the number of included variables. We conclude that there could be a value of including both isolate- and gene-based sewage data for predictions of resistance rates in clinical isolates, while emphasizing the value of linking predictors to specific species and classes of antibiotics.}, }
@article {pmid42381921, year = {2026}, author = {Salah, R and AbdElaal, KR and Ghonaim, L and Awe, OI and Moustafa, A}, title = {DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag166}, pmid = {42381921}, issn = {2635-0041}, abstract = {MOTIVATION: Accurate species-level classification of prokaryotic 16S rRNA sequences remains difficult: existing tools rely on exact alignment, k-mer heuristics, or phylogenetic placement and are limited by incomplete reference databases. Deep learning approaches in microbial genomics have focused largely on whole-genome metagenomics, leaving 16S taxonomy under-supported.<br><br>RESULTS: We present DeepTaxa, a hybrid CNN-BERT framework that pairs a multiscale CNN with a transformer trained from scratch on the DNABERT-2 BPE vocabulary, producing parallel rank-specific predictions across the seven Linnean ranks. On the Greengenes2 2024.09 test set, DeepTaxa achieves species-level accuracy of 92.96% and F1 of 0.9212 (3-seed mean; cross-seed standard deviation &#x2264; 0.0008 F1 at every rank), with F1 above 0.99 from domain through class and a species-level expected calibration error of 0.0242. DeepTaxa exceeds DADA2 (90.05%) and QIIME 2 (85.01%) at the species rank on the same held-out test set, with larger gains over the k-mer-based classifiers SINTAX and Kraken 2. Performance degrades smoothly with decreasing training-set similarity (species F1 from 0.95 to 0.45), and a dedicated V3-V4 amplicon checkpoint reaches 87.55% species accuracy from an approximately 420&#x2009;bp window.<br><br>Source code, trained checkpoints for full-length 16S and V3-V4 amplicons, curated datasets, and reproducible workflows are publicly available at github.com/systems-genomics-lab/deeptaxa and huggingface.co/systems-genomics-lab/deeptaxa.}, }
@article {pmid42382111, year = {2026}, author = {Sachula, W and Huimin, L and Yaxing, Z and Ding, Y and Shangxiong, Z and Shengli, L and Haizhou, S and Chunhua, Z}, title = {An integrative multi-omics investigation into the influence of forage type on the volatile flavor profile of Ujumqin sheep mutton.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1856240}, pmid = {42382111}, issn = {2297-1769}, abstract = {China ranks among the leading producers and consumers of mutton globally and the development of nutritional strategies to improve meat quality and sensory attributes. This study investigated the effect of three high-quality forages, i.e., alfalfa hay (ALFA), Leymus chinensis hay (LEYM) and oat hay (OATS) compared to corn stalks-based control diet (CORN) on rumen microbiota, metabolomics profiles, and muscle volatile flavor compounds in lambs through a multi-omics integration approach. Forty male lambs were randomly allocated into four dietary groups (n = 10/group) and fed a concentrated forage supplement for 91 days. From each group, six lambs (n = 6/group; totla 24) were slaughtered. Rumen fluid and longissimus dorsi muscle samples were collected for metagenomics, untargeted metabolomics, and volatile flavor analysis. Differential microbial taxa were identified using LEfSe analysis, followed by integrated Pearson correlation and MetoOrigin analysis to link microbiota, metabolites, and metabolic pathways. Associations with muscle volatile flavor compounds were also assessed. LEfSe analysis identified 4, 3, and 7 differentially abundant rumen microbial taxa in the ALFA, LEYM and OATS groups, respectively, compared to CORN. Integrated analysis showed these taxa correlated with 4, 9 and 11 rumen metabolites via 3, 11 and 7 microbial or host-microbial co-metabolic routes, respectively. These metabolic changes were strongly associated to alterations in muscle volatile flavor compounds. Particularly, the ALFA diet increased volatile compounds associated with fresh, grassy, floral, and citrus-like odors reduced mutton-related Pyrazine (2,5-dimethyl-). The LEYM diet reduced Pentaborane(9) and Pyrazine, which are associated with undesirable mutton like odors. The OATS diet increased 2-Nonanone and Phenylethyl Alcohol (fruity and floral smells), while suppressing n-Decanoic acid and n-Octanoic acid (associated with characteristic mutton aroma). These results showed that high-quality forages improve the mutton flavor by regulating the rumen micro-ecological network and associated metabolic pathways along the forage-microbiota-metabolites-muscle flavor axis. These findings provide a theoretical foundation for precise nutritional interventions aimed at enhancing meat quality in lambs.}, }
@article {pmid42382141, year = {2026}, author = {Chigwada, AD and Tekere, M}, title = {Archaea-driven bioremediation of polyolefins and polyesters in extreme environments.}, journal = {Biodesign research}, volume = {8}, number = {3}, pages = {100092}, pmid = {42382141}, issn = {2693-1257}, abstract = {Global plastic production surpassed 436 million metric tonnes in 2023, with polyolefins, polyethylene and polypropylene, and polyesters, polyethylene terephthalate and polybutylene adipate terephthalate dominating the persistent fraction. In extreme environments, these recalcitrant polymers accumulate rapidly: hadal-trench sediments contain microplastic abundances of 71.1 items per kilogram dry weight, while bottom waters reach 2.06-13.51 particles per litre. Abiotic degradation is severely limited by hydrostatic pressure, hypersalinity, low temperature, and anaerobiosis. Although bacterial and fungal pathways have received primary attention, archaea adapted to polyextreme conditions represent an underexplored resource. Landmark discoveries include PET46, a lid-containing feruloyl esterase from uncultured Candidatus Bathyarchaeota in Guaymas Basin deep-sea sediments that hydrolyses semi-crystalline polyethylene terephthalate powder at rates comparable to established bacterial PETases while outperforming them on oligomers. Subsequent metagenomic prospecting identified GuaPA, a distinct Bathyarchaeia-derived PETase capable of film depolymerisation. Deep-sea plastispheres, hypersaline basins, and extraterrestrial analog sites further reveal archaeal colonisation and metabolic versatility. This review synthesises metagenomic, enzymatic, and community-level evidence, critically evaluates archaeal advantages relative to bacteria and fungi, addresses persistent gaps, including limited polyolefin mineralisation and cultivation bias, and outlines priorities for enzyme engineering and consortia design. The work advances sustainable bioremediation strategies aligned with climate-action goals and circular-economy frameworks in extreme and space environments.}, }
@article {pmid42382346, year = {2026}, author = {He, B and Xiao, Z and Zou, L and Wei, J and Xiang, Z and Sang, F and Guo, X}, title = {Unveiling the unique gut microbial signatures in colorectal adenomas: establishment and validation of a cross-kingdom microbiome predictive model.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1854806}, pmid = {42382346}, issn = {1664-302X}, abstract = {BACKGROUND: Colorectal adenoma (CA), the main precancerous lesion of colorectal cancer (CRC), originates in approximately 85-90% of CRC cases. With increasing demands for early diagnosis and treatment, gut microbiome research has become a forefront area. While numerous studies have shown that gut bacteria are closely related to the development of colorectal adenomas and cancer, research on viruses, archaea, and fungi is limited.<br><br>METHODS: From January 2019 to January 2024, this study collected 296 fecal samples from multiple centers and performed metagenomic analysis using shotgun sequencing. Principal coordinate analysis (PCoA) was conducted based on Bray-Curtis distance at the species level, &#x3b1;-diversity was calculated, and LEfSe analysis identified differential microorganisms. A random forest model was developed to distinguish adenoma patients from healthy individuals, with performance evaluated through internal validation using Bootstrap sampling and external validation with an independent cohort.<br><br>FINDINGS: Significant differences in the relative abundance of certain bacteria (e.g., Phocaeicola_vulgatus and Prevotella_copri), fungi (Candida_albicans), archaea (Methanobrevibacter_oralis), and viruses (Streptococcus satellite phage Javan301) were observed in adenoma patients. Spearman correlation analysis revealed complex network relationships among these microorganisms. The prediction model achieved a mean AUC of 0.80&#x202f;&#xb1;&#x202f;0.05 and an external validation AUC of 0.75, demonstrating stability and generalizability.<br><br>CONCLUSION: This study shows significant cross-kingdom microbial signatures in colorectal adenoma patients, providing potential for developing new preventive and therapeutic methods. The predictive model, based on these differential microorganisms, exhibits robust and promising classification performance, offering potential for early adenoma detection.}, }
@article {pmid42382358, year = {2026}, author = {Mengjia, C and Bujiang, W and Honghui, C and Qiying, H and Haojun, S}, title = {Biliary tract microbes and common bile duct stones: current status and prospects.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818256}, pmid = {42382358}, issn = {1664-302X}, abstract = {Common bile duct stones is a common digestive system disease, and about 5%-30% of patients with cholelithiasis are complicated with common bile duct stones. It poses significant challenges to clinical diagnosis and treatment. Although its occurrence is related to traditional factors such as abnormal bile composition and biliary dynamics disorders, the exact pathogenesis has not been fully clarified. In recent years, with the rapid development of high-throughput sequencing and metagenomics and other microbiome technologies, researchers have begun to pay attention to the role of biliary microbiota in the formation of common bile duct stones. More and more evidence indicates that the biliary tract microbes may has been associated with the occurrence and development of stones. This review firstly examines the literature implicating between biliary microorganisms and different types of common bile duct stones. We discuss the various mechanisms of action of biliary tract microorganisms in the occurrence of common bile duct stones. We also evaluated the specific value of microbial markers for diagnostic typing and prediction of recurrence.}, }
@article {pmid42382773, year = {2026}, author = {Zhang, D and Song, Y and Bai, Y and Yan, J and Shen, R}, title = {Autoimmune GFAP astrocytopathy with eosinophils on cerebrospinal fluid cytology and isolated spinal cord lesions on MRI: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1865920}, pmid = {42382773}, issn = {1664-3224}, mesh = {Humans ; Female ; Adult ; *Glial Fibrillary Acidic Protein/immunology ; Magnetic Resonance Imaging ; *Astrocytes/immunology/pathology ; *Spinal Cord/pathology/diagnostic imaging/immunology ; *Eosinophils/immunology/pathology ; Biomarkers ; Autoantibodies/immunology ; }, abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy is an autoimmune inflammatory disorder of the central nervous system associated with GFAP-IgG. It most commonly presents as meningoencephalitis, myelitis, or meningoencephalomyelitis. Although MRI abnormalities in the brain and spinal cord are common, isolated spinal cord lesions without corresponding brain MRI abnormalities are uncommon and may pose a diagnostic challenge. Eosinophils identified on cerebrospinal fluid cytology have rarely been reported in this disorder.<br><br>CASE PRESENTATION: A 31-year-old woman presented with fever, headache, urinary retention, and meningeal irritation signs. Despite these findings, brain magnetic resonance imaging (MRI) was unremarkable, whereas spinal MRI revealed discontinuous patchy long-segment intramedullary lesions in the thoracic cord. Cerebrospinal fluid (CSF) analysis showed elevated opening pressure, pleocytosis, increased protein, and 10% eosinophils on cytological examination. Infectious studies, including CSF culture and metagenomic next-generation sequencing, were negative. Serum and CSF antibodies against aquaporin-4, myelin oligodendrocyte glycoprotein, and myelin basic protein were negative, whereas CSF GFAP-IgG was positive at a titer of 1:32, while serum GFAP-IgG was negative. Following high-dose intravenous methylprednisolone and an oral prednisone taper, the patient showed marked clinical, CSF, and radiological improvement, with complete resolution of thoracic cord lesions on follow-up MRI.<br><br>CONCLUSION: Isolated spinal cord lesions on MRI may represent an important clue to autoimmune GFAP astrocytopathy and should prompt consideration of this diagnosis even in the absence of brain MRI abnormalities. The presence of eosinophils on cerebrospinal fluid cytology may further suggest a distinct inflammatory profile and offer insight into the pathophysiology of the disease.}, }
@article {pmid42382960, year = {2026}, author = {Zhang, WJ and Yang, Z and She, JQ and Wu, HL and Xia, ZY and Zhang, D and Suo, LG and Pan, Z and Zhang, Y and Wang, HZ and Hong, J and Zhang, C}, title = {Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.}, journal = {International journal of ophthalmology}, volume = {19}, number = {7}, pages = {1235-1248}, pmid = {42382960}, issn = {2222-3959}, abstract = {AIM: To characterize the composition and functional features of the aqueous humor microbiome in common ocular diseases, including myopia, cataract, primary open angle glaucoma (POAG), and Posner-Schlossman syndrome (PSS).<br><br>METHODS: We performed metagenomic sequencing on 176 aqueous humor samples from patients with cataract (n=37), POAG (n=66), PSS (n=35), and myopia patients (n=38, as controls). Taxonomic profiling, functional annotation, and diversity analyses were conducted to characterize microbial communities, with adjustments for age and gender where appropriate. Associations between microbial features and clinical parameters were evaluated using correlation analyses.<br><br>RESULTS: We identified 6635 bacterial, 141 archaeal, 96 eukaryotic, and 108 viral operational taxonomic units (OTUs) in the aqueous humor. The microbiome was dominated by Actinomycetota and Pseudomonadota at the phylum level. Compared to myopia controls, POAG and PSS patients showed significantly reduced alpha diversity after age adjustment (P<0.05), whereas cataract patients showed no significant difference. Additionally, we identified disease-specific microbial signatures including enrichment of Cytomegalovirus (CMV) in PSS. Functional analysis revealed enrichment of distinct metabolic pathways. Finally, correlations were observed between microbiota/pathway abundance and clinical phenotype, though none remained significant after multiple testing correction.<br><br>CONCLUSION: This study provides a preliminary characterization of the aqueous humor microbiome in patients with POAG, PSS, cataract, and myopia controls. The identified microbial signatures and functional pathways offer new insights into potential microbiome-mediated mechanisms in ocular pathophysiology and may inform future diagnostic and therapeutic strategies.}, }
@article {pmid42383698, year = {2026}, author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO}, title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585261454207}, doi = {10.1177/13524585261454207}, pmid = {42383698}, issn = {1477-0970}, abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.<br><br>OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.<br><br>METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N&#x2009;=&#x2009;266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.<br><br>RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).<br><br>CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.}, }
@article {pmid42384485, year = {2026}, author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ}, title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {116334}, doi = {10.1016/j.celrep.2025.116334}, pmid = {42384485}, issn = {2211-1247}, abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.}, }
@article {pmid42384916, year = {2026}, author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA}, title = {Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag422}, pmid = {42384916}, issn = {1367-4811}, abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on January 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.<br><br>AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42384962, year = {2026}, author = {Narayanan, AK and Philosof, A and Murali, R and Connon, SA and Wegener, G and Orphan, VJ}, title = {Viral communities from long-term anaerobic alkane-oxidizing enrichments encode predicted cell surface adhesion functions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag172}, pmid = {42384962}, issn = {1751-7370}, abstract = {The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.}, }
@article {pmid42385223, year = {2026}, author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A}, title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.}, journal = {MicrobiologyOpen}, volume = {15}, number = {4}, pages = {e70359}, doi = {10.1002/mbo3.70359}, pmid = {42385223}, issn = {2045-8827}, mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; }, abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.}, }
@article {pmid42385456, year = {2026}, author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A}, title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.}, journal = {Ticks and tick-borne diseases}, volume = {17}, number = {4}, pages = {102679}, doi = {10.1016/j.ttbdis.2026.102679}, pmid = {42385456}, issn = {1877-9603}, abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.}, }
@article {pmid42385542, year = {2026}, author = {Zhong, X and Sun, Z and Wu, H and Li, E and Fang, G}, title = {Response of soil nitrogen-cycling functional genes and their associations to nitrogen enrichment in a typical subtropical estuary (Min River), Southeast China.}, journal = {Marine pollution bulletin}, volume = {232}, number = {}, pages = {120078}, doi = {10.1016/j.marpolbul.2026.120078}, pmid = {42385542}, issn = {1879-3363}, abstract = {Soil N-cycling functional genes are easily modified by environmental changes, but insufficient information is available regarding the response of their elaborate associations to nitrogen (N) enrichment in estuarine marsh ecosystem. In this study, a field experiment with four N enrichment levels (NN, 0.0 g N m[-2] yr[-1]; NL, 37.5 g N m[-2] yr[-1]; NM, 50.0 g N m[-2] yr[-1]; and NH, 100.0 g N m[-2] yr[-1]) was conducted in a typical Cyperus malaccensis marsh in the Min River estuary of southeastern China. After 28 and 40 months of sustained N additions (represented by T28 and T40 periods, respectively), the potential impacts of N enrichment on soil N-cycling functional genes and their associations were investigated by metagenomic sequencing. Results showed that although the composition of functional microbial communities showed causality with N enrichment levels, its variation was primarily driven by N-enriched duration as evidenced by the higher interpretability (64.7%). With prolonged the experiment, the diversity of soil N-cycling microbial communities dropped markedly while their richness showed no statistically significant alteration. Within each sampling period, the relative abundances of functional genes involved in organic N metabolism (ONM, glnB, GDH2 and GLT1), assimilatory nitrate reduction (ANRA, narB, nirA, NR and NIT-6), denitrification (nirS, norC and napB), N fixation (nifK/D, vnfH/K/G and anfG), dissimilatory nitrate reduction (DNRA, nrfA and nirB/D), N transport (nrtC/B) and nitrification (pmoB/C-amoB/C) significantly increased with increasing N additions. Compared with the T28 period, the relative abundances of genes involved in ONM (GDH2 and K00261_gdhA), denitrification (narI and nirS), N fixation (nifD/H and vnf/H/K) and N transport (NRT2 and nrtA/C) elevated significantly at T40 period, while those participated in DNRA (nrfH), nitrification (hao) and anammox (hzsB/C) declined markedly. Under N-enriched conditions, the network complexity of functional genes displayed decreases in the LN and MN treatments, followed by a significant increase in the HN treatment. With prolonged the experiment, the positive correlations among functional genes were weakened and the succession of functional microbial communities was driven in a more functionally specialized direction by a few dominant species. This paper found that sustained N enrichment drove the phased reconstruction of gene networks with a continuous weakening of positive associations among functional genes. The findings can guide the policymaking of targeted N load control and estuarine marsh conservation.}, }
@article {pmid42385547, year = {2026}, author = {Paietta, EN and Lefkowitz, EJ and Van Der Pol, WJ and Hendrickson, RC and Johnston, RA and Randrianarisoa, SF and Kraberger, S and Razanamahenina, TT and Ramboninarimalala, A and Raherinirina, TG and Raveloson, L and Finley, NL and Scotch, M and Baitchman, E and Yoder, AD and Varsani, A}, title = {Divergent poxvirus identified in a non-native black rat from Madagascar.}, journal = {Virology}, volume = {623}, number = {}, pages = {111021}, doi = {10.1016/j.virol.2026.111021}, pmid = {42385547}, issn = {1096-0341}, abstract = {Non-native rodents serve as bridges between anthropogenic and natural landscapes. They have expanded across the planet alongside humans while bringing competition, predation, and pathogens, such as poxviruses, to naïve ecosystems. Although rodents serve as reservoirs for multiple zoonotic poxviruses, limited research has focused on rodents for identification of unknown poxviruses. Here, we characterized a divergent metagenome-assembled poxvirus, madamurpox virus, from the oral swab of a black rat in southeastern Madagascar. While madamurpox virus shares a phylogenetic relationship with human-infecting molluscum contagiosum virus and bat-associated Rousettus poxvirus, madamurpox virus presents extensive genetic variation and represents a putative new species and genus in the Chordopoxvirinae subfamily. Further, although madamurpox virus has a similar genome organization to molluscum contagiosum virus and Rousettus poxvirus, madamurpox virus lacks key immune modulators seen in molluscum contagiosum virus. Our findings highlight that substantial unexplored poxvirus diversity likely exists in rodents, with globally distributed, non-native rodent populations of increased interest.}, }
@article {pmid42385579, year = {2026}, author = {Han, YH and Zou, MZ and Wei, XM and Chen, X and Tong, LC and Zhang, Y and Zhang, H and Chen, Z}, title = {Mining rare earth elements with ammonium sulfate as a leaching agent provokes a significant perturbation in soil microbial function.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142856}, doi = {10.1016/j.jhazmat.2026.142856}, pmid = {42385579}, issn = {1873-3336}, abstract = {The mining of rare earth elements (REEs), which are critical for modern technologies, frequently leads to severe soil degradation, particularly through ammonium sulfate-based in-situ leaching. This study provided a comprehensive metagenomic assessment of how REEs mining reshapes soil ecosystems. We analyzed paired samples from a mined site and an adjacent unmined control in a typical ion-adsorption REEs deposit region in China. Mining activity was associated with profound alterations in soil geochemical profiles. While soil pH decreased from 4.72 to 4.42, total carbon (TC) declined by over two-thirds (from 1.05 to 0.31 g kg[-1]), and total nitrogen (TN) exhibited a significant 22% increase (from 215.60 to 263.26 mg kg[-1]). Regarding REEs, mining caused an approximately 53% reduction in their total content (from 475.83 to 218.82 mg kg[-1]) and a restructured composition (cerium from 28% to 75%, lanthanum from 23% to 5.4%, and neodymium from 18% to 4.8%). Metagenomic analysis revealed that microbial diversity was significantly lower in the post-mining area compared to the unmined control. Bacterial communities shifted from a balanced composition to an oligotroph-dominated state, with p_Acidobacteriota increasing to 41% and the copiotrophic p_Actinomycetota declining from 23% to 10%. Fungal communities transitioned from a p_Basidiomycota-rich (31%) symbiotic state to an p_Ascomycota-dominated (77%), saprotrophic condition. Mantel tests and path analysis identified the mining-induced deterioration of soil physicochemical and nutrient properties (especially pH, TC, and Mg) as a key factor associated with microbial restructuring, rather than REEs depletion itself. Functionally, Kyoto Encyclopedia of Genes and Genomes annotation revealed a widespread suppression of metabolic pathways critical for ecosystem functioning, including C fixation, N metabolism, energy production, and environmental adaptation. The identification of key microbial taxa (e.g., declining p_Actinomycetota and p_Chloroflexota) as biomarkers for soil health, and their strong linkage to decreased C and N cycling functions, offers potential genomic targets for monitoring and guiding the recovery of soil ecosystem services in post-mining landscapes.}, }
@article {pmid42385824, year = {2026}, author = {Zhang, W and Ran, G and Li, P and Ke, J and Ji, S and Gao, Y and Bian, R and Wang, Z}, title = {Multi-scale analysis of patterns, risks, and mechanisms of edaphic antibiotic resistance genes on the Qinghai-Tibet Plateau: Integrating regional and national perspectives.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128686}, doi = {10.1016/j.envpol.2026.128686}, pmid = {42385824}, issn = {1873-6424}, abstract = {The Qinghai-Tibet Plateau (QTP), acclaimed as the "Third Pole"," is an ecologically vulnerable region pivotal to global biogeochemical cycles. However, our knowledge of edaphic antibiotic resistance genes (ARGs) across its heterogeneous land-use regimes remains limited. Here, we systematically characterized the patterns, potential risks, and driving mechanisms of ARGs by analyzing soil samples encompassing anthropogenically disturbed soils (ADS) and pristine alpine meadows on the QTP, coupled with comparative analysis of national cropland metagenomic datasets. Metagenomic analysis identified 897 ARG subtypes, with ADS harboring significantly higher ARG abundance, diversity, and horizontal transfer potential compared to pristine alpine meadows. Source tracking analysis confirmed yak feces as the predominant source of soil ARGs, contributing 31.35%-38.33% across different land-use types. At the national scale, QTP croplands exhibited a distinct resistome profile containing 158 unique ARG subtypes, and the abundance of ARG-carrying pathogens was 1.4-fold higher than the national average, with human pathogens being the most prevalent. Non-dominant ARGs were pinpointed as pivotal biomarkers for differentiating land-use types and geographic regions. Rare microorganisms were critical drivers shaping ARG distribution, whereas mobile genetic elements and virulence factors augmented ARG transmissibility and pathogenicity. This study presents the first comprehensive characterization of the soil resistome on the QTP, highlighting that anthropogenic activities have triggered non-negligible ARG contamination in this ecologically vulnerable ecosystem. These findings underscore the urgency of implementing "One Health" strategies to mitigate the spread of antibiotic resistance in high-altitude regions, with far-reaching implications for global public health and ecological security.}, }
@article {pmid42385828, year = {2026}, author = {Yin, Z and Zhang, Y and Song, S and Li, C and Shi, J and Yin, Y and Cai, Y}, title = {Co-contamination of antimony and arsenic reshapes resistome, virulome, and virome in poultry feces near the world's largest antimony mine.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128684}, doi = {10.1016/j.envpol.2026.128684}, pmid = {42385828}, issn = {1873-6424}, abstract = {The poultry microbiome and virome are integral to the One Health framework, with significant implications for ecosystem and human health, but their responses to arsenic (As) and antimony (Sb) exposure remain overlooked. Here, we conducted a comprehensive metagenomic characterization of the metal resistome, antibiotic resistome, virulome, and virome in poultry feces collected from the world's largest antimony mining area. We found that As and Sb co-contamination was significantly associated with elevated resistance and virulence. The abundance of metal resistance genes (MRGs) was 1.8-fold higher in the high-Sb group than in the low-Sb group (15,022.27 ± 3,538.47 vs 8,370.24 ± 4,502.07 TPM, P = 0.008), with arsR, arsB, and arsC dominating the MRG profiles. Similarly, antibiotic resistance genes (ARGs) abundance was 1.6-fold higher in the high-Sb group than in the low-Sb group (7,251.00 ± 1,844.34 vs 4,478.95 ± 2,302.69 TPM, P = 0.026), with multidrug resistance genes being the predominant class (8.09% - 58.48%). Metagenome-assembled genomes (MAGs) analysis and contig analysis suggest co-selection of MRGs, ARGs, and virulence factor genes (VFGs). We identified 100,819 viral contigs clustered into 91,004 viral operational taxonomic units (vOTUs), revealing a highly diverse viral community. Members of Enterobacteriaceae (e.g., Klebsiella) and Enterococcaceae (i.e., Enterococcus) were identified as key drivers mediating resistance and virulence dynamics, acting as resistome supercarriers, opportunistic pathogens, and viral hosts. These findings suggest that As-Sb co-contamination is an overlooked but potentially important driver of poultry antimicrobial resistance and pathogenicity, and highlight potential ecological and public health risks in mining-impacted poultry-associated environments.}, }
@article {pmid42385829, year = {2026}, author = {Wei, C and Yun, CW and Li, XQ and Lai, LH and Gao, JP and Tang, MP and Zhou, CN and Zhang, YL and Xu, HJ}, title = {Regulatory mechanisms of N2O emissions from latosolic red soil by different ecotypes of earthworms: insights from microbial diversity and metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128682}, doi = {10.1016/j.envpol.2026.128682}, pmid = {42385829}, issn = {1873-6424}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas pollutant, but the mechanisms by which different earthworm ecotypes regulate N2O emissions in latosolic red soils remain poorly understood. To address this issue, a microcosm incubation experiment was conducted using three earthworm ecological categories, epigeic Eisenia foetida, endogeic Pontoscolex corethrurus, and anecic Pheretima guillelmi, to investigate their effects on N2O emissions, soil nitrogen-cycling processes, microbial communities, and nitrogen-cycling functional genes in latosolic red soil. The results showed that the three earthworm ecological categories differentially affected N2O emissions by altering soil physicochemical properties, regulating related enzyme activities, and promoting inorganic nitrogen transformation, with endogeic and anecic earthworms exerting stronger stimulatory effects. Earthworm activity reshaped microbial community interactions and altered the relative abundances of key functional genes involved in nitrification, denitrification, assimilatory nitrate reduction, and dissimilatory nitrate reduction to ammonium (DNRA). Integrated analysis indicated that earthworms may jointly influence soil nitrogen transformation and N2O emissions by modifying the soil environment, promoting soil nitrogen transformation processes, and regulating microbial community structure and the relative abundance of nitrogen-cycling functional genes. Due to differences in activity patterns and disturbance intensity, the effects of different earthworm ecological categories varied substantially, with cumulative N2O emissions generally following the order: anecic > endogeic > epigeic.}, }
@article {pmid42385873, year = {2026}, author = {Chen, P and Si, H and Wang, J and Xie, J and Gu, C and Ma, W and Liu, X and Sun, Q}, title = {Metagenomic insights into microbial responses to soil amendments and oat cultivar identity in saline-alkali soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125147}, doi = {10.1016/j.envres.2026.125147}, pmid = {42385873}, issn = {1096-0953}, abstract = {Host cultivar identity can influence rhizosphere microbiomes, yet its relative importance compared with soil amendment regime in saline-alkali farmland remains insufficiently resolved. Here, we compared how two oat (Avena sativa) cultivars shape soil microbial communities and functions under contrasting amendment regimes. In a field experiment, two oat cultivars, Tianyan 60 (TY60) and Musite (MST), were grown under five treatments: control, bacterial agent, organic manure, silica fume, and their combination. Soil physicochemical properties, enzyme activities, and metagenomic sequencing were used to characterize microbial taxonomic and functional profiles. Amendment regimes strongly altered soil nutrient and enzyme variables, whereas cultivar identity explained more variation than amendment regime in microbial community structure and beta diversity under the tested field conditions. Taxonomically, TY60 showed stronger amendment-associated reassembly, including enrichment of Bacteroidota, Pseudomonadota, and Ascomycota under selected treatments, whereas MST retained a comparatively more stable higher-rank backbone. Network analysis further indicated cultivar-associated differences in microbial community organization. Functionally, organic manure and the combination treatments (MIX3) produced the broadest shifts in C, N, P, and S cycling gene modules, particularly in TY60-associated soils. Null-model analyses showed that stochastic assembly dominated overall, but the dominant stochastic component differed among kingdoms, with bacteria mainly governed by drift, archaea by homogeneous dispersal, and fungi by a more balanced contribution of the drift and homogeneous dispersal. These results indicate that cultivar identity played a stronger role than amendment regime in shaping amendment-associated microbiome and functional shifts in this two-cultivar comparison, highlighting the potential value of combining cultivar choice with organic-microbial inputs to improve rhizosphere multifunctionality in saline-alkali agroecosystems.}, }
@article {pmid42385907, year = {2026}, author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Chen, L and Zhang, X and Zhang, Y}, title = {Exogenous S[0] enhances the degradation of lignocellulose residues in anaerobic digestion: by driving the coenzyme A-dependent NAD(P)H sulforeductase pathway and persulfidation modification of cellulase.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135285}, doi = {10.1016/j.biortech.2026.135285}, pmid = {42385907}, issn = {1873-2976}, abstract = {Lignocellulose residues in food wastes are encapsulated by polysaccharide matrices, forming a "biomass barrier" that hinders their degradation during anaerobic digestion. This study demonstrates that elemental sulfur (S[0]) can serve as a low-cost in-situ enhancer, effectively breaking down this biomass barrier and significantly improving the degradation efficiency and CH4 yield of lignocellulose residues. Anaerobic fermentation experiment showed that the addition of S[0] increased cellulose and hemicellulose removal efficiencies to 94.89% and 96.78%, respectively, while VFAs concentration increased by 54.72%. Methanogenesis experiment further revealed that the optimal S[0] dosage (20 mg/L) achieved a CH4 yield of 378 mL CH4/g VS, which was 1.72 times that of the control. Microbial community analysis indicated a significant enrichment of cellulolytic bacteria, sulfur-reducing bacteria, and syntrophic acidogenic microorganisms. Metagenomic analysis further revealed that S[0] induced the sulfur reduction pathway mediated by Coenzyme A-dependent NAD(P)H Sulfide Oxidoreductase (NSR), with NSR abundance significantly increasing by 74.28%. This pathway can regenerate NAD[+] and maintain redox balance, thereby promoting the degradation of lignocellulose substrates. In addition, the sulfide generated by S[0] reduction stimulated S-persulfidation modification of cellulase active site, converting -SH to the more polar -SSH, enhancing the affinity between cellulases and lignocellulose substrates. This study demonstrates that S[0] can serve as a low-cost in-situ enhancer, effectively breaking down the biomass barrier in food wastes lignocellulosic residues and significantly improving degradation efficiency and CH4 yield.}, }
@article {pmid42374043, year = {2026}, author = {Wu, J and Zhang, B and Ma, Y and Kuang, C and Hong, Y}, title = {Recovery of 178 metagenome-assembled genomes from sediments in subterranean estuary.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07716-z}, pmid = {42374043}, issn = {2052-4463}, support = {42476141//National Natural Science Foundation of China/ ; 42276130//National Natural Science Foundation of China/ ; 2025001//Open Fund of Hainan Xisha Marine Environment National Observation and Research Station/ ; 2024312281//Graduate Innovative Research Grant Program of Guangzhou Education Bureau/ ; 2023B1515120029//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A03J3103//Science and Technology Projects in Guangzhou/ ; }, abstract = {Subterranean estuaries (STEs), the mixing zones between terrestrial groundwater and seawater, function as critical biogeochemical reactors that buffer anthropogenic pollutants from entering the open ocean. To date, microbial diversity and community structure within STEs remain poorly characterized. Here, we reconstructed 178 metagenome-assembled genomes (MAGs) exclusively from bacteria (no archaeal MAGs identified). All MAGs met medium-quality standards (>70% completeness, <10% contamination), including 59 near-complete (>90%), 47 with completeness over 80%, and 23 over 75% complete genomes. These MAGs spanned 17 bacterial phyla, with Pseudomonadota dominating (30.9%). Crucially, 157 MAGs (88%) are unclassified at the species level based on GTDB assessment, potentially representing novel taxa, including 1 candidate family, 28 candidate genera, and 128 candidate species. This study provides a genomic resource for studying the functional roles of these unclassified taxa in STEs.}, }
@article {pmid42374196, year = {2026}, author = {Ye, J and Mao, P and Li, B and Hao, Y and Chen, Y and Li, K}, title = {Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05346-4}, pmid = {42374196}, issn = {1471-2180}, abstract = {BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort.<br><br>METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16&#xa0;S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis.<br><br>RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients.<br><br>CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.}, }
@article {pmid42374517, year = {2026}, author = {Harvey, E and Van Brussel, K and Holmes, EC}, title = {Empowering One Health with metagenomics.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-026-00225-4}, pmid = {42374517}, issn = {2524-4655}, support = {GNT2017197//National Health and Medical Research Council/ ; }, abstract = {In an increasingly connected world a global One Health approach to the management of human, animal and ecosystem health will be critical to effective infectious disease responses. The emergence and rapid global spread of several emerging and re-emerging pathogens in the past decade has highlighted the need for rapid, sensitive and accurate diagnostics. Metagenomics, while commonly used for research purposes for almost two decades, entered the global spotlight during the COVID-19 pandemic. In this review we discuss the impacts that metagenomic studies have had on our understanding of origins, aetiology and ecology of infectious diseases within a One Health context. We also discuss the role of metagenomics in the future of diagnostics and disease surveillance, and outline the challenges and limitations of current metagenomic methods.}, }
@article {pmid42374552, year = {2026}, author = {Wan, LY and Zou, J and Li, XM and Zhao, R and Yang, G and Zhang, MY and Xiao, QY and Wei, YD and Gao, JM and Yang, BP and Zhang, C and Jiao, YM and Wang, FS and Song, JW}, title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals pathogen spectrum and mortality predictors among patients with advanced HIV-1 disease at a tertiary hospital in China.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03234-x}, pmid = {42374552}, issn = {1743-422X}, support = {No. 20250484882//Beijing Nova Program, China/ ; No. 2025ZD01904603//National Science and Technology Major Project/ ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections remain the major causes of morbidity and mortality among people living with HIV-1 (PLWH), particularly in resource-limited settings. However, the clinical characteristics and prognostic indicators of PLWH with suspected CNS infections are not well defined. In this study, we aim to characterize the spectrum of CNS pathogens, clinical characteristics, in-hospital mortality, and factors associated with death among people with advanced HIV-1 disease (AHD) in Guangxi, China.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was performed to analyze types of infection in cerebrospinal fluid (CSF) from 61 treatment-naive PLWH with suspected CNS infections. Clinical data, routine laboratory tests, and biochemical tests were collected and analyzed.<br><br>RESULTS: Among the 61 CSF samples, primarily with AHD, a total of 206 pathogens were identified. Viral pathogens predominated, with Epstein-Barr virus being the most frequently identified, followed by cytomegalovirus. Compared with patients with single-pathogen infection, those with multiple infections (viral, bacterial, and fungal) exhibited significantly lower CD4 T cell counts, higher C-reactive protein levels, and markedly reduced lipid metabolism parameters. However, infection types were not significantly associated with in-hospital death. Multivariate logistic regression analysis identified plasma low density lipoprotein (LDL) and CSF lactate dehydrogenase (LDH) as independent predictors of in-hospital death.<br><br>CONCLUSION: In PLWH with AHD and suspected CNS infections, multiple pathogens frequently coexist in the CSF. Plasma LDL and CSF LDH levels were independent predictors of death, indicating their potential value as early risk stratification in AHD.}, }
@article {pmid42374590, year = {2026}, author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB}, title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02383-z}, pmid = {42374590}, issn = {2049-2618}, support = {Heritage_2020-005_RESTOROMIC//&#xd6;sterreichischen Akademie der Wissenschaften/ ; }, abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.<br><br>RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.<br><br>CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.}, }
@article {pmid42375904, year = {2026}, author = {Panagiotidi, K and Markidis, A and Karamatzanis, I and Almomani, M and Omirou, R and Kosmidou, P}, title = {The Nasopharyngeal Microbiome: A Narrative Review of the Hidden Regulator of Ear, Nose, and Throat (ENT) Inflammations.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e109921}, pmid = {42375904}, issn = {2168-8184}, abstract = {The nasopharyngeal microbiome is a central regulator of respiratory health. The upper airway microbial community acts as the primary gatekeeper against respiratory pathogens and maintains homeostasis in the upper respiratory tract (URT). This community is established at birth and influenced by the delivery method and antibiotic exposure. Disruptions to this balance are recognised as a major driver of chronic inflammatory ear, nose, and throat (ENT) diseases. This review analyses the literature on the relationship between the nasopharyngeal microbiome and inflammatory ENT diseases. We searched recent literature (2015-2025) via PubMed and Scopus, focusing on 16S rRNA and metagenomic studies of the upper respiratory tract. We examined papers that linked microbial shifts to clinical outcomes in otitis media, rhinosinusitis, and allergic rhinitis, as well as studies applying machine learning to diagnostic modelling. Clinical health is associated with stable colonisation by Dolosigranulum and Corynebacterium. These commensals protect the host by maintaining the mucosal barrier and competing against pathogens. Chronic disease, in contrast, is marked by a bloom of Streptococcus, Haemophilus, or Moraxella. In chronic rhinosinusitis, loss of bacterial diversity and S. aureus biofilm formation often lead to treatment failure. Machine learning tools like Random Forest and XGBoost classifiers have been applied to nasopharyngeal microbiome data. In published cohorts, these models have achieved sensitivity and specificity values of 80-90% for identifying dysbiotic profiles associated with disease, outperforming standard culture in speed and taxonomic resolution. These findings support a shift from broad antibiotic use toward microbiome-informed treatment. Standardising sampling and sequencing methods remains the next necessary step.}, }
@article {pmid42376027, year = {2026}, author = {Dong, X and Xiao, R and Gao, C and Huang, S and Meng, X and Yan, X and Bai, Z and Wu, S}, title = {Ruxolitinib combined with azithromycin for scrub typhus-associated hemophagocytic lymphohistiocytosis in a child: a case report and narrative literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1852110}, pmid = {42376027}, issn = {2296-2360}, abstract = {BACKGROUND: Scrub typhus-associated hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening complication in children, with reported mortality of 11.9%-30%. Conventional immunomodulation with corticosteroids and intravenous immunoglobulin often provides insufficient control of the hyperinflammatory state, while etoposide-based chemotherapy carries significant toxicity. JAK1/2 inhibition targeting the interferon-gamma pathway represents a promising therapeutic strategy, but its application in scrub typhus-associated HLH has not been previously reported.<br><br>CASE PRESENTATION: A 5-year-11-month-old girl with no prior medical history presented with persistent fever, tachypnea, hepatosplenomegaly, and a 0.5&#x2005;cm eschar in the left axilla after travel to Yunnan Province, China. Laboratory findings revealed pancytopenia (platelets 40&#xd7; 10[9]/L), hyperferritinemia (>2,000&#x2005;ng/mL), hypofibrinogenemia (1&#x2005;g/L), and elevated interferon-gamma (135.48&#x2005;pg/mL). Bone marrow aspiration demonstrated hemophagocytosis. Metagenomic next-generation sequencing confirmed Orientia tsutsugamushi infection. The patient met six of eight HLH-2004 diagnostic criteria. She was treated with oral ruxolitinib (5&#x2005;mg twice daily) initiated on the day of admission, followed by intravenous azithromycin (10&#x2005;mg/kg once daily) after confirmatory testing. Fever resolved within 72&#x2005;h. Ruxolitinib was temporally associated with rapid clinical improvement, although causal attribution cannot be established due to concurrent therapies. By day 8, platelet count normalized to 240&#xd7; 10[9]/L, ferritin declined to 1,246&#x2005;ng/mL, and fibrinogen recovered to 2.4&#x2005;g/L. The patient was discharged on day 13 with ruxolitinib tapered to 2.5&#x2005;mg daily. At 3-month follow-up, she remained well with normal laboratory parameters.<br><br>LITERATURE REVIEW: Narrative literature review of 66 previously reported pediatric cases from Chinese and English databases (inception to May 2026) plus the present case revealed an overall mortality of 11.94% (8/67). Among these patients, 43 (64.2%) received corticosteroids, 34 (50.7%) received intravenous immunoglobulin, and only 3 (4.5%) received etoposide. The published cases suggest that absence or delay of anti-rickettsial therapy is associated with poor outcomes, though the evidence is limited by case-report bias and confounding.<br><br>CONCLUSION: This is the first report of successful JAK1/2 inhibitor therapy in scrub typhus-associated HLH. This case raises a hypothesis worth investigating further-that ruxolitinib combined with azithromycin may achieve rapid disease control with good tolerability. Prospective studies are needed to evaluate the role of targeted JAK inhibition in infection-triggered HLH.}, }
@article {pmid42376290, year = {2026}, author = {Onumanyi, V and Ogola, HJO and Ijoma, GN and Semenya, K}, title = {PacBio HiFi sequencing datasets of culture-enriched airborne microbial cave communities from dolomitic Sudwala Caves, South Africa.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112970}, pmid = {42376290}, issn = {2352-3409}, abstract = {We present a dataset integrating physico-chemical air quality measurements with long-read PacBio HiFi shotgun metagenomic sequences from culture-enriched airborne samples collected in Sudwala Caves, one of the oldest known cave systems in South Africa. This resource provides baseline characterization of airborne microbial communities and associated environmental parameters within a subterranean karst ecosystem. A total of 106 air samples were collected across six different cave compartments and three external reference sites spanning two seasonal periods, the winter-spring transition (September-October 2024) and the summer-autumn window (February-March 2025). Environmental metadata include temperature, relative humidity, particulate matter (PM1.0, PM2.5, PM10), and formaldehyde (HCHO) concentrations, enabling direct linkage between microbial composition and air quality dynamics. Post-quality control of eighteen (18) culture-enriched metagenome datasets yielded 7.7 × 10[4] to 7.8 × 10[5] HiFi reads per sample corresponding to 0.63-6.71 Gb of high-accuracy sequence data per sample. Kaiju classification assigned 65.1-83.4% of assembled sequences to reference taxa. Domain-level profiles were dominated by Bacteria (98.7-99.9% of classified sequences), with minor representation of Eukaryota (0.06-0.15%) and extremely low abundances of Archaea (0.002-0.009%) and Viruses (0.000-0.001%). At the phylum level, airborne bacterial communities were consistently dominated by Bacillota (mean relative abundance: 46.92%), Pseudomonadota (34.28%), and Actinomycetota (15.71%) across all sampling sites and seasons, with Pseudomonadota and Actinomycetota exhibiting proportionally higher representation within cave interior environments relative to outdoor reference sites. At the genus level, Staphylococcus, Bacillus, Microbacterium, Arthrobacter, and Pseudomonas were among the most consistently detected and abundant airborne genera within cave compartments, whilst outdoor aerobiome communities were characterised by greater relative abundances of Planococcus, Sphingomonas, Stenotrophomonas, and Arthrobacter. Functional annotation using the DRAM pipeline identified 1205,651 predicted genes, with 579,682 KEGG orthologs (KO), 62,261 MEROPs peptidases, 904,193 Pfam domains, and 21,859 CAZy genes annotated. This dataset supports investigations of culturable airborne microbial composition, functional capacity, bioaerosol dynamics, and environmental health indicators in dolomitic subterranean karst systems, providing a reference framework for comparative studies of low-biomass atmospheric environments.}, }
@article {pmid42376319, year = {2026}, author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S}, title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1828012}, pmid = {42376319}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; }, abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.<br><br>METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.<br><br>RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p&#xa0;=&#xa0;0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p&#xa0;=&#xa0;0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.}, }
@article {pmid42376322, year = {2026}, author = {Qin, Q and Ning, YC and Zhu, SN and Ma, JH and Chen, W and Tian, W and Wang, CM and Wu, YF and Li, SL}, title = {Performance of metagenomic next-generation sequencing for bloodstream infections in perioperative critically ill patients- a post-hoc analysis of a prospective, multi-center cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1814969}, pmid = {42376322}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; Female ; *Metagenomics/methods ; Critical Illness ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Intensive Care Units ; *Bacteremia/diagnosis/microbiology ; Aged ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation &amp; purification ; Blood Culture ; *Sepsis/diagnosis/microbiology ; }, abstract = {BACKGROUND: Bloodstream infections (BSI) in intensive care unit (ICU) patients are associated with high morbidity and mortality, necessitating rapid and accurate pathogen identification to guide early antimicrobial therapy. However, traditional blood culture (BC) is limited by the long turnaround time and low sensitivity. Metagenomic next-generation sequencing (mNGS) has been applied in infectious disease diagnostics, but its clinical utility for perioperative ICU patients with BSI requires further evaluation.<br><br>METHODS: This post-hoc analysis included 219 perioperative ICU patients (from a prospective, multi-center cohort, July 2020-June 2023) who underwent concurrent mNGS and BC testing. The study compared pathogen detection differences between the two methods, and evaluated the diagnostic value of mNGS for clinical BSI based on mNGS-assisted clinical diagnostic criteria. Additionally, the impact of mNGS findings on clinical antimicrobial management was assessed.<br><br>RESULTS: mNGS demonstrated a higher overall pathogen detection rate than BC in the 219 enrolled patients (25.1% vs. 9.6%, p&#xa0;<&#xa0;0.001), with significant advantages in detecting Gram-negative bacteria (13.2% vs. 5.9%, p&#xa0;=&#xa0;0.009), anaerobes (3.6% vs. 0.5%, p&#xa0;=&#xa0;0.018), and fungi (6.4% vs. 0.9%, p&#xa0;=&#xa0;0.002). Mixed-pathogen infections were identified in 20% of mNGS-positive clinical BSI cases, whereas BC-positive cases exclusively had single-pathogen infections. Ultimately, 64 patients (29.2%) were diagnosed with clinical BSIs. The sensitivity and specificity of the mNGS were 85.9% (95% CI: 74.5%-93.0%), and 80.6% (95% CI: 73.4%-86.4%), respectively, and the area under the receiver operating characteristic curve was 0.833 (95% CI: 0.772-0.894). The positive predictive value and negative predictive value were 64.7% (95% CI: 53.5%-74.6%) and 93.3% (95% CI: 87.3%-96.7%), respectively. Additionally, mNGS led to a positive impact in 56 patients (25.6%), manifested by the identification of new pathogens and guidance for targeted therapy, a negative impact in 11 patients (5.0%), and no clinical impact in 152 patients (69.4%).<br><br>CONCLUSIONS: For perioperative ICU patients, mNGS demonstrated superior pathogen detection rates, broader microbial spectrum coverage, and enhanced polymicrobial infection detection capability versus BC. mNGS exhibited high diagnostic value for clinical BSI, with the potential to facilitate targeted antimicrobial therapy adjustments.}, }
@article {pmid42376574, year = {2026}, author = {Biełło, K and Rodríguez-Caballero, G and Becerra-Mora, D and Dorado-Blanco, N and Sáez-Melero, LP and Moreno-Vivián, C and Luque-Almagro, VM and Olaya-Abril, A and Roldán, MD}, title = {Exploring the Tenebrio molitor gut microbiota response to LDPE and PET: putative genetic indicators and methodological insights.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1746922}, pmid = {42376574}, issn = {1664-302X}, abstract = {Insect gut microbiomes are recognized as potential reservoirs of enzymatic activities relevant to plastic metabolism. Here, we investigated the taxonomic and functional dynamics of the Tenebrio molitor gut microbiota under dietary exposure to low-density polyethylene (LDPE) and polyethylene terephthalate (PET) using 16S rRNA sequencing and shotgun metagenomics. Significant compositional shifts were detected at the ASV level, with plastic-fed cohorts showing enrichment of taxa implicated in xenobiotic metabolism. Predicted functional changes suggested altered abundance of pathways related to aromatic compound processing and redox homeostasis. Metagenomic assembly and functional annotation, performed through a reproducible open-source workflow, revealed several putative proteins with distant homology to enzymes such as phthalate dioxygenases, urethanases, and polyhydroxyalkanoate depolymerases. A metagenome-assembled genome (MAG) assigned to Enterococcus accounted for most recovered protein-coding sequences. Although gene-level comparisons did not show statistically significant differences, Gene Set Enrichment Analysis (GSEA) highlighted ABC transporter signatures and stress-response ATPases under plastic-exposed conditions. Overall, this exploratory study reveals microbial shifts and putative genetic indicators of metabolic potential within the T. molitor gut, providing a reproducible analytical framework for future investigations into the microbial role in plastic bioconversion.}, }
@article {pmid42376617, year = {2026}, author = {Lee, YS and Kuo, TF and Yang, G and Liang, YC and Yang, WC}, title = {Bidens pilosa extract and bentonite, a phytogenic formulation, as a feed additive to improve diarrhea and gut microbiota in calves: Effects on feed use and regulation of gut microbiota.}, journal = {Veterinary and animal science}, volume = {34}, number = {}, pages = {100732}, pmid = {42376617}, issn = {2451-943X}, abstract = {Phytogenics are emerging as an alternative approach to maintain animal health and productivity without using antibiotics in the livestock industry. This study investigated the function and mechanism of a phytogenic formulation composed of Bidens pilosa extract and bentonite (BPB) on diarrhea, gut microbiota and growth performance in calves. Twenty-six 15-day-old Holstein Friesian calves were fed control or 0.5% BPB diets for 4 weeks. Their diarrhea, gut microbiota, fecal IgA, and bacterial growth were analyzed using culture-based methods, 16S rRNA sequencing, and statistical analyses. BPB (0.5%) significantly reduced diarrhea, fecal scores, and fecal IgA levels, but increased body weight in calves. Furthermore, metagenomic analysis and selective agar assays indicated that 0.5% BPB decreased three bacterial genera, Campylobacter, Clostridium_sensu_stricto_1, and Escherichia/Shigella, but increased seven other bacterial genera, including Lactobacillus, Ruminococcus, and Bacteroides, in the feces of calves. Mechanistic studies suggested that BPB augmented the proliferation of bacteria associated with beneficial effects, subsequently inhibiting the growth of bacteria associated with harmful effects in the intestines of calves. In conclusion, BPB mitigated diarrhea and gut inflammation and increased body weight gain in calves by modulating the gut microbiota. This modulation involved the upregulation of bacteria with beneficial potential that antagonize the growth of bacteria with pathogenic potential.}, }
@article {pmid42376710, year = {2026}, author = {Arguelles, EDLR and Mugikura, K and Sato, S}, title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70195}, pmid = {42376710}, issn = {1529-8817}, support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.}, }
@article {pmid42377028, year = {2026}, author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K}, title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048926}, doi = {10.1128/msystems.00489-26}, pmid = {42377028}, issn = {2379-5077}, abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.}, }
@article {pmid42377463, year = {2026}, author = {Brenner, T and Skarabis, A and Schaller, SJ and von Groote, T and Putensen, C and Günther, U and Sauer, M and Decker, SO and Dusse, F and Weiss, M and Suchodolski, K and Simon, TP and Rosenberger, P and Moerer, O and Unterberg, M and Schewe, JC and Bracht, H and Hutzl, S and Feißt, M and Marschall, U and Brandenburg, P and Stevens, P and Schmidt, J and Pletz, MW and Berger, MM and , }, title = {Effects of a clinical metagenomics intervention on clinical outcomes, healthcare costs, and health-related quality of life in patients with sepsis or septic shock: results of the randomized-controlled DigiSep trial.}, journal = {Intensive care medicine}, volume = {}, number = {}, pages = {}, pmid = {42377463}, issn = {1432-1238}, support = {01NVF20013//German Innovation Fund/ ; }, abstract = {PURPOSE: Early pathogen detection is crucial in sepsis. We hypothesized that detection of microbial circulating cell-free DNA by metagenomic next-generation sequencing (mNGS) improves clinical outcomes and health-related quality of life without increasing healthcare costs.<br><br>METHODS: This randomized, controlled, interventional, open-label, multicenter trial was conducted in 24 intensive care units across Germany. The intervention group (n&#x2009;=&#x2009;200) received mNGS diagnostics in addition to standard-of-care microbiology, compared with standard-of-care microbiology alone (control group; n&#x2009;=&#x2009;189). The primary endpoint was the Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk (DOOR/RADAR) score.<br><br>RESULTS: The DOOR/RADAR score was not significantly improved at 28&#xa0;days after sepsis onset (intervention group: 3.21&#x2009;&#xb1;&#x2009;1.54; control group: 3.49&#x2009;&#xb1;&#x2009;1.51; 95% CI&#x2009;-&#x2009;0.58 to 0.03). However, other secondary endpoints were improved, including a reduced duration of mechanical ventilation (intervention group: 6.6&#x2009;&#xb1;&#x2009;9.4&#xa0;days; control group: 9.3&#x2009;&#xb1;&#x2009;10.6&#xa0;days; 95% CI&#x2009;-&#x2009;5.03 to&#x2009;-&#x2009;0.34) and faster shock resolution (intervention group: 6.9&#x2009;&#xb1;&#x2009;7.4&#xa0;days; control group: 8.8&#x2009;&#xb1;&#x2009;8.5&#xa0;days; 95% CI&#x2009;-&#x2009;3.75 to&#x2009;-&#x2009;0.04). Health-related quality of life at 90&#xa0;days (EQ-5D-5L) was improved in the intervention group (0.312&#x2009;&#xb1;&#x2009;0.386) compared with the control group (0.208&#x2009;&#xb1;&#x2009;0.373; p&#x2009;=&#x2009;0.047). In the subgroup with available claims data (33.2% of participating patients), healthcare costs over 180&#xa0;days did not differ.<br><br>CONCLUSION: The DOOR/RADAR score as primary endpoint was not significantly improved by mNGS. Exploratory secondary analyses revealed improvements in secondary endpoints. (Funding: German Innovation Fund; ClinicalTrials.gov number, NCT04571801, registration: 25.8.2020).}, }
@article {pmid42377624, year = {2026}, author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C}, title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42377624}, issn = {1573-0972}, mesh = {*Wastewater/microbiology ; *Microalgae/growth &amp; development/microbiology ; Phylogeny ; *Bacteria/isolation &amp; purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; }, abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.}, }
@article {pmid42377631, year = {2026}, author = {Thakur, A and Gupta, P and Sethi, S and Apreja, M and Ahmed, S and Sharma, L}, title = {Exploring the antibacterial potential of a designed peptide against Gardnerella vaginalis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42377631}, issn = {1573-4978}, mesh = {*Gardnerella vaginalis/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Antimicrobial Peptides/pharmacology ; Female ; Vaginosis, Bacterial/drug therapy/microbiology ; Hemolysis/drug effects ; Cell Survival/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Peptides, Cyclic/pharmacology ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal dysbiosis caused by Gardnerella vaginalis, a facultative anaerobic bacillus. The failure of conventional antibiotics and recurrence of bacterial vaginosis call for alternative novel therapeutic strategies. Antimicrobial peptides (AMPs) provide a targeted, resistance-sparing alternative with their broad-spectrum activity and distinct mode of action.<br><br>METHODS: Two AMPs, i.e., TCCP-1 (cyclic) and ZMLP-2 (linear), were designed in silico from proteome sequences of Thymbra capitata and Zataria multiflora already available in NCBI. The designed peptides were chemically synthesized, evaluated for their antibacterial activity, cytotoxicity, hemolytic effects and mechanism of action against G.vaginalis.<br><br>RESULTS: TCCP-1, a cyclic peptide with an MIC of 1.95&#xa0;&#xb5;g/mL against G. vaginalis showed minimal cytotoxicity even at 100&#xa0;&#xb5;g/mL, which is much higher than its MIC value (1.95&#xa0;&#xb5;g/mL). TCCP-1 maintained high cell viability at lower concentrations, while a concentration-dependent reduction in viability was observed at higher concentrations. In contrast, ZMLP-2, a linear AMP, showed weak antimicrobial activity with an MIC of 100&#xa0;&#xb5;g/mL, exhibited a moderate reduction in cell viability (~&#x2009;70-75%) when tested at 100&#xa0;&#xb5;g/mL or a concentration below its MIC. Both peptides showed the disruption of bacterial membranes and, therefore, support the re-establishment of healthy vaginal flora. More significantly, TCCP-1 demonstrated efficient antimicrobial activity against G.vaginalis along with decreased cytotoxicity, making it an excellent candidate for future in vivo studies and possible clinical uses.<br><br>CONCLUSIONS: Thus, plant-derived AMPs could prove to be useful, targeted, and sustainable alternatives to BV prevention while treating both resistance and recurrence.}, }
@article {pmid42377725, year = {2025}, author = {Yun, S and Seo, Y and Yoon, Y}, title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.}, journal = {Food science of animal resources}, volume = {45}, number = {6}, pages = {1710-1723}, doi = {10.5851/kosfa.2025.e14}, pmid = {42377725}, issn = {2636-0780}, abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.}, }
@article {pmid42377908, year = {2026}, author = {Deng, Y and Borton, MA and Nesbø, CL and Forster, MD and Konhauser, KO and Gingras, MK and Goss, GG and Wrighton, KC and Lanoil, BD and Zhong, C and Alessi, DS}, title = {Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag070}, pmid = {42377908}, issn = {1574-6941}, abstract = {Microbial communities inhabiting hydraulically fractured subsurface waters are increasingly recognized as important components of unconventional oil and gas systems because they can influence water quality, infrastructure integrity, and biogeochemical processes during flowback and production. However, a quantitative cross-basin understanding of their taxonomic diversity, ecological organization, and potential functional variation remains limited. In this study, we analyzed 16S rRNA gene amplicons, metagenomes, and geochemical data from flowback and produced water (FPW) from the Sichuan Basin, China, and conducted a quantitative comparison to data previously reported from the same basin and hydraulic fracturing (HF) regions in North America. Our findings revealed strong co-occurrence patterns among fermentative, sulfidogenic, and methanogenic microorganisms, which emerged as core members of microbial communities across all fractured subsurface environments. Notably, microbial diversity and selected metabolic traits differed across basins in the low-salinity systems of China, whereas high-salinity basins in North America exhibited reduced diversity and more constrained metabolic capabilities. These differences are consistent with salinity acting as an important ecological filter across the analyzed basins. Our results indicate that basin-specific geochemical context, particularly salinity, is closely associated with cross-basin differences in microbial diversity, community composition, and selected metabolic traits in fractured subsurface waters. These findings support the value of integrating geological, geochemical, and microbiological information when interpreting microbial risks and water-management strategies in hydraulic fracturing systems.}, }
@article {pmid42378511, year = {2026}, author = {Zhang, R and Wang, B and Lu, J and Wu, J and Liu, X and Zhang, R and Marsili, E and Gong, C}, title = {The Food Additives p-Coumaric Acid Production from Corn Stalk Catalyzed by a Cold-Adapted Carboxylesterase.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c05955}, pmid = {42378511}, issn = {1520-5118}, abstract = {p-Coumaric acid is a widely utilized food additive with beneficial biological activities. A novel enzymatic catalysis strategy for the production of p-coumaric acid from lignocellulosic biomass is proposed herein. The gene encoding a carboxylesterase was identified in metagenome-assembled genome and further characterized in the isolated Glutamicibacter soli Em07. The target protein, with a molecular weight of 53 kDa, was successfully obtained through heterologous expression. The carboxylesterase exhibited cold adaptation, with optimal activity at 35 °C and pH 7.0 using 1-naphthyl acetate as substrate, and maintained over 75% of the maximum activity after incubation at 25 °C for 2 h. At 25 °C, 35.9 ± 0.4 μg of p-coumaric acid was obtained from 20 mg of corn stalk via carboxylesterase-mediated catalysis. This work achieves a high p-CA yield from lignocellulosic biomass via low-temperature enzymatic catalysis without pretreatment. The results offer valuable progress toward manufacturing high-value food additives, including p-CA.}, }
@article {pmid42378616, year = {2026}, author = {Tyler, RS and Charles, DW and Mills, AG and Alkabab, Y}, title = {Disseminated Mycobacterium immunogenum -associated Hemophagocytic Lymphohistiocytosis after Stem Cell Transplantation.}, journal = {International journal of mycobacteriology}, volume = {15}, number = {2}, pages = {179-182}, pmid = {42378616}, issn = {2212-554X}, abstract = {Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome most commonly triggered by infection, malignancy, or transplant-related immune dysregulation. Rapidly growing mycobacteria are uncommon causes of disseminated infection and have only rarely been reported as infectious triggers of HLH. A 56-year-old immunocompromised woman with a history of allogeneic hematopoietic stem cell transplant presented with recurrent fever, progressive transaminitis, and laboratory features consistent with secondary HLH. Liver biopsy showed granulomatous hepatitis with iron overload. Initial treatment with dexamethasone and anakinra resulted in transient clinical improvement. Less than 2 weeks later, she was readmitted with worsening hepatic dysfunction and found to have acid-fast bacilli in blood and bone marrow cultures, later identified as Mycobacterium immunogenum. Despite targeted antimicrobial therapy, the patient developed progressive hepatic and renal failure and died. To our knowledge, this case represents the first reported case of disseminated M. immunogenum infection precipitating secondary HLH, expanding the recognized clinical spectrum of this rapidly growing nontuberculous mycobacterium and highlights the diagnostic challenges of atypical mycobacterial infection in immunocompromised hosts.}, }
@article {pmid42378712, year = {2026}, author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M}, title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.}, journal = {Journal of Crohn's &amp; colitis}, volume = {20}, number = {6}, pages = {}, doi = {10.1093/ecco-jcc/jjag080}, pmid = {42378712}, issn = {1876-4479}, support = {//Takeda Pharmaceutical Company Ltd/ ; }, abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.<br><br>DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n&#x2009;=&#x2009;23) or CgF (n&#x2009;=&#x2009;17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.<br><br>RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.<br><br>CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.}, }
@article {pmid42378762, year = {2026}, author = {Liu, J and Tan, Y and Fan, X and Xie, S and Xu, X and Zhu, L}, title = {Exogenous vitamin B12 alleviated inhibition of salinity on anaerobic dichloromethane degradation by reducing cofactor-related constraints and reshaping community functional potential.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142823}, doi = {10.1016/j.jhazmat.2026.142823}, pmid = {42378762}, issn = {1873-3336}, abstract = {Dichloromethane (DCM) frequently co-occurs with high salinity in industrial wastewater, imposing dual stress on anaerobic treatment. However, how anaerobic DCM degraders respond to salt stress and whether exogenous vitamin B12 (VB12, a key cofactor in DCM transformation) can facilitate DCM degradation remain poorly understood. Here, we established long-term enrichments (>800 days) of DCM-degrading consortia under non-saline and salt-stressed conditions (10 g/L NaCl) to investigate how VB12 affected degradation performance, community assembly, and functional potential. Salt stress significantly inhibited DCM degradation, reducing the maximum degradation rate by 71.5%, whereas VB12 substantially alleviated this inhibition and increased the degradation rate to 55.9% of the non-saline control. Metagenomic and co-occurrence network analyses indicated that salinity drove community reassembly and niche differentiation, linking DCM degraders, methanogens/homoacetogens, and fermenters within an inferred producer-cooperator-cross-feeder framework that maintained community stability under salt stress. Functional analyses showed that VB12 was associated with shifts in community functional potential toward hydrogenotrophic/acetoclastic methanogenesis and osmoadaptive metabolism, supporting stress adaptation under saline conditions. Further analysis of the mec (methylene chloride catabolism) cassette suggested that VB12 likely reduced cofactor-related constraints and reinforced downstream product-consuming functions, thereby contributing to the enhanced degradation performance. Notably, a previously uncharacterized Dehalobacteriaceae MAG, D_MAG.168, emerged as a dominant candidate DCM degrader under salt stress. Overall, these findings provide insight into the functional responses of DCM-degrading consortia to VB12 supplementation under salt stress and support the further development of VB12-assisted bioaugmentation strategies for DCM-contaminated saline industrial wastewater.}, }
@article {pmid42378793, year = {2026}, author = {Torres, MC and Breyer, GM and da Silva, MERJ and Jank, L and Barreto, F and Dorn, M and Cardoso, MRI and Siqueira, FM}, title = {Swine waste stabilization ponds as hotspots for antimicrobial resistance gene accumulation: a longitudinal metagenomic study.}, journal = {International journal of hygiene and environmental health}, volume = {276}, number = {}, pages = {114857}, doi = {10.1016/j.ijheh.2026.114857}, pmid = {42378793}, issn = {1618-131X}, abstract = {Using next-generation sequencing, this study provides a comprehensive longitudinal assessment of bacterial communities, antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), and metabolic pathways in a full-scale swine waste treatment system in Brazil. Samples were collected from the first (WSP1) and final (WSP4) waste stabilization ponds of a farrow-to-finish farm during four sampling events between October 2022 and January 2023. Antibiotic molecules were additionally identified and quantified using solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry. Bacterial community composition remained remarkably stable over time. Similarly, the resistome and mobilome showed pronounced temporal stability, although a consistently higher relative abundance of ARGs and MGEs was observed in the final treatment process (WSP4). Genes encoding resistance markers of human-health relevance were detected in WSP4, including Paer_PhoP_CST, associated with polymyxin (colistin) resistance; PRC-1, linked to resistance to third-generation cephalosporins; and quinolone resistance determinants such as adeF, Paer_parE_FLO, and Mtub_gyrB_FLO. Genes encoding efflux pump complexes associated with multidrug resistance were also identified, including Paer_CpxR, PmpM, YajC, MuxB, and MexW. Supporting these findings, fluoroquinolones (ciprofloxacin and norfloxacin), lincomycin, and tetracycline molecules were detected in the waste ponds, indicating sustained selective pressure within the system. The accumulation of clinically relevant resistance determinants in the final of the waste treatment process, whose effluent is reused for agricultural irrigation, highlights waste stabilization ponds as potential hotspots for the persistence and environmental dissemination of antimicrobial resistance. These findings underscore the urgent need for improved monitoring and management of livestock waste treatment systems to mitigate antimicrobial resistance dissemination across agroecosystems.}, }
@article {pmid42378969, year = {2026}, author = {Xing, BS and Wu, YF and Zhang, Y and Wang, XC and Li, YY and Chen, R}, title = {Carbon cloth-mediated direct interspecies electron transfer effect on the intensification mechanism of high-load codigestion dynamic membrane bioreactors.}, journal = {Water research}, volume = {304}, number = {}, pages = {126376}, doi = {10.1016/j.watres.2026.126376}, pmid = {42378969}, issn = {1879-2448}, abstract = {Acidification under high organic loading conditions and control of dynamic membrane (DM) thickness remain major challenges in the development of anaerobic dynamic membrane bioreactors (AnDMBR). In anaerobic digestion (AD), conductive materials can promote electron exchange between electron donors and acceptors, thereby accelerating electron transfer and enhancing direct interspecies electron transfer (DIET). These processes can improve methane yield and process stability at higher organic loading rates (OLRs). In this study, a carbon cloth anaerobic dynamic membrane bioreactor (CC-AnDMBR) was constructed and compared with a common nylon mesh anaerobic dynamic membrane bioreactor (NM-AnDMBR) to investigate the impact of DIET reinforcement on system performance and stability. The maximum load tolerance of the system and changes in microorganisms during this process were further evaluated to elucidate the mechanisms underlying enhanced system resilience. At a hydraulic retention time of 6.25 days (OLR of 20.13 g COD/L/day), the methane production rate of the carbon cloth reactor (313.74 ± 41.06 mL/g COD) was significantly greater than that of the nylon mesh reactor (256.02 ± 63.29 mL/g COD). Metagenomic analysis revealed that carbon cloth membranes are more conducive to the enrichment of Geobacter, which can exchange electrons with the dominant archaeal genus Methanosarcina, thereby accelerating the DIET rate within the CC-AnDMBR. The enhanced performance of the carbon cloth reactor was attributed to the higher electrical conductivity, more negative oxidation-reduction potential value, and higher electron transport system activity of the sludge. These characteristics together created a more conducive environment for conductive microorganisms and improved the system's electron transfer rate.}, }
@article {pmid42378973, year = {2026}, author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B}, title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.}, journal = {Water research}, volume = {304}, number = {}, pages = {126351}, doi = {10.1016/j.watres.2026.126351}, pmid = {42378973}, issn = {1879-2448}, abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.}, }
@article {pmid42379260, year = {2026}, author = {Alamri, MM and Proctor, G and Garcia-Guevara, F and Guennec, AL and Mainas, G and Shoaie, S and Nibali, L}, title = {Multiomics Analyses in Young Grade C Molar Incisor Pattern Periodontitis.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {106871}, doi = {10.1016/j.jdent.2026.106871}, pmid = {42379260}, issn = {1879-176X}, abstract = {OBJECTIVE: To explore the microbial profiles in plaque and saliva and metabolic profiles in saliva and serum collected from young patients (≤25 years old) with grade C molar incisor pattern periodontitis (C/MIP), to compare them to age-matched controls and integrate both omics to elucidate C/MIP pathogenesis.<br><br>MATERIAL AND METHOD: Thirty-one young patients with C/MIP and 31 periodontally healthy age-matched controls were recruited. Bacterial profiles were investigated in unstimulated saliva and subgingival plaque using shotgun sequencing metagenomics while metabolic profiles were assessed in saliva using nuclear magnetic resonance and serum using mass spectrometry. Data from both omics analyses were integrated and visualised as interaction networks using Cytoscape software.<br><br>RESULTS: C/MIP showed significantly lower levels of several salivary (e.g., dimethylamine, proline, glycine) and serum metabolites, and higher levels of others including methyl indole-3-acetate and sulfosalicylic acid, compared to controls (P<0.001). Fifteen bacteria, of which twelve were associated with C/MIP, were differentially prevalent between groups. The plaque microbiome in C/MIP was enriched with pathogenic species such as D. oralis, C. rectus, T. denticola, and P. endodontalis, while health-associated bacteria like R. mucilaginosa and L. hongkongensis were more prevalent in controls. D. oralis and GGB10485-SGB49305 emerged as potential microbial biomarkers. Notably, metabolites such as DL-glutamine and taurine were significantly associated with periodontal pathogens.<br><br>CONCLUSION: C/MIP is marked by a distinct dysbiotic microbiome and altered metabolic profile. While key pathogens and metabolites likely contribute to disease progression, the underlying mechanisms remain only partially understood due to the complexity and incomplete characterisation of many associated factors.<br><br>CLINICAL SIGNIFICANCE: This study highlighted the multifactorial nature of C/MIP, driven by microbial dysbiosis, immune disturbances, and metabolic alterations. A comprehensive multi-omics approach offered a foundation for understanding microbial-metabolite dynamics in young patients, and highlighted candidate biomarkers for future diagnostics and therapeutics.}, }
@article {pmid42379362, year = {2026}, author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF}, title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28174}, pmid = {42379362}, issn = {1525-3198}, abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD), were used in a replicated 4 × 4 Latin Square design experiment with 4-wk periods. Treatments were: 0, 10, 20 and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass silage and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order: CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat-and-protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45 ± 0.2 and 32.0 ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk crude protein (3.39 ± 0.2%) or fat (4.06 ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h post-feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h post-feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the impact of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat-and-protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.}, }
@article {pmid42282649, year = {2026}, author = {Boyd, AI and Quintanilla, KA and Escapa, IF and Lewis, MA and Kafer, LA and Zeng, XL and Blutt, SE and Ibberson, CB and Lemon, KP}, title = {D-alanine aminotransferase (Dat) promotes Staphylococcus aureus colonization fitness on human nasal respiratory epithelium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42282649}, issn = {2692-8205}, abstract = {Nasal colonization by Staphylococcus aureus is an established risk factor for invasive infection, yet bacterial determinants promoting fitness on human nasal mucosa remain incompletely defined. To identify genes required for early colonization of human nasal respiratory epithelium, we colonized human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) with a high-density transposon (Tn) library of the methicillin-resistant USA300 strain LAC. TnSeq analysis identified 165 genes that met our threshold for candidate colonization fitness factors. Among these, genes involved in D-alanine biosynthesis and use were enriched, including two encoding the enzymes that separately synthesize D-alanine in S. aureus: alanine racemase 1 (alr1) and D-alanine aminotransferase (dat). Disruption of dat reduced colonization fitness in competition with the parental strain by ≥ 1,000 fold across 4 different strains from clonal complexes 8, 5, and 30. In competition with the parental strain during HNO-ALI colonization, a dat::Tn mutant was 34-fold less fit than an alr1::Tn mutant. Genetic complementation with single-copy dat expressed from its native operon promoter restored parental colonization levels. Supplementation with exogenous D-alanine or L-alanine also rescued the dat::Tn colonization defect, whereas D-glutamate did not, consistent with Dat primarily producing D-alanine on nasal mucosa. Complementation with dat under control of a putative 5' intra-operon promoter substantially restored colonization but failed to support growth in chemically defined medium lacking L-alanine, suggesting a new layer of environment-specific regulation of dat transcription. Together, these findings demonstrate that Dat is a major source of D-alanine during colonization of human nasal mucosa and is required for S. aureus fitness in this environment.}, }
@article {pmid42366391, year = {2026}, author = {Lai, T and Liu, Y and Duan, Z and Su, S and Ding, H and Dai, Y and Gao, M and Ji, M and Liao, L}, title = {Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00919-2}, pmid = {42366391}, issn = {2524-6372}, support = {2022YFC2807501//National Key Research and Development Program of China/ ; 42476264//National Natural Science Foundation of China/ ; }, abstract = {The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains poorly characterized. To address this gap and evaluate its potential as a bioindicator of Antarctic marine environmental health, we employed shotgun metagenomics and 16S rRNA amplicon sequencing on fresh fecal samples collected from four Antarctic fur seals (designated S59, S62, S63, and S64) at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including an immunodeficiency-associated Lentivirus. Chitin-degrading capacity was ubiquitous, consistent with the host's krill-based diet. Metagenome-assembled genomes (MAGs) resolved distinct taxonomic contributions to discrete steps of chitin hydrolysis, suggesting that complete depolymerization requires metabolic cross-feeding among functionally complementary taxa. Notably, Helicobacter MAGs were abundant in individual S62, suggesting potential pathogenicity. Additionally, 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. These findings not only elucidate the community composition, functional potential, and ecological adaptation of the Antarctic fur seal gut microbiota but also establish a comprehensive baseline for assessing environmental change and human impacts on the Antarctic marine ecosystem, thereby offering valuable scientific data and methodological insights for the conservation of polar marine mammals.}, }
@article {pmid42366413, year = {2026}, author = {Li, X and Li, Z and Sun, X and Guo, Y and Pang, Z and Niu, G}, title = {Honghe Bunya-like virus: a novel virus identified in mosquitoes from Yunnan, China.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-13112-z}, pmid = {42366413}, issn = {1471-2164}, support = {SDYJSJGC2025059//Shandong Provincial Department of Education/ ; }, abstract = {BACKGROUND: Arboviruses represent a persistent and escalating threat to global public health, with mosquitoes serving as the principal vectors in their natural transmission cycles and geographic dissemination. Yunnan Province, southwestern China, is a recognized hotspot for arboviral diversity, yet the full spectrum of mosquito-borne viruses circulating in this region remains incompletely characterized.<br><br>RESULTS: A total of 3,300 female mosquitoes of four species across four genera were collected from rural areas of Honghe County, Yunnan Province in 2024, and subjected to viral metatranscriptomic sequencing. A previously undescribed bunya-like virus, designated Honghe Bunya-like virus, was identified in two locally dominant hematophagous mosquito species, with minimum infection rates of 0.2% and 0.3%, respectively. The viral genome comprises three single-stranded negative-sense RNA segments (L, M, and S) encoding the RdRp, glycoprotein, and nucleoprotein, respectively, consistent with the canonical architecture of the genus Orthobunyavirus. Phylogenetic analyses placed the virus within Orthobunyavirus across all three segments, though inter-segment topological incongruence was observed; amino acid identities to known orthobunyaviruses (49.7%-71.6%) fell below conspecific thresholds, suggesting a novel species.<br><br>CONCLUSIONS: This study expands the known genetic diversity of mosquito-associated virus in southwestern China and, given the phylogenetic affinity to pathogenic orthobunyaviruses and the hematophagous nature of the vector species, raises the possibility of vertebrate infection potential warranting further investigation.}, }
@article {pmid42366525, year = {2026}, author = {Kan, J and Morales-Amador, A and Hernandez, Y and Burian, J and Ternei, MA and Brady, SF}, title = {Resistance-CONKAT-seq Guided Discovery of a ClpP Active Natural Product from a Soil Metagenome.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.6c00347}, pmid = {42366525}, issn = {1554-8937}, abstract = {The discovery of natural products with specific molecular targets from metagenomes remains challenging. To address this limitation, we developed resistance-CONKAT-seq (resistance co-occurrence network analysis of targeted sequences) which links metagenomic BGCs (biosynthetic gene clusters) to potential modes of action through the identification of colocalized molecular target-based resistance genes. Applying this approach to a soil metagenomic library, we identified the uncharacterized metagenomic azetidopyrroline (MTA) BGC associated with a potential clpP self-resistance gene. Genetic engineering and heterologous expression of the MTA BGC led to the discovery of metaze A and B, which are structurally related azetidopyrroline- and bicyclocarbamate-based natural products, respectively. Metaze B inhibited Mycobacterium tuberculosis caseinolytic protease proteolytic subunit (ClpP) with an IC50 of 1.35 μM. This study expands the chemical diversity of natural product ClpP inhibitors and further demonstrates the applicability of resistance-CONKAT-seq for target-guided discovery of natural products with specific modes of action from complex metagenomes.}, }
@article {pmid42366537, year = {2026}, author = {Meusel, I and Manheim, D and Delaney, O and Greene, D and Tobolsky, R and Palya, H and Shapiro, N and Sharma, S}, title = {A Metagenomic Biosurveillance Network for Emerging Infectious Diseases: A Simulation-Based Model.}, journal = {Health security}, volume = {}, number = {}, pages = {23265094261453732}, doi = {10.1177/23265094261453732}, pmid = {42366537}, issn = {2326-5108}, abstract = {In this article, we propose a metagenomic next-generation sequencing (mNGS) system for symptomatic clinical respiratory disease samples in Israel to enable detection early enough to contain novel pathogen outbreaks, limit international spread and expedite countermeasure development. We built an open-source, interactive SEIR (susceptible, exposed, infectious, recovered)-based model extending the work of Sharma et al (2023) for 7 representative known respiratory pathogens with pandemic potential, aiming to estimate costs and detection time for the identification of a novel respiratory pathogen in Israel through a network of mNGS monitoring in hospitals. We find that a novel pathogen with SARS-CoV-2-like characteristics could be detected within 68 days (interquartile range [IQR]: 53 to 80) after the first 2 emergency department presentations and 213 (IQR: 94 to 429) total infections across Israel. This surveillance system would cost US$24 million annually over 10 years when implemented in Israel's 6 largest hospitals, covering 37% of the population. Our open-source interactive model allows policymakers and experts to explore different system configurations and their associated tradeoffs between cost, detection speed, and population coverage.}, }
@article {pmid42366621, year = {2026}, author = {Tawfiq, R and Kulmanov, M and Hoehndorf, R}, title = {Evaluating completeness, coherence, and consistency of genome-scale function annotations.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, doi = {10.1093/bib/bbag336}, pmid = {42366621}, issn = {1477-4054}, support = {URF/1/5041-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5235-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/4938-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5659-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; 5932//King Abdullah University of Science and Technology (KAUST)-KAUST Center of Excellence for Smart Health (KCSH)/ ; 5940//King Abdullah University of Science and Technology (KAUST)-Center of Excellence for Generative AI/ ; //KAUST Supercomputing Laboratory/ ; }, mesh = {*Molecular Sequence Annotation/methods ; Systems Biology/methods ; *Genome ; *Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Protein function annotation traditionally follows a reductionist approach, assigning functions to individual proteins acting in isolation. This treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated networks where their functions depend on genomic context and interacting partners. This needs to be reflected in function annotation and evaluation frameworks. We assess whether annotated protein functions could plausibly coexist within a living organism. To achieve this goal, we formalize three criteria grounded in systems biology principles: completeness (presence of essential functions), coherence (satisfaction of functional dependencies), and consistency (absence of mutually exclusive functions). We applied this framework to manually curated function annotations from six model organisms and computational function predictions from seven methods. While model organism annotations largely satisfied our constraints, computational function prediction methods systematically failed to produce biologically plausible genome-scale annotations. Our review reveals a measurable gap between the per-protein objectives of current annotation methods and the system-level criteria that an annotation set must satisfy to describe a viable organism. Our evaluation framework grounded in systems biology principles provides quantitative metrics for evaluating biological plausibility and establishes a foundation for developing system-aware annotation approaches. Augmenting protein-level annotation with system-level criteria offers a tractable path to improving annotation of the rapidly growing collection of sequenced genomes and metagenomes.}, }
@article {pmid42366665, year = {2026}, author = {Kuzbekov, SR}, title = {[Microbiota and microbiome of the lacrimal drainage system].}, journal = {Vestnik oftalmologii}, volume = {142}, number = {3}, pages = {91-100}, doi = {10.17116/oftalma202614203191}, pmid = {42366665}, issn = {0042-465X}, mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.}, }
@article {pmid42366735, year = {2026}, author = {Guo, X and Lai, CY and Zhao, HP}, title = {Targeted Acclimation Unlocks Adaptive Evolution of a Methanotrophic Consortium Enabling 3A5MI Elimination and Enhanced Sulfamethoxazole Biodegradation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02194}, pmid = {42366735}, issn = {1520-5851}, abstract = {Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.}, }
@article {pmid42367190, year = {2026}, author = {Teng, Y and Saghaï, A}, title = {Fermentative nitrite ammonifiers are abundant in soils and ecologically distinct from NrfA-dependent ammonifiers.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag144}, pmid = {42367190}, issn = {2730-6151}, abstract = {Microorganisms can use different enzymes to perform nitrite ammonification, the reduction of nitrite to ammonium, an important process to retain nitrogen in soils. Yet, the organisms mediating this process and their distribution in terrestrial ecosystems remain poorly resolved. Here, we determined the phylogenetic diversity of bacteria performing fermentative nitrite ammonification via the NAD(P)H-dependent nitrite reductase NirB, assessed their distribution across terrestrial ecosystems, and identified their environmental preferences. We found that these organisms are broadly distributed, spanning 29 phyla including Bacillota, Pseudomonadota and Actinomycetota. Screening 1587 globally distributed soil metagenomes using a phylogeny-based approach revealed that fermentative nitrite ammonifiers are ubiquitous across biomes and particularly abundant in Mediterranean forests and desert soils. In these ecosystems, they outnumbered NrfA-dependent ammonifiers, the best characterized ammonifier group to date, suggesting distinct ecological niches for the two groups. Consistent with this, random forest modelling revealed a negative relationship between fermentative nitrite ammonifiers and the carbon-to-nitrate ratio, which contrasts with a preference for high carbon-to-nitrate conditions in NrfA-dependent ammonifiers. However, moisture and salinity emerged as the strongest predictors of the abundance of fermentative nitrite ammonifiers, indicating a high tolerance to osmotic stress in this group. Overall, our results demonstrate that fermentative nitrite ammonifiers are both phylogenetically diverse and environmentally widespread, calling for future efforts to determine the conditions under which they contribute to nitrogen retention in soils.}, }
@article {pmid42367193, year = {2026}, author = {Guo, S and McNamara, NP and Bending, GD and Mushinski, RM}, title = {Phosphorus availability mediates pathway-specific nitrogen cycling in stratified peatland microbiomes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag143}, pmid = {42367193}, issn = {2730-6151}, abstract = {Peatland microbiomes regulate nitrogen (N) cycling processes that control nutrient retention and greenhouse gas emissions in carbon-rich ecosystems. Although depth-driven redox gradients structure microbial communities, how physicochemical stratification shapes the functional versus taxonomic organization of N-cycling microorganisms remains unclear. We used shotgun metagenomics to characterize N-cycling gene distributions, taxonomic affiliations, and metagenome-assembled genomes (MAGs) across depth and vegetation gradients in a temperate blanket bog. Depth emerged as the primary structuring factor, creating functional-taxonomic decoupling. Surface peat (0-20 cm) harbored functionally diverse but taxonomically constrained communities assembled deterministically around nitrification and labile N acquisition, while subsurface peat (20-40 cm) supported taxonomically richer but functionally-simpler communities assembled stochastically and enriched in denitrification and dissimilatory nitrate reduction. Linear mixed-effects models revealed pathway-specific controls on N cycling. Denitrification increased with depth (β = 11.53, P < .05), whereas organic N transformation declined (β = -5.81, P < .05); depth effects on nitrification and N fixation became non-significant after accounting for environmental variables. Phosphorus (P) emerged as the strongest environmental predictor, regulating nitrification (β = 95.40, P < .01), N fixation (β = 128.33, P < .01), organic N transformation (β = 80.53, P < .01), and denitrification (β = -109.63, P < .05), highlighting the importance of P availability in structuring microbial N cycling. This challenges traditional N-limitation paradigms in ombrotrophic systems. MAGs revealed Pseudomonadota as the dominant N-cycling lineage, while incomplete denitrification capacity indicated genetic potential for N2O accumulation in subsurface layers. These findings demonstrate that P availability, rather than N content alone, regulates microbial N transformation capacity in peatlands, with implications for predicting nutrient dynamics under altered hydrological and nutrient deposition regimes.}, }
@article {pmid42367641, year = {2026}, author = {Xu, C and Liu, T and Zhang, X and Feng, S}, title = {Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.}, journal = {Blood science (Baltimore, Md.)}, volume = {8}, number = {3}, pages = {e00304}, pmid = {42367641}, issn = {2543-6368}, abstract = {In patients with hematological disorders, the high risk of complex infections caused by immune dysfunction and intensive therapies poses a major challenge to the use of conventional microbiological tests (CMTs). Plasma cell-free DNA (cfDNA) metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary noninvasive tool that enables unbiased, broad-spectrum, and rapid pathogen identification directly from blood samples. This review summarizes the core applications of plasma cfDNA mNGS in patients with hematological disorders, including the diagnosis of febrile neutropenia, bloodstream infections, focal infections, and infections caused by uncommon/fastidious pathogens. It highlights the advantages of this technology in overcoming antibiotic interference, enabling early detection, and providing diagnostic value in cases without clear infection foci or when invasive sampling is not feasible. This review further discusses how China has facilitated the widespread adoption of this technology through a localized application model, cost reduction, and the development of clinically relevant interpretation models. Nevertheless, challenges remain, such as lower sensitivity than site-specific specimens in focal infections, and the difficulty in predicting antimicrobial resistance (AMR) on the basis of cfDNA mNGS. Future developmental directions should focus on technical optimization (eg, combined plasma cell-fraction testing), quality assurance and quality control management, multidimensional data integration (eg, host immune response analysis), artificial intelligence (AI)-assisted interpretation, and cost reduction through technology popularization and insurance coverage. These efforts will advance cfDNA mNGS from a pathogen detection tool toward an intelligent clinical decision-support platform, ultimately improving the diagnostic accuracy and clinical outcomes of hematological patients with infections.}, }
@article {pmid42367778, year = {2026}, author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y}, title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1868704}, pmid = {42367778}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; }, abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.<br><br>METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.<br><br>RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P&#xa0;<&#xa0;0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P&#xa0;=&#xa0;0.003) and depletion of Roseburia (1.05% vs. 3.77%, P&#xa0;=&#xa0;0.005) and Ruminococcus (5.98% vs. 7.85%, P&#xa0;=&#xa0;0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P&#xa0;=&#xa0;0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.<br><br>CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably&#xa0;Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.}, }
@article {pmid42367784, year = {2026}, author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X}, title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1859206}, pmid = {42367784}, issn = {1664-3224}, mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; }, abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.}, }
@article {pmid42367847, year = {2026}, author = {Sparagon, WJ and Lary, S and Ioh, MT and Lin, A and Dhungana, I and Fullmer, CR and Handel, CR and Paudel, R and Burden, J and Deubel, JN and Tayo, MAG and Rodriguez, FE and Swift, SOI and Nakayama, KK and Maaz, TM and Nguyen, NH}, title = {Soil Resistomes in a Tropical Watershed are Indirectly Structured by Bacterial Community Interactions with Soil Properties.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.18.733189}, pmid = {42367847}, issn = {2692-8205}, abstract = {Soils are recognized as reservoirs of antibiotic resistance genes (ARGs) with the potential to transfer to clinical pathogens, creating antimicrobial resistance (AMR) that poses a threat to human health. While large-scale AMR surveys have profiled how diverse biomes shape soil resistomes, less is known about the influence of specific soil properties. Here, we combined metagenomics and 16S rRNA amplicon sequencing with isolate-based approaches to investigate drivers of soil AMR across a tropical watershed from beach to mountaintop in Waimea Valley, O'ahu, Hawai□i. We leveraged functional- and taxonomic-classification of resistances to unravel how soil properties interact with bacterial taxa to structure resistomes. Metagenomic- and isolate-resistomes showed remarkable consistency, including a general gradient of increasing AMR from ridge to beach. Resistome functional composition was significantly correlated with total bacterial community structure. The relationship between resistances and soil properties was primarily dictated by taxonomic composition of each resistance. Rifampin- and Vancomycin-ARGs associated with Actinomycetes negatively correlated with soil physical properties, while resistant genes and isolates from Gammaproteobacteria positively correlated with enzymatic activity metrics. These findings indicate that soil properties structure the resistome indirectly through taxonomic filtering of microbial hosts and challenge the notion that AMR is decoupled from phylogenetic relatedness.}, }
@article {pmid42367895, year = {2026}, author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and De Souza, ML and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH}, title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.13.732064}, pmid = {42367895}, issn = {2692-8205}, abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1 - 3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.}, }
@article {pmid42368165, year = {2026}, author = {Tinker, KA and Ross, DE and Beebe, MN and Bagwell, CE and Smallwood, CR and Davis, RW and Gulliver, DM}, title = {Biogeochemical Assessment of Short-Term Hydrogen Storage in Methane Reservoirs with Field Sample Characterization and Reactor Experiments.}, journal = {ACS omega}, volume = {11}, number = {24}, pages = {34976-34986}, pmid = {42368165}, issn = {2470-1343}, abstract = {Hydrogen is a valuable commodity due to its high energy density and properties as a flexible energy carrier. It is possible to store hydrogen by blending it with methane and utilizing existing natural gas infrastructure. However, adapting current methane storage strategies to withstand the expected biogeochemical processes caused by H2 injection has not been fully explored. In this study, a series of experiments were designed to identify potential geochemical and microbial challenges of storing hydrogen/methane gas blends in existing methane reservoirs. First, fluid samples were collected from two methane reservoirs located in the western United States. The geochemical composition, microbial taxonomy, and metabolic potential of each fluid sample were characterized by utilizing ion chromatography (IC), inductively coupled plasma optical emission spectroscopy (ICP-OES), a Total Organic Carbon (TOC) analyzer, 16S rRNA gene amplicon sequencing, and metagenomic sequencing. Next, fluid samples from one field site (Site 2) were used to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ∼1000 psi) for natural gas (100% CH4) and hydrogen blend (80% CH4/20% H2) storage environments. Both biotic and abiotic (sterilized) measurements were conducted to accurately understand and decouple abiotic and microbially driven processes, with the goal of linking these processes to storage impacts. Overall, the two reservoirs had a high, but variable, total dissolved solids (TDS) concentration, with various organic acids including acetate and propionate. The field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across these reactors, there was minimal change in the fluid geochemistry and a minimal (0-5%) decrease of hydrogen gas during the initial storage event (days 1-3). This work contributes to the understanding of the complexities of hydrogen storage and demonstrates the need for additional research.}, }
@article {pmid42368245, year = {2026}, author = {Bahr, NC and Kasibante, J and Nsangi, L and Kagimu, E and Ssebambulidde, K and Rutakingirwa, MK and Tugume, L and Ramachandran, PS and Cresswell, F and Meya, DB and Boulware, DR and Wilson, MR and Ellis, J}, title = {Central Nervous System Toxoplasmosis is an Under-Recognized Opportunistic infection in Uganda.}, journal = {Journal of tropical medicine}, volume = {2026}, number = {}, pages = {2158978}, pmid = {42368245}, issn = {1687-9686}, abstract = {In Uganda, Toxoplasma meningoencephalitis remains underdiagnosed due to the low sensitivities and specificities of available diagnostics. In our recent publication, we identified 15 cases of possible Toxoplasma gondii meningoencephalitis by cerebrospinal fluid metagenomic next-generation sequencing in patients with suspected meningitis. We herein discuss, in detail, these cases to highlight the ongoing limitations of utilizing clinical symptoms to diagnose Toxoplasma gondii meningoencephalitis, the importance of access to rapid diagnostics, and the frequency of toxoplasmosis as a possible co-infection with other opportunistic diseases among people with advanced HIV.}, }
@article {pmid42368276, year = {2026}, author = {Zhu, H and Lin, Y and Liao, H and Li, X and Xie, Q and Zheng, Y}, title = {Infantile pulmonary abscess due to Mycobacterium abscessus subsp. massiliense identified by integrated mNGS and targeted NGS: a rare case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1828339}, pmid = {42368276}, issn = {2296-2360}, abstract = {BACKGROUND: To describe a rare case of pulmonary infection caused by Mycobacterium abscessus in an infant and to evaluate the complementary diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying non-tuberculous mycobacterial (NTM) infections when conventional testing is inconclusive.<br><br>CASE PRESENTATION: A 3-month-old male infant presented with a persistent cough and a right upper-lobe mass, initially suspected to be a congenital malformation or neoplasm. Following inconclusive routine examinations, mNGS was performed on bronchoalveolar lavage fluid (BALF). mNGS detected a single read of M. abscessus in BALF, providing an initial diagnostic clue. Subsequently, a tNGS assay was conducted on both BALF and resected lung tissue to achieve precise species identification. tNGS identified 13,272 reads of M. abscessus subsp. massiliense in BALF and 31,474 reads in lung tissue, confirming the pathogen and enabling precise molecular diagnosis. Histopathological examination revealed granulomatous inflammation with multinucleated giant cells, consistent with NTM infection. Guided by these results, the patient initially received azithromycin and was transferred to a specialized chest hospital, where a multidrug anti-NTM regimen was formulated, including azithromycin, imipenem-cilastatin, cefoxitin, and linezolid. After continued treatment at a local municipal hospital, respiratory symptoms resolved, inflammatory markers improved, follow-up CT showed progressive absorption of the right upper-lobe lesion with a small residual cavity, and the patient was discharged in stable condition without recurrent infections during available follow-up.<br><br>CONCLUSION: This case highlights the diagnostic utility of integrating mNGS and tNGS for the accurate identification of rare NTM infections in infants, particularly when routine microbiological tests and imaging findings are inconclusive.}, }
@article {pmid42368287, year = {2026}, author = {Li, M and Sun, Z and Jia, T and Ma, M}, title = {Insights into the mechanism of intestinal flora imbalance and immune disorder in co-morbidity of pneumonia and diarrhea in children.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1836762}, pmid = {42368287}, issn = {2296-2360}, abstract = {Pneumonia and diarrhea are the two leading causes of death in children under five years of age, and these two conditions often present as a comorbidity, where the same child experiences respiratory and digestive system infection symptoms simultaneously or sequentially. Clinical data indicate that the incidence of secondary diarrhea in children hospitalized with pneumonia is high, significantly prolonging hospital stays and affecting prognosis. In recent years, the proposal of the gut-lung axis theory has provided a novel perspective for understanding this comorbidity phenomenon. The gut-lung axis refers to the bidirectional regulatory pathway between the gut microbiota and the pulmonary immune system, with the lungs and intestines sharing embryonic origin and a common mucosal immune system. This review systematically reviews the characteristics of gut microbiota dysbiosis and the mechanisms of immune disorders in the context of pediatric pneumonia-diarrhea comorbidity. Clinical studies have shown that children with comorbidity exhibit significant gut microbiota dysbiosis, characterized by a reduction in beneficial bacteria such as Bifidobacterium, an increase in opportunistic pathogens such as Escherichia coli, and decreased microbial diversity. Gut microbiota dysbiosis leads to immune disorders through multiple mechanisms, including reduced short-chain fatty acids, skewed immune cell differentiation, and dysregulated inflammatory factor networks, resulting in Th1/Th2 imbalance, decreased regulatory T cell function, and exacerbated systemic inflammatory responses. Supplementation with microecological preparations such as Saccharomyces boulardii has been shown to significantly shorten hospital stays, diarrhea duration, and fever resolution time, while improving peripheral blood immunoglobulin levels and T-cell subsets, providing evidence-based support for clinical intervention. This review also systematically reviews clinical laboratory indicators associated with comorbidity, including inflammatory markers, immune status indicators, intestinal barrier function markers, and microbiota detection methods, which have important application value in early identification, disease assessment, and treatment monitoring of comorbidity. Future research should further employ metagenomic approaches combined with longitudinal follow-up designs to elucidate the roles of specific bacterial species/strains in gut-lung axis regulation, providing new strategies for precision prevention and treatment of pediatric pneumonia-diarrhea comorbidity.}, }
@article {pmid42368316, year = {2026}, author = {Zheng, H and Zhuang, J and Lin, Q and Wang, T and Guo, G and Huang, L and Lin, W}, title = {Study on the role and clinical relevance of gut microbiota in diabetic foot ulcers.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {287}, pmid = {42368316}, issn = {2190-572X}, abstract = {UNLABELLED: Diabetic foot ulcers (DFU) are severe and costly complications of diabetes, predisposing to infection, amputation, and mortality, highlighting the urgent need to clarify their mechanisms for optimized clinical management. This study integrated clinical biochemistry data and multi-omics analyses (including metagenomic sequencing) from 11 patients to reveal the critical role of gut microbiota in the pathogenesis of DFU. Results showed significant host metabolic disorders in DFU patients, characterized by hypoalbuminemia (mean ± SD:32.35 ± 6.02 g/L), persistent hyperglycemia (mean ± SD:8.25 ± 3.21 mmol/L), and imbalances in trace elements such as magnesium (mean ± SD:0.84 ± 0.08 mmol/L). Concurrently, the gut microbiota composition was markedly altered, with enrichment of the phylum Bacillota_A (formerly Firmicutes; 48.7% in patients vs. 32.1% in controls) and elevated genetic potential of virulence genes (e.g., type VI secretion systems, capsular polysaccharide gene cps4J/L). Metagenomic tracing revealed that antibiotic resistance genes (ARGs) such as tet(A) and blaOXA-1 were co-localized with mobile genetic elements (MGEs) including IncF plasmids and tnpA transposases. 99.2% of key ARGs shared sequence homology with gut-derived metagenome-assembled genomes (MAGs) and co-localized with MGEs, indicating potential cross-niche transfer capacity. Furthermore, renal (mean ± SD:11.81 ± 5.75 mmol/L) and hepatic (ALT: 35.67 ± 18.22 U/L) dysfunction correlated with aggravated gut dysbiosis and ARG enrichment. In conclusion, this study confirms that host metabolic deficiencies contribute to DFU refractoriness by altering gut microbiota ecology and enhancing horizontal gene transfer of virulence and resistance determinants, providing a novel framework for precision therapies targeting the host-microbe metabolic interface.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04745-8.}, }
@article {pmid42368546, year = {2026}, author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W}, title = {Erratum: Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1899816}, doi = {10.3389/fpls.2026.1899816}, pmid = {42368546}, issn = {1664-462X}, abstract = {[This corrects the article DOI: 10.3389/fpls.2026.1726191.].}, }
@article {pmid42368826, year = {2026}, author = {Martínez-Noriega, M and Jean-Louis, P and Philippon, M and Sanchez-Flores, A and Gonzalez-Rizzo, S}, title = {Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag034}, pmid = {42368826}, issn = {2633-6685}, abstract = {White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including Ferrimicrobium, Thermonospora, Alcanivorax, and Serratia, which has been previously associated with human-induced environmental changes. In contrast, Prosthecochloris and Chlorobaculum were highly abundant in protected sites, whereas Sulfurovum and Sulfurimonas dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.}, }
@article {pmid42368984, year = {2026}, author = {Basbouss-Serhal, I and Fayad, F}, title = {Familial Mediterranean Fever and the Gut Microbiota: A Dual Perspective Review of Current Evidence.}, journal = {Mediterranean journal of rheumatology}, volume = {37}, number = {2}, pages = {302-308}, pmid = {42368984}, issn = {2529-198X}, abstract = {Familial Mediterranean Fever is a well-known autoinflammatory disease resulting from mutations in the MEFV gene. A recent development has linked FMF pathogenesis and mode of expression to the gut micro-biota. There may be a change in the gut microbiota profile of FMF patients, characterised by low diversity and a depletion of beneficial bacteria. Dysbiosis tends to be linked to increased gut permeability, systemic inflammation, and low response to colchicine treatment. Probiotics and prebiotics, in this case, may help restore the previous idyllic state of the microbial balance, along with a reduction in inflammatory markers, thereby demonstrating therapeutic merit. Notably, however, it did argue in some instances that changes in the microbiota were secondary to the genetic and inflammatory nature of FMF itself. It is still important to carry out longitudinal studies of naïve patients that will integrate metagenomics with immune profiling to ascertain whether microbial changes arise from causes, contributions, or coincidence in the pathogenesis of FMF.}, }
@article {pmid42369126, year = {2026}, author = {Pang, H and Pi, C and Shen, P and Tang, Z and Bao, E and Luo, X and Zhang, Q}, title = {Case Report: pharmaceutical care in a case of complicated urinary tract infection combined with disseminated Nocardia brasiliensis infection.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1839868}, pmid = {42369126}, issn = {2296-858X}, abstract = {Given the increasing prevalence of multidrug-resistant opportunistic pathogens and the high mortality rate associated with delayed diagnosis of disseminated infections, there is an urgent need for rapid diagnostic tools and closely monitored, individualized anti-infective strategies. This study aimed to explore the critical role of comprehensive pharmaceutical care in managing disseminated Nocardia infections complicated by complicated urinary tract infection (cUTI). Through detailed documentation of a 67-year-old male patient, this study focuses on optimizing antimicrobial regimens based on pathogenetic findings and adjusting treatments for severe adverse reactions. The patient was diagnosed with disseminated Nocardia brasiliensis infection complicated by Enterococcus faecalis urinary tract infection using metagenomic next-generation sequencing (mNGS). The treatment process underwent two critical adjustments. First, during the efficacy optimization phase, the initial empirical meropenem therapy was modified to a reinforced regimen centered on trimethoprim-sulfamethoxazole (TMP-SMX), combined with linezolid and short-term amikacin, effectively controlling the spread of infection. Subsequently, during the safety optimization phase, the patient developed severe thrombocytopenia during sequential oral therapy. Prompt identification and switching to amoxicillin/clavulanate potassium resolved the adverse reactions, enabling successful continuation of subsequent treatment. Follow-up revealed a favorable patient recovery. This case demonstrates that for such complex mixed infections, rapid pathogen diagnosis represented by mNGS serves as the starting point for precision treatment, whereas the intensive combination regimen centered on TMP-SMX forms the foundation for controlling disseminated Nocardia infection. More importantly, the core insight from this case is that successful treatment relies not only on appropriate initial medication, but more critically, on proactive, dynamic pharmaceutical monitoring throughout long-term therapy. This enables early intervention for severe adverse drug reactions and timely, flexible adjustments to treatment regimens, which are essential components for ensuring ultimate therapeutic success in patients with such complex infections.}, }
@article {pmid42369553, year = {2026}, author = {Xu, S and Jia, M and Guo, X and Liang, W and Pan, Y and Lin, Y and Li, X and Qiu, H and Hu, D and Yan, D}, title = {Metagenomics and metabolomics analyses of the mechanism of non-expression of natural mating behavior in captive male Malayan pangolins (Manis javanica).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1828282}, pmid = {42369553}, issn = {1664-302X}, abstract = {Ex situ conservation and captive breeding are important measures for conserving endangered species. However, the reproduction of some wild animals, especially males, is inhibited in captivity, but the underlying mechanism has not yet been elucidated. This study aimed to investigate the microbiota and their functions, metabolites, and their metabolic pathways impacting reproduction employing metagenomics and metabolomics analyses and using male Malayan pangolins with normal (with natural mating behavior) and abnormal (no natural mating behavior) reproduction as the research objects. The results showed that the relative abundance of Proteobacteria, Escherichia coli, and Shigella spp. was significantly higher in the abnormal reproduction (AR) group. However, the relative abundance of Firmicutes and Staphylococcus aureus was significantly higher in the normal reproduction (NR) group. Kyoto Encyclopedia of Genes and Genomes functional pathway enrichment analysis found that citrate cycle (TCA cycle, KO00020) and pyruvate metabolism (KO00620) were significantly enriched in pangolins with AR, whereas gonadotropin-releasing hormone secretion (KO04929) was significantly enriched in pangolins with NR. Metabolites such as tryptophan, arginine, and androgen were significantly enriched in pangolins with AR, whereas L-proline, taurine, choline, and spermidine were significantly enriched in pangolins with NR. Microbiota dysbiosis, energy metabolism disorder, deficiencies in key metabolic pathways and metabolites, and hormonal disturbances are all potential factors contributing to the inability of male Malayan pangolin to express natural reproductive behavior. This study provides evidence for AR of captive pangolins and offers important insights for the conservation of captive endangered species.}, }
@article {pmid42369554, year = {2026}, author = {Zi, GR and Zhang, DJ and He, DL and Shu, F and Ou, Y and Ke, CX}, title = {Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1843102}, pmid = {42369554}, issn = {1664-302X}, abstract = {Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.}, }
@article {pmid42369768, year = {2026}, author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G}, title = {A foundational quantum framework for multi-pattern string matching in k-mer detection.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1802517}, pmid = {42369768}, issn = {2673-7647}, abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.<br><br>METHOD: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (&#x221a;S) query complexity for S text positions but requiring O (m &#xb7; L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (&#x221a;S &#xb7; &#x221a;m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation.<br><br>RESULTS: This work introduces two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.<br><br>CONCLUSION: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.<br><br>To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.}, }
@article {pmid42369969, year = {2026}, author = {Wei, M and Xiao, Z and Du, X and Cao, J and Wu, S and Zhang, R and Yang, X and Fan, C and Lian, J and Kang, W and Wang, C and Ye, C}, title = {mNGS-Identified Mycobacterium porcinum Infection in a Newly Diagnosed Person With HIV Presenting With Recurrent Suppurative Cervical Lymphadenitis.}, journal = {Open forum infectious diseases}, volume = {13}, number = {6}, pages = {ofag373}, pmid = {42369969}, issn = {2328-8957}, abstract = {Although reports of human infection caused by Mycobacterium porcinum (M. porcinum) have gradually increased in recent years, cases occurring in people with HIV (PWH) remain rare, and the association between M. porcinum infection and suppurative cervical lymphadenitis in PWH has not been previously reported. In this case, metagenomic next-generation sequencing was used to rapidly identify M. porcinum from a pus specimen obtained from a newly diagnosed person with HIV presenting with suppurative cervical lymphadenitis as the initial manifestation. Recognition of these rare clinical features may improve understanding of non-tuberculous mycobacterial infections in PWH and their diverse clinical presentations.}, }
@article {pmid42370219, year = {2026}, author = {Niu, X and Yu, Q and Gu, J and Lu, B and Shen, W and Tian, J}, title = {Disseminated Mycobacterium avium Complex Infection in an HIV Patient with a History of Talaromyces marneffei: Diagnostic Value of Blind Subculture and Suspected Management Challenges of Immune Reconstitution Inflammatory Syndrome.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {606947}, pmid = {42370219}, issn = {1178-6973}, abstract = {This study reported a 33-year-old male acquired immune deficiency syndrome (AIDS) patient with a 10-year human immunodeficiency virus (HIV) infection history, poor antiretroviral therapy (ART) adherence, and two previous Talaromyces marneffei infections. Self-discontinuation of ART led to severe immunosuppression and disseminated Mycobacterium avium complex (MAC) infection involving the bloodstream and bone marrow. After the restart of ART, the patient developed persistent high fever, which was clinically suspected to be MAC-associated immune reconstitution inflammatory syndrome (IRIS). However, due to the lack of serial HIV viral load and CD4[+] T lymphocyte data, a definitive diagnosis could not be established. The patient was admitted with fatigue, anorexia, and black stool as the main symptoms. MAC infection was confirmed by blood culture, bone marrow culture, and bone marrow metagenomic next-generation sequencing (mNGS) at a higher-level hospital. Notably, after transfer to our hospital, the microbiology laboratory performed blind subculture on routinely negative blood culture bottles and extended the incubation period to 15 days, successfully isolating MAC. This highlights the crucial significance of close clinical-laboratory collaboration and optimized pathogen detection for diagnosing non-tuberculous mycobacteria (NTM) infections. After initial infection control and ART restart, the patient developed recurrent fever. Given the temporal association with ART reinitiation and the dose-dependent correlation between fever and glucocorticoid adjustments, possible MAC-associated IRIS was suspected. The patient's clinical symptoms improved with glucocorticoid therapy, though this does not confirm the diagnosis. Complications including cytomegalovirus reactivation, adverse drug reactions, and human rhinovirus co-infection were managed in a standardized manner. This case suggests that the diagnosis of disseminated MAC infection in severely immunocompromised AIDS patients relies on efficient collaboration between clinicians and laboratories. However, in the absence of confirmatory immunological and virological evidence, the diagnosis of IRIS remains uncertain. Clinicians should remain vigilant for suspected IRIS when restarting ART while acknowledge that limited data may preclude a definitive diagnosis. Individualized comprehensive strategies covering anti-infection, immunomodulation, anti-inflammation, and supportive treatment are the key to managing such complex HIV-related opportunistic infections.}, }
@article {pmid42370222, year = {2026}, author = {Chen, M and An, W and Fang, S and Zhang, M}, title = {Efficacy and Safety of Omadacycline in Patients with Mycoplasma Pneumoniae Harboring the 23S rRNA A2063G Mutation.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {601060}, pmid = {42370222}, issn = {1178-6973}, abstract = {OBJECTIVE: Mycoplasma pneumoniae is a major pathogen of community-acquired bacterial pneumonia (CABP). Macrolide-resistant Mycoplasma pneumoniae (MRMP) harboring the 23S rRNA A2063G mutation poses a global therapeutic challenge. Omadacycline, a novel aminomethylcycline approved for CABP, exhibits activity against MRMP. However, real-world data on omadacycline for A2063G-mutated MRMP pneumonia remain limited. In this study, we present our clinical experience with intravenous omadacycline in patients with genetically confirmed A2063G-mutated MRMP pneumonia.<br><br>METHODS: We retrospectively analyzed the clinical data of eight patients with MRMP pneumonia confirmed by metagenomic next-generation sequencing (mNGS). All patients had failed prior macrolide or fluoroquinolone therapy and received a 7-day course of intravenous omadacycline. Clinical symptoms, inflammatory parameters, chest CT findings, and safety were evaluated.<br><br>RESULTS: Eight patients were included. Significant reductions in inflammatory markers were observed after treatment: the neutrophil count decreased from (6.92 &#xb1; 2.13)&#xd7;10[9]/L to (4.67 &#xb1; 1.03)&#xd7;10[9]/L (P = 0.02), C-reactive protein decreased from (68.17 &#xb1; 50.35) mg/L to (14.77 &#xb1; 19.34) mg/L (P = 0.01), and serum amyloid A decreased from (497.28 &#xb1; 319.79) mg/L to (28.35 &#xb1; 32.28) mg/L (P < 0.01). Chest CT showed marked resolution of pulmonary lesions in seven patients. No treatment-related adverse events requiring discontinuation were reported.<br><br>CONCLUSION: Omadacycline demonstrates promising clinical efficacy and a favorable safety profile for the treatment of pneumonia caused by A2063G-mutated MRMP, promoting both clinical and radiological recovery. Larger prospective controlled studies are warranted to confirm these findings.}, }
@article {pmid42370333, year = {2026}, author = {Mahlich, Y and Sohi, H and Veličković, M and Piehowski, PD and McDermott, JE and Gosline, SJC}, title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag163}, pmid = {42370333}, issn = {2635-0041}, abstract = {MOTIVATION: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.<br><br>RESULTS: To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with the goal of integration across multiple data types (e.g. sequencing, metabolites, proteins) within the same tissue.<br><br>spammR is implemented in R. The package is currently installable from GitHub (https://pnnl-compbio.github.io/spammR/).}, }
@article {pmid42370706, year = {2026}, author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, M&#xd8;}, title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057726}, doi = {10.1128/msystems.00577-26}, pmid = {42370706}, issn = {2379-5077}, abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.}, }
@article {pmid42370707, year = {2026}, author = {Victorsen, A and Knutson, TP and Bolender, L and Jung, S and Ferrieri, P and Thyagarajan, B and Hilt, EE}, title = {Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0366625}, doi = {10.1128/spectrum.03666-25}, pmid = {42370707}, issn = {2165-0497}, abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this technology a gold standard for infectious disease diagnostic testing. One major challenge is being able to distinguish between the clinically relevant organisms from background contamination. We performed a validation study for mNGS on cerebrospinal fluid (CSF) that utilized positive clinical samples and contrived samples that incorporated a bioinformatics pipeline that can better distinguish between background contamination and clinically relevant organisms and used a three-tiered reporting algorithm meant to decrease the inherent subjectivity that comes with interpreting and reporting data from clinical metagenomic sequencing. The validation of this assay and category-based reporting pipeline revealed an overall concordance of 91.8%, with a sensitivity of 100% and a specificity of 72.4%. In addition, we improved the detection of clinically relevant RNA viruses to almost 100% in the CSF by modifying the wet lab processing of the sample. This bioinformatics pipeline with a category-based reporting algorithm will provide more confidence in reporting microorganisms detected with this technology, mNGS, and improving patient care.<br><br>IMPORTANCE: Metagenomic next-generation sequencing (mNGS) can offer a broad, unbiased approach for the detection of infectious pathogens and has shown promise in diagnosing central nervous system infections. Despite its potential, clinical implementation remains limited by challenges in distinguishing clinically relevant organisms from background contamination. This study validated an mNGS assay for cerebrospinal fluid that incorporates an optimized bioinformatics pipeline with a three-tiered reporting algorithm designed to reduce subjectivity and enhance diagnostic confidence. The assay also has improved detection of clinically relevant RNA viruses through modified wet-lab processing. These findings support the clinical utility of a structured, category-based reporting approach for mNGS, advancing its reliability as a diagnostic tool in infectious disease testing.}, }
@article {pmid42370713, year = {2026}, author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ}, title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0113625}, doi = {10.1128/msystems.01136-25}, pmid = {42370713}, issn = {2379-5077}, abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.}, }
@article {pmid42370731, year = {2026}, author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L}, title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0040726}, doi = {10.1128/msystems.00407-26}, pmid = {42370731}, issn = {2379-5077}, abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.}, }
@article {pmid42370747, year = {2026}, author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE}, title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.}, journal = {mBio}, volume = {}, number = {}, pages = {e0338225}, doi = {10.1128/mbio.03382-25}, pmid = {42370747}, issn = {2150-7511}, abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.}, }
@article {pmid42371112, year = {2026}, author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X}, title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42371112}, issn = {1436-6215}, support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; }, mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; }, abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.<br><br>METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500&#xa0;ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).<br><br>RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P&#x2009;<&#x2009;0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.<br><br>CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.<br><br>CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).}, }
@article {pmid42371206, year = {2026}, author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T}, title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42371206}, issn = {1573-0972}, support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; }, mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth &amp; development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenome ; China ; Microbiota/genetics ; }, abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.}, }
@article {pmid42371248, year = {2026}, author = {Tlaskalová-Hogenová, H and Hrnčíř, T and Štěpánková, R and Trebichavský, I and Hudcovic, T and Šplíchal, I and Šplíchalová, A and Šinkora, M and Funda, D and Sánchez, D and Kverka, M and Jirásková Zákostelská, Z and Kostovčíková, K and Coufal, &#x160; and Procházková, P and Roubalová, R and Vannucci, L and Miler, I}, title = {Gnotobiology: from 19th-century global foundations to 21st-century omics - six decades of Czech contribution to microbiome research.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42371248}, issn = {1874-9356}, support = {22-12533S, 22-21356S, 23-05645S, 25-16094S, 26-21469S//Czech Science Foundation (GA&#x10c;R)/ ; LUAUS23014//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//European Union - Next Generation EU (Operational Programme Johannes Amos Comenius)/ ; LX22NPO5102//European Union - Next Generation EU (National Institute for Cancer Research, Programme EXCELES)/ ; RVO: 61388971//Institute of Microbiology of the Czech Academy of Sciences/ ; NU21-04-00443, NU22-09-00493, NU22J-05-00056, NU23-01-00288, NU23-04-00381, NU23-05-00133, NW24-06-00509, NW24-07-00042, NW25-04-00079//Czech Health Research Council (AZV &#x10c;R)/ ; }, abstract = {Gnotobiology, from the Greek gnotos (meaning 'known') and bios (meaning 'life'), is a research discipline that uses organisms with a defined microbiological status to study the interaction between hosts and microbes. This review traces six decades of Czech gnotobiology, beginning with the launch of a dedicated gnotobiology programme at Nový Hrádek in 1962 by Jaroslav Šterzl, whose visionary aims anticipated by decades the current recognition of the microbiota as a central determinant of immune and broader physiological function. The site - originally established in 1953 as the Biological Station - was thereby transformed into one of only four gnotobiological laboratories worldwide at that time and the first in Central and Eastern Europe. The facility pioneered the rearing of germ-free piglets, rats, rabbits, and mice, establishing the experimental foundation for the laboratory's work on immune ontogeny, mucosal immunity and tolerance, and microbiota-host interactions in immune development and regulation. This review discusses the key discoveries made using these models. Among them, work at the Institute of Microbiology (Prague and Nový Hrádek) demonstrated that germ-free animals have underdeveloped lymphoid tissue and impaired adaptive immunity. The review also describes the subsequent development of gnotobiotic models of human metabolic, immune-mediated, neoplastic, and neuropsychiatric diseases. The completion of the Human Genome Project in 2001 and the emergence of microbial metagenomics in the early 2000s sparked renewed interest in host-microbe interactions and led to a rediscovery of gnotobiotic approaches as essential tools for establishing causation in microbiome research. We examine how integrating these approaches with high-throughput sequencing, metabolomics, and other omics technologies has shifted the focus from cataloguing the microbiome to mechanistically dissecting host-microbe interactions. Finally, we outline future directions, including humanized gnotobiotic models, microbiota-based therapeutics, and the convergence of gnotobiology with personalized medicine and synthetic biology.}, }
@article {pmid42371328, year = {2026}, author = {Pattani, V and Kaneriya, J and Joshi, K and Sanghvi, G}, title = {Microbial Metabolic Strategies for Environmental Detoxification: From Enzymatic Mechanisms to Synthetic Biology and Omics.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42371328}, issn = {1559-0291}, abstract = {Microorganisms play a pivotal role in environmental detoxification by utilizing their metabolic pathways to degrade, transform, or immobilize toxic pollutants such as hydrocarbons, heavy metals, pesticides, and industrial effluents. This review explores microbial enzymatic systems, including oxidoreductases, hydrolases, and transferases, that facilitate pollutant breakdown. Various bioremediation strategies, such as bioaugmentation, biostimulation, and phytoremediation-assisted microbial degradation, are discussed alongside advances in synthetic biology and metabolic engineering, which enhance microbial efficiency for targeted detoxification. The potential of microbial consortia in tackling complex contamination scenarios is also examined. Additionally, omics-based approaches, including metagenomics, transcriptomics, and proteomics, provide deeper insights into microbial community dynamics and metabolic capabilities. Challenges such as environmental limitations, regulatory concerns, and sustainability issues are critically analyzed. By integrating microbiology with biotechnological innovations, microbial metabolism can be effectively harnessed for large-scale pollution mitigation, offering ecofriendly and cost-effective solutions to address global environmental challenges and promote sustainable industrial practices.}, }
@article {pmid42372060, year = {2026}, author = {Jiang, H and Zhang, M and Khan, RAA and Zhao, J and Hou, J and Liu, T}, title = {Trichoderma enriches Burkholderia via cross-feeding of degradation intermediates to enhance atrazine degradation and alleviate soybean phytotoxicity.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag152}, pmid = {42372060}, issn = {1751-7370}, abstract = {The widespread agricultural use of atrazine threatens soil health, and residual phytotoxicity in corn-soybean rotation systems necessitates sustainable remediation strategies. By leveraging the atrazine-degrading fungus Trichoderma lentiforme HN154, we achieved an 80.3% removal of atrazine (500 mg/kg) in non-sterilized soils from a corn planting system within 14 days, 22.1% higher degradation than in sterilized soil, while concurrently alleviating phytotoxic symptoms in soybean plants. Metagenomic analysis revealed that colonization by T. lentiforme HN154 drove restructuring of microbial networks, enriching the keystone family Burkholderiaceae, which was strongly associated with atrazine catabolism and four key catabolic enzymes (EC 3.5.4.43 (atzB), EC 3.5.1.131 (atzE), EC 3.5.1.54 (atzF), EC 3.5.4.42 (atzC)). Among 23 rhizosphere isolates, the Burkholderia strains Bur-4, Bur-5, and Bur-14 showed the highest atrazine degradation rates (26.3% - 29.4%) within 72 h. A Trichoderma-Burkholderia synthetic consortium further enhanced remediation by boosting plant antioxidant defenses (SOD, POD, CAT) and reducing oxidative damage (MDA). Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h). This study reveals tripartite interactions among exogenous microbial degraders, pollutant metabolites, and indigenous microbiota, offering a strategic foundation for microbiome-guided, precision bioaugmentation to restore soil ecological health and crop resilience.}, }
@article {pmid42372843, year = {2026}, author = {Capuano, N and Giannattasio, A and Impemba, S and Belgiorno, V and Folliero, V and Buonerba, A and Franci, G}, title = {Microplastics as Emerging Viral Vectors: Nexus, Mechanisms, Ecological Implications and Health Risks.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125138}, doi = {10.1016/j.envres.2026.125138}, pmid = {42372843}, issn = {1096-0953}, abstract = {Microplastics (MPs) have emerged as pervasive environmental pollutants with complex implications for ecological and human health. Beyond their chemical toxicity and persistence, MPs act as dynamic microhabitats supporting microbial colonization and viral adsorption. This review provides a comprehensive overview of the physicochemical characteristics, environmental distribution, and degradation pathways of the most common polymeric MPs, including polystyrene, polyethylene, polypropylene, polyvinyl chloride, polyurethane, polyethylene terephthalate, polydimethylsiloxane, and biobased polyesters. Particular attention is given to the virus-microplastic interface, highlighting how MPs serve as vectors that enhance viral persistence, transport, and infectivity. Experimental and metagenomic evidence demonstrates that both enveloped and non-enveloped viruses can adhere to MPs via electrostatic and hydrophobic interactions, often mediated by biofilm and eco-corona formation. These interactions extend viral stability across environmental compartments and can modulate host immune responses, exacerbating infection outcomes. By integrating physicochemical, microbiological, and toxicological perspectives, this review emphasizes that MPs are not inert residues but active ecological interfaces that can reshape viral ecology and increase public-health risks. Future studies combining molecular, environmental, and epidemiological approaches are essential to quantify the real impact of MP-virus interactions on ecosystem balance and infectious-disease dynamics.}, }
@article {pmid42372850, year = {2026}, author = {Gong, X and Zhang, L and Xu, A and Huang, Z and Wang, C and Yang, T and Liang, H and Zhang, M and Zhan, X and Peng, Y and Gao, D}, title = {Root Exudates Recruit Beneficial Microbes to Promote Anammox-Driven Nitrogen Cycling in Wetland.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125149}, doi = {10.1016/j.envres.2026.125149}, pmid = {42372850}, issn = {1096-0953}, abstract = {Anammox bacteria serve as a major biological sink in nitrogen (N) cycling within wetland, yet the hydrophyte root exudates-mediated microbial interplay mechanism that sustain their activity and ecosystem function remain unclear. To address this gap, we established flow-controlled microcosms planted with Iris pseudacorus, combined with [15]N stable isotope tracing and metagenome-assembled genomes (MAGs) analysis. Our findings revealed that root exudates significantly enhanced in-situ anammox rates (rhizosphere: 5.9±2.0 mg N/(m[3]·d), non-rhizosphere: 0.4±0.02 mg N/(m[3]·d), p<0.001), leading to a remarkable enrichment of anammox bacteria in the rhizosphere (6.5×10[7] copies/g dry sludge, p<0.001). We further uncovered a previously overlooked partial denitrification pathway that supplied nitrite, substantially increasing anammox contributions to rhizosphere N removal (16.6±4.1%). Key bioactive components, flavonoids and amino acids, selectively recruited beneficial rhizobacteria affiliated to Pseudomonadota and Bacteroidota. MAGs-based analysis revealed that these microbial taxa encoded pathways for producing essential substrates (nitrite loop) and metabolites (cofactor, biotin) supporting anammox metabolism. The symbiotic interaction facilitated the survival and metabolic activity of anammox bacteria in the oligotrophic rhizosphere habitat. These findings unveil a natural plant-microbiota interaction that effectively enhances the sustainability of N cycling and provide new insights for optimizing nitrogen removal strategies in engineered wetland systems.}, }
@article {pmid42372852, year = {2026}, author = {Wang, Y and Yan, C and Jin, J and Li, Z and Zhou, H and Tang, J and Wang, X and Li, H}, title = {Straw incorporation and strawsphere formation shape the fate of antibiotic-resistant human pathogens in agricultural soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125142}, doi = {10.1016/j.envres.2026.125142}, pmid = {42372852}, issn = {1096-0953}, abstract = {Antibiotic-resistant human pathogens (ARPs) in soil pose a latent threat to public health. However, how ARPs evolve in agricultural soil after straw incorporation remains unclear. This study combined a metagenomic analysis of 230 soil samples from typical straw-incorporated regions in China and controlled microcosm experiments to assess the effects of straw incorporation on soil ARPs. The influence of straw incorporation on ARPs was management practice-dependent. Semi-quantity short (4 cm) straw incorporation significantly decreased the total abundances of ARPs by 17.4%. A redundancy analysis revealed that elevated levels of alkali hydrolyzable nitrogen, available potassium and total organic carbon as well as virus abundance were key factors associated with the reduction in ARPs in straw-incorporated soil. Moreover, scanning electron micrographs revealed that the straw surface developed a coccoid bacterium-dominated biofilm, forming a distinct ecological niche, the strawsphere. A KEGG pathway annotation suggested that lignocellulose-degrading microbes in the strawsphere serve as a potential source of ARP-antagonistic microorganisms. Structural equation models further identified straw fragment length as a critical parameter for the fates of ARPs both in soil and the strawsphere. The study elucidated the critical roles of straw incorporation and the resulting 'strawsphere' in controlling ARPs in agricultural soil.}, }
@article {pmid42372901, year = {2026}, author = {Edwards, M and Sanchez-Ramos, L}, title = {Likelihood ratios enhance clinical interpretation of metagenomic prediction of early-onset neonatal sepsis in preterm premature rupture of membranes (Letter-to-the-Editor).}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2026.06.023}, pmid = {42372901}, issn = {1097-6868}, }
@article {pmid42372926, year = {2026}, author = {Kwon, CY and Choi, YH and Kim, H and Han, K and Jang, D and Hwangbo, H}, title = {Gut microbial signature for frailty discrimination: a metagenomic meta-analysis of 28 independent cohorts.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {113223}, doi = {10.1016/j.exger.2026.113223}, pmid = {42372926}, issn = {1873-6815}, abstract = {Frailty, a clinical syndrome of multisystem decline and homeostatic vulnerability, is a critical public health priority. While the gut microbiome regulates immune and metabolic signaling, current evidence remains fragmented. We performed a metagenomic meta-analysis of 955 individuals from 28 independent cohorts across 24 countries to identify universal microbial signatures and develop a generalizable discriminative model. Frailty was determined using a Proxy Frailty Index based on the deficit accumulation model. Following refinement to isolate signatures from disease-specific dysbiosis, we used Firth's penalized regression for biomarker discovery and validated a Random Forest (RF) model via leave-one-study-out cross-validation. Shannon diversity exhibited a significant and sharp decline during the transition from robust to pre-frail states (p = 0.0006), manifesting at the earliest stages of physiological decline. We identified 16 microbial biomarkers characterized by the progressive attrition of core symbionts, such as Coprococcus eutactus, and the opportunistic expansion of pathobionts, including Enterococcus gallinarum. Sensitivity analysis in a healthy sub-cohort (n = 499) confirmed that these shifts occur independently of chronic clinical diagnoses and their associated confounding effects (p = 0.036). The 16-species RF model, predominantly driven by Collinsella massiliensis, achieved a corrected mean area under the receiver operating characteristic curve of 0.7572 across 5 eligible cohorts. Gut microbial restructuring is a sentinel biological hallmark of frailty that occurs independently of aging-related diseases. This study establishes a microbial signature broadly applicable across European and East Asian populations that serves as a high-fidelity, non-invasive metric for precision geriatric assessment.}, }
@article {pmid42372963, year = {2026}, author = {Cui, Q and Wang, F and Shan, X and Ding, L and Qiu, X and Zhang, B and Li, X and Liang, X and Guo, X}, title = {Biodegradable polylactic acid microplastics affect nutrient cycling during the entire crop growth cycle: Implications for soil ecosystem multifunctionality.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128664}, doi = {10.1016/j.envpol.2026.128664}, pmid = {42372963}, issn = {1873-6424}, abstract = {While microplastics (MPs) have been extensively studied for their effects on soil nutrient cycling, their influence on ecosystem multifunctionality (EMF) across the entire crop growth cycle remains poorly understood. This study systematically investigated the impacts of a model biodegradable MP, polylactic acid (PLA), on soil microbiomes and EMF across different maize incubation periods. Results of 16S rRNA amplicon sequencing and metagenomic analysis revealed that PLA-MPs decreased bacterial community α-diversity, co-occurrence network complexity, and stability throughout the 120-day incubation period. Particularly, PLA-MPs exerted more pronounced effects at early incubation stages (30 and 60 days), and these effects were intensified with increasing PLA-MP concentrations. PLA-MPs suppressed anaerobic carbon fixation (porA, porB, frda) and pyruvate metabolism (ppdk), while promoting fermentation (L-lactate dehydrogenase), nitrogen fixation (nifD, nifH, nifK, anfG), and microbial phosphorus (P) acquisition (phoD, phn cluster). Over the entire incubation period, PLA-MP-induced shifts in nutrient cycling enhanced soil carbon (C) function by 37.6-569%, while decreasing nitrogen (N) and P functions by 8.40-22.4% and 16.8-56.2%, respectively. Path analysis revealed that PLA-MPs altered soil properties and bacterial community diversity, which in turn regulated functional genes and these individual soil functions, thereby reducing EMF by 2.05-27.0% (R[2] = 0.923), with bacterial community diversity as the primary driver of EMF (standardized path coefficient of 0.978). These findings underscore the impacts of PLA-MPs on EMF in the soil-crop system throughout the entire maize growth cycle, advancing the understanding of the agroecological safety of biodegradable MPs.}, }
@article {pmid42373490, year = {2026}, author = {Shen, Y and Zhang, DT and Shi, WX and Ma, CN and Huo, D and Yang, P and Wang, QY and Feng, ZM}, title = {[Epidemiological characteristics of test-negative severe acute respiratory infections during the 2024-2025 surveillance years in Beijing].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {47}, number = {6}, pages = {1114-1119}, doi = {10.3760/cma.j.cn112338-20260104-00004}, pmid = {42373490}, issn = {0254-6450}, support = {2026-2G-30124//Capital's Funds for Health Improvement and Research/ ; BJRID2026-001//Beijing Research Center for Respiratory Infectious Diseases/ ; 20252D01900800//National Science and Technology Major Project of China/ ; }, mesh = {Humans ; Middle Aged ; Adult ; Adolescent ; Child ; Child, Preschool ; *Respiratory Tract Infections/epidemiology/microbiology ; Male ; Female ; Young Adult ; Infant ; Beijing/epidemiology ; Aged ; Infant, Newborn ; High-Throughput Nucleotide Sequencing ; Acute Disease ; }, abstract = {Objective: To analyze the epidemiological characteristics of cases with severe acute respiratory infection (SARI) in Beijing who tested negative for 22 common respiratory pathogens by nucleic acid testing, and to explore the potential pathogen spectrum using metagenomic next-generation sequencing (mNGS). Methods: Data were obtained from the Beijing Acute Respiratory Infectious Disease Surveillance Network. Hospitalized SARI cases from week 40 of 2024 to week 39 of 2025 were included. All cases were tested for 22 common respiratory pathogens using nucleic acid assays. Among those test-negative results, 50 specimens were randomly selected for mNGS analysis. Multivariable logistic regression was performed to identify factors associated with test-negative results. Results: A total of 7 202 SARI cases were included, of whom 4 212 (58.5%) tested negative for all 22 common respiratory pathogens. The proportion of negative results increased with age, with 32.9% (322/978) in children aged 0-5 years, 69.1% (972/1 407) in adults aged 18-59 years, and 65.0% (2 506/3 856) in those aged ≥60 years, the difference was statistically significant (all P<0.001). Multivariable analysis showed that age was independently associated with negative results (18-59 years: aOR=4.62, 95%CI:3.85-5.55; ≥60 years: aOR=4.08, 95%CI:3.49-4.78). Upper respiratory samples were more likely to test negative. Among 48 valid mNGS samples, 32 pathogens were identified. At least one pathogen was detected in 44 cases (93.6%), and multiple infections were common (37 cases, 84.1%). Human herpesvirus 7 (20 cases) was most frequently detected, followed by Stenotrophomonas maltophilia (16 cases), Human herpesvirus (15 cases), and Streptococcus pneumoniae (12 cases). Conclusions: A high proportion of SARI cases in Beijing tested negative for common respiratory pathogens, and age played an important role. mNGS identified predominantly opportunistic pathogens and herpesviruses, and did not detect novel pathogens with clear respiratory significance. These findings indicate that the current SARI surveillance covers the most common respiratory pathogens.}, }
@article {pmid42373646, year = {2026}, author = {Howells, AEG and Robinson, K and Silva, MG and Cook, E and Fifer, L and Boyer, G and Hoehler, T and Shock, EL}, title = {Methanotrophy under extreme alkalinity in a serpentinizing system.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72513-6}, pmid = {42373646}, issn = {2041-1723}, support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; EAR-1515513//National Science Foundation (NSF)/ ; EAR-1949030//National Science Foundation (NSF)/ ; EAR-2149016//National Science Foundation (NSF)/ ; }, abstract = {Serpentinization produces hyperalkaline, H2- and CH4-rich fluids that support microbial life and serve as analogs for ocean worlds such as Enceladus. While methane production in these systems has been well studied, methane consumption-especially under high pH-remains poorly understood. Here, we present isotopic, geochemical, and genomic evidence for hyperalkaliphilic (pH > 11) methanotrophy in the Samail ophiolite of Oman. Using models that account for fluid mixing and gas exsolution, we identify δ[13]CH4 enrichment that cannot be explained by abiotic processes alone. The enrichment of [13]CH4 co-occurs with methanotroph 16S rRNA gene sequences, particularly in fluids formed by mixing CH4-rich, reduced fluids with oxidant-rich waters. Shotgun metagenome sequencing reveals a metagenome-assembled genome affiliated with Methylovulum, encoding a complete methane oxidation pathway, multiple carbon assimilation routes, and Na[+]/H[+] antiporters-adaptations likely enabling growth above pH 11. Our findings highlight the viability of methanotrophy under extreme high pH conditions and provide a framework for interpreting δ[13]CH4 signals in serpentinizing environments on Earth and beyond.}, }
@article {pmid42374042, year = {2026}, author = {Chen, X and Chen, C and Zhang, P and OuYang, X and Ma, H and Chen, W and Li, T and Han, J and Wang, Y and Wang, H and Zhou, Q and Cheng, G and Zhou, W and Yu, Z and Zhou, W and Wang, M and Zeng, S}, title = {Bifidobacterium animalis reshapes the bile acid pool and prevents neonatal jaundice: a clinical microbiome study from correlation to causation.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01057-w}, pmid = {42374042}, issn = {2055-5008}, support = {2024YFC2707700//National Key R&amp;D Program of China, Key Special Project for "Reproductive Health and Maternal and Child Health Security"/ ; 82571963//the National Natural Science Foundation of China/ ; 2025A1515012162//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20250604145739052//Shenzhen Science and Technology Innovation Bureau/ ; Y2024001//the Research Initiation Fund of Longgang District Maternity &amp; Child Healthcare Hospital of Shenzhen City/ ; }, abstract = {Neonatal jaundice (NJ) affects 60-80% of neonates, yet the underlying microbial mechanisms remain elucidated, despite known links between gut dysbiosis and bilirubin and bile acid (BA) metabolism. Through two-stage shotgun metagenomic-metabolomic analysis of 150 fecal samples from 120 neonates, we identified key taxa linked to bile acid (BA) metabolism in moderate-to-severe NJ. Furthermore, multi-omics integration revealed significant interkingdom correlations among gut phages, bacteria, and BAs. Dysbiosis featured enriched Streptococcus and Escherichia, depleted Bifidobacterium animalis, and group-specific phage signatures. In the independent clinical validation cohort, jaundice intervention normalized the dysbiotic profile, demonstrating significant suppression of pathogenic taxa concomitant with restoration of B. animalis abundance. In vitro, B. animalis subsp. lactis Y103-OTU5 remodeled BA via deconjugation. In a phenylhydrazine hydrochloride (PHZ)-induced murine model of hemolytic jaundice, oral administration of isolated B. animalis subsp. lactis Y103-OTU5 significantly attenuated hyperbilirubinemia and hepatic inflammation, likely via Cyp7a1/Cyp7b1-dependent modulation of BA synthesis and detoxification pathways. Structural equation modeling revealed a tripartite regulatory network: phages indirectly modulated BA through bacterial remodeling, while B. animalis directly regulated BA pathways, positioning it as a potential therapeutic candidate for hemolysis-associated neonatal jaundice. Collectively, these findings reveal a gut phage-bacteria-BA network in NJ, highlighting B. animalis as a therapeutic candidate with dual modulation of BA metabolism and phage-bacteria interactions.}, }
@article {pmid42365131, year = {2026}, author = {Zhu, S and Yang, Z and Zhao, H and Ma, Y and Chen, K and Qi, D}, title = {Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02823-1}, pmid = {42365131}, issn = {1432-184X}, support = {Qing[2025]TG04//Demonstration of Techniques for Wetland Protection, Restoration, and Carbon Sink Capacity Enhancement in the Qinghai Lake Basin - Qinghai Provincial Finance Budget/ ; }, abstract = {The alpine wetlands of the Qinghai-Tibet Plateau are confronting significant ecological challenges due to drastic shifts in precipitation patterns. Elucidating the response mechanisms of rhizosphere microbial communities in wetland plants to precipitation events is critical to understanding ecosystem resilience. In this study, sandy wetlands at Niaodao and riverine wetlands at Haergai in the Qinghai Lake basin were selected as study sites. Using Poa alpigena rhizosphere and non-rhizosphere soils as the research subjects, metagenomic DNA sequencing combined with environmental factor analysis was employed to compare the microbial community responses before and after a single pulse precipitation event. The results showed that Proteobacteria and Actinobacteria were the dominant phyla in both wetland types (combined relative abundance > 70%). Rainfall induced a differentiated restructuring of soil microbial community composition across different habitats. In rhizosphere soils, rainfall significantly reduced microbial alpha diversity. Co-occurrence network analysis revealed that the rhizosphere community shifted from a competition-coexistence pattern before rainfall to a cooperative adaptation pattern after rainfall, with significant increases in modular cohesion and the proportion of positive correlations. Metagenomic analysis indicated that the number of differentially abundant metabolic pathways in soil microorganisms increased markedly after rainfall, rising to 46 and 40 pathways in the rhizosphere and non-rhizosphere, respectively (compared to 3 and 31 before rainfall), indicating a shift from carbon reserve metabolism to energy-producing metabolism. Total carbon and water content were identified as the core environmental factors jointly regulating community assembly. This study reveals the mechanism by which regional background, precipitation disturbance, and the rhizosphere effect synergistically drive the succession of microbial communities in alpine wetlands, providing a new paradigm for understanding ecosystem adaptation to climate change.}, }
@article {pmid42365389, year = {2026}, author = {Park, JH and Lee, KL and Lee, YM and Choi, JY and Heo, YR and Oh, SM and Lee, D and Kim, S and Lee, HW and Poon, CTC and Hong, WH and Moon, HB and Mok, S and Lee, CY and Kim, MA and Yuen, AHL and Seok, SH and Kim, BY and Kim, SW}, title = {From traumatic oral fibroma to fatal pneumonia: a multidisciplinary postmortem investigation in a long-term monitored Indo-Pacific bottlenose dolphin (Tursiops aduncus).}, journal = {BMC zoology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40850-026-00277-z}, pmid = {42365389}, issn = {2056-3132}, support = {No. RS-2025-25432543//National Research Foundation of Korea/ ; No. RS-2022-NR072403//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: An Indo-Pacific bottlenose dolphin (Tursiops aduncus) in the coastal waters of Jeju Island, Republic of Korea, exhibited an oral mass and mandibular deformity over a documented 6-year period, including 3 years of intensive longitudinal monitoring by our research team. A multidisciplinary approach combining imaging, pathology, microbiology, and omics analyses was used to assess the dolphin.<br><br>RESULTS: Post-mortem computed tomography confirmed a mandibular fracture at the oral mass site. Histopathological examination of the oral mass revealed prominent fibroblast proliferation and collagen deposition. Fibropapillomas and desmoid tumors were excluded based on viral detection assays and &#x3b2;-catenin accumulation analysis, supporting a diagnosis of trauma-induced fibroma. Transcriptomic analysis of the tumor tissues identified highly expressed genes associated with extracellular matrix remodeling, myofibroblast activation, and epithelial differentiation, supporting a reactive fibrotic rather than malignant phenotype. Gross necropsy revealed multiple suppurative pulmonary lesions, abundant foamy fluid within the respiratory tract, and diatoms within the pulmonary tissue. Metagenomic sequencing revealed a polymicrobial infection, with Parvimonas micra as the predominant organism. Collectively, these findings are most consistent with aspiration pneumonia, with severe secondary pulmonary infection considered a major contributor to death. In addition, analysis of halogenated organic contaminants revealed accumulation levels consistent with those typically observed in aged individuals, and no evidence was identified indicating a direct causal role in the terminal disease process.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first study to characterize the pathological features and proposed pathogenic mechanism of traumatic fibroma in a marine mammal, and the first confirmed case of pulmonary abscessation associated with Parvimonas micra infection in this taxonomic group. Overall, these findings provide valuable baseline data for the health monitoring and conservation of marine mammal populations.}, }
@article {pmid42365784, year = {2026}, author = {Chen, Q and Zheng, J and Zeng, L and You, Y and Zhuang, X and Meng, F and Wang, L}, title = {A 1-year-old boy with near-complete tracheobronchial obstruction from endobronchial tuberculosis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117533}, doi = {10.1016/j.diagmicrobio.2026.117533}, pmid = {42365784}, issn = {1879-0070}, abstract = {A one-year-old boy was referred to our respiratory department for further evaluation of obstructing endobronchial lesions. The lesions were detected on chest computed tomography (CT) performed at another hospital after the patient presented with cough and worsening wheezing. Physical examination revealed tachypnea and diminished breath sounds bilaterally without rales. The patient was receiving supplemental oxygen. Notably, his medical history was significant for an admission at 21 days of age for persistent cough, right upper lung atelectasis, and sputum analysis that revealed Bordetella pertussis, Acinetobacter baumannii, and rhinovirus. Despite advanced testing, including bronchoalveolar lavage acid-fast staining, tuberculin skin testing, and metagenomic next-generation sequencing, the diagnosis was initially missed and was ultimately established only after multi-institutional pathology review with deeper histologic recuts identifying a rare acid-fast bacillus. This case demonstrates a rare but high-risk presentation of pediatric tuberculosis: near-complete tracheobronchial obstruction due to endobronchial tuberculosis (EBTB) in an infant.}, }
@article {pmid42365883, year = {2026}, author = {Wu, W and Wang, W and Liu, H and Ganigué, R and Zhang, J and Liu, B and Liu, G and Wang, A}, title = {Multi-omics analysis reveals propanol is superior electron donor for odd-chain elongation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135265}, doi = {10.1016/j.biortech.2026.135265}, pmid = {42365883}, issn = {1873-2976}, abstract = {Chain elongation from organic wastes has primarily targeted even-chain carboxylates, leaving the production of equally valuable odd-chain compounds underexplored. Propanol, abundant in industrial wastewater, offers a promising electron donor to address this gap, yet the underlying metabolic pathways and microbial consortia driving efficient odd-chain elongation remain unclear. The present study systematically investigated the characteristics of odd-chain elongation. The results demonstrated that the propanol-acetate (PA) group, using propanol as the electron donor and acetate as the electron acceptor, achieved an excellent selectivity of 84% for n-valerate and n-heptanoate, compared with 55% in the conventional ethanol-propionate (EP) group. Multi-omics analysis guided the specialized metabolic route construction, showing that electrons from propanol oxidation are channeled to drive acetyl-CoA synthesis from acetate and activate the reverse β-oxidation pathway. The propionate generated from propanol oxidation serves as the initial three-carbon backbone for odd-chain carboxylates generation. The keystone microorganisms for propanol-based odd-chain elongation are suggested to be Clostridium kluyveri and Oscillibacter valericigenes. Techno-economic analysis confirmed the metabolic selectivity inherent to the PA group confers superior economic resilience, yielding higher profitability than the EP group. This work positions propanol-based chain elongation as an efficient and economically viable strategy for the targeted production of valuable odd-chain carboxylates from propanol-containing wastewater.}, }
@article {pmid42366019, year = {2026}, author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J}, title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70367}, doi = {10.1111/1462-2920.70367}, pmid = {42366019}, issn = {1462-2920}, support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation &amp; purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; }, abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.}, }
@article {pmid42050399, year = {2026}, author = {Li, CJ and Zhao, Y and Tang, M and Chu, X and Zhan, PC and Jiang, XW and Tian, JY and Hai, X and Lu, YF and Yang, LL and Zhi, XY}, title = {Comparative population genomics reveal the genetic features associated with the plant host adaptation of Clostridium butyricum.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42050399}, issn = {1471-2164}, support = {32560005//National Natural Science Foundation of China/ ; }, mesh = {*Clostridium butyricum/genetics/physiology/classification/isolation &amp; purification ; *Host Adaptation/genetics ; Phylogeny ; Genetic Variation ; *Metagenomics ; Genomics ; Genetics, Population ; Genome, Bacterial ; }, abstract = {BACKGROUND: Plants are increasingly considered as secondary reservoirs for enterics. However, little is known about their population dynamics and the genetic mechanisms during plant colonization. Clostridium butyricum is a gut symbiont of humans and animals and, rarely, a pathogen. Here, 55 strains of C. butyricum isolated from the roots of Paris polyphylla var. yunnanensis provided a new model for understanding plant-host adaptation of enterics. RESULTS: These strains, along with 67 non-endophytic C. butyricum strains (nECB), were examined for population structure, revealing that they diverged into four well-defined lineages, whereas endophytic C. butyricum strains (ECB) from different sources were scattered across two lineages. The population diversity estimate confirmed the genetic distinctiveness among four lineages and uncovered distinct evolutionary processes that might drive the divergence of ECB-related lineages. Frequent gene flow between ECB and nECB suggested that plant-host colonization does not lead to genetic isolation. Extensive recombinations within and between lineages demonstrated the major role of recombination in shaping population genetic structure and diversification in C. butyricum. Additionally, the endophytic variance analysis identified several genes associated with CRISPR, defense systems, and metabolism that contribute to endophytic colonization by C. butyricum. CONCLUSION: This study provides novel insights into the ongoing adaptation of C. butyricum to plant hosts and illuminates the genetic mechanisms underlying this host transition. By elucidating population structure, gene flow, recombination patterns, and candidate adaptive genes, our findings advance the understanding of host-associated evolution in enteric bacteria.}, }
@article {pmid42363297, year = {2026}, author = {Wang, Y and Liu, M and Dogra, SK and Vidal, K and Godin, JP and Darwish, N and Wei, X and Reymond, L and Li, Q and Dong, J and Vyllioti, AT and Bettler, J and Kennedy, E and Wang, K and Zhai, Q and O'Regan, J and Samuel, TM and Cai, W}, title = {Effects of an infant formula containing a whey protein concentrate on feeding tolerance and markers of intestinal immune defense in Chinese infants.}, journal = {BMC nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40795-026-01395-0}, pmid = {42363297}, issn = {2055-0928}, abstract = {BACKGROUND: Human milk (HM) bioactive components can have immune modulatory functions, impact the gut microbiome, and may result in functional benefits when added to infant formula (IF). In this single-arm, prospective, intervention study, we tested the effectiveness of an IF with a whey protein concentrate co-enriched in α-lactalbumin, milk fat globule membrane (MFGM), and Sn-2 palmitate resulting in protein and lipid profiles observed in HM. The outcomes tested were feeding tolerance, Bifidobacteria abundance, and intestinal and immune health of Chinese infants.<br><br>METHODS: Predominantly formula-fed (FF) and breastfed (BF) infants were enrolled between 3 and 28&#xa0;days and assigned to the FF (N&#x2009;=&#x2009;60) or BF (N&#x2009;=&#x2009;60) group, per their feeding practice, for 6&#xa0;weeks. The primary endpoint was Infant Gastrointestinal Symptom Questionnaire (IGSQ) index score assessed using a validated IGSQ-13 questionnaire after 6&#xa0;weeks of intervention; non-inferiority of FF vs BF was tested. Secondary endpoints included fecal Bifidobacteria abundance assessed using shotgun metagenomics sequencing; fecal short chain fatty acids (SCFAs) analyzed by ultra-performance liquid chromatography-tandem mass spectrometry; fecal markers of immune response, inflammation, intestinal barrier integrity (secretory immunoglobulin A sIgA), cytokines, calprotectin, &#x3b1;1 antitrypsin, lipocalin-2) assessed using enzyme-linked immunosorbent assay; stool consistency assessed using gastrointestinal (GI) diary; anthropometric assessments; quality of life; physician reported adverse events; and use of medications.<br><br>RESULTS: Good GI tolerance was observed in both groups at V2 (mean&#x2009;&#xb1;&#x2009;SD IGSQ score FF: 19.9&#x2009;&#xb1;&#x2009;7.4; BF: 16.8&#x2009;&#xb1;&#x2009;4.2); difference of means 1.35 [95% CI: -1.312, 4.012]). After 6&#xa0;weeks, Bifidobacterium genus relative abundance was not significantly different between the groups. Total SCFAs were significantly higher (p&#x2009;<&#x2009;0.05) in the FF versus BF group, driven by increased levels of valeric and propanoic acids (p&#x2009;<&#x2009;0.05 for both). The IGSQ domain scores, stool consistency, fecal markers of immunity, inflammation, and intestinal barrier integrity (except lipocalin-2 which was significantly higher in BF vs FF), anthropometric Z-scores, common illnesses, antibiotic use, and adverse events were not significantly different between groups at week 6.<br><br>CONCLUSIONS: Our results support the effectiveness of this tested infant formula in supporting good GI tolerance, growth, specific intestinal and immune health markers, and Bifidobacteria abundance similar to that of the BF group.<br><br>TRIAL REGISTRATION: NCT04880083 (2021-05-06).}, }
@article {pmid42363646, year = {2026}, author = {Torres Sánchez, ED and Martínez Nieto, M and González Alvarez, GE and Rodríguez Montaño, R and Alarcón-Sánchez, MA and Heboyan, A and Gutiérrez Maldonado, AF and Varela Hernández, JJ and Lomelí Martínez, SM}, title = {Helicobacter pylori in oral and gastric pathologies: a narrative review of potential bidirectional pathogenic interactions.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2533434}, doi = {10.1080/07853890.2025.2533434}, pmid = {42363646}, issn = {1365-2060}, mesh = {Humans ; *Helicobacter pylori/pathogenicity/isolation &amp; purification ; *Helicobacter Infections/microbiology/complications/immunology ; *Periodontitis/microbiology ; *Mouth/microbiology ; *Gastritis/microbiology ; }, abstract = {The association between periodontal diseases and gastrointestinal conditions, particularly those associated with Helicobacter pylori and systemic inflammation, has garnered increased scientific attention because of its clinical and public health implications. These diseases, which affect both the oral cavity and the digestive system, have shared pathophysiological mechanisms that link inflammatory processes and bacterial transmission pathways. The possible presence of H. pylori in the oral cavity has sparked interest regarding its potential colonization of periodontal tissues and acting as an extragastric reservoir. This narrative review describes H. pylori's possible survival mechanisms in this oral microenvironment and its clinical significance in the interaction between oral and gastric conditions. We propose that periodontitis might promote gastric H. pylori infection by stimulating systemic inflammation, and oral colonization might serve as a reservoir for gastric reinfection. Future studies may involve advanced technologies such as metagenomics and proteomics. The eradication of H. pylori in the oral cavity may provide a strategy to prevent gastric reinfection. The findings described herein highlight the importance of this bacterium in two different pathologies sharing a close anatomical relationship.}, }
@article {pmid42363687, year = {2026}, author = {Redmile, C and Sutherland, D and Devane, M and Taylor, W and Busby, I and Glackin, A and Gilpin, B and Chambers, T}, title = {The Establishment of an Indigenous-Led Drinking Water Monitoring Program Leveraging qPCR and Metagenomics Testing in New Zealand.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {7}, pages = {e70471}, doi = {10.1002/wer.70471}, pmid = {42363687}, issn = {1554-7531}, support = {ESR2411//Ministry of Business, Innovation and Employment/ ; TN/PWC/19/UoOWTC//Ministry of Business, Innovation and Employment/ ; }, mesh = {New Zealand ; *Drinking Water/microbiology/analysis ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; Water Quality ; Water Microbiology ; Maori People ; }, abstract = {An Indigenous-led monitoring program was established in partnership with the South Island Māori (Indigenous population of New Zealand [NZ]) tribe of NZ to understand and improve local drinking water safety. The aims of the project were to: (1) establish an Indigenous-led drinking water monitoring program; (2) utilize a full suite of monitoring tools to understand source water hazards and treatment efficacy; and (3) test the effectiveness of advanced water sampling techniques in Indigenous communities. Advanced sampling techniques were used for fecal source tracking to identify existing public health hazards and to provide assurance that any remedial interventions were effective. The program trained a total of 27 individuals from 16 different Indigenous communities in water quality sampling and helped to identify and address six microbial water quality issues. This project underscored the benefits of engaging Indigenous Peoples in governance and decision-making processes and in alleviating systemic barriers that prevent Indigenous communities from realizing safe water quality and sufficient water infrastructure.}, }
@article {pmid42363849, year = {2026}, author = {Wang, X and Wang, H and Wang, X and Zhang, M and Cui, Y and Liao, H and Yang, J and Zou, Y and Jiang, L and Li, X and Yang, Y}, title = {Metagenome-assembled genome of Oscillospiraceae bacterium strain ZGZL, an anaerobic chloromethane-degrading bacterium enriched from rice paddy soil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0028726}, doi = {10.1128/mra.00287-26}, pmid = {42363849}, issn = {2576-098X}, abstract = {Oscillospiraceae sp. strain ZGZL is an anaerobic bacterium capable of degrading chloromethane. Here, we report the metagenome-assembled genome sequence of strain ZGZL, which has a genome size of 2.04 Mb and a G+C content of 52.56%.}, }
@article {pmid42363855, year = {2026}, author = {Pham, EQ and Gaulke, CA and Eisen, JA and Dandekar, S}, title = {Metagenome-assembled genomes recovered from the gut microbiomes of simian immunodeficiency virus-infected rhesus macaques.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0042826}, doi = {10.1128/mra.00428-26}, pmid = {42363855}, issn = {2576-098X}, abstract = {Rhesus macaques are widely used model organisms for studying human biology, yet relatively few metagenome-assembled genomes (MAGs) are available from their microbiome. Here, we report 159 MAGs recovered from simian immunodeficiency virus-infected macaques, including those treated either with antiretroviral therapy or 10-hydroxystearic acid.}, }
@article {pmid42364055, year = {2026}, author = {Xu, Q and Sun, L and Han, X and Zhang, Q and Jiang, W and Zhu, S}, title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay in multiple type 2 diabetes cohorts.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42364055}, issn = {1869-1889}, abstract = {The role of the gut microbiome in type 2 diabetes (T2D) remains incompletely defined, particularly across microbial kingdoms and diverse populations. Here, we conducted a meta-analysis of 3,857 fecal metagenomes from six international cohorts, profiling bacteria, fungi, archaea, and viruses. Using supervised machine-learning models trained on harmonized multi-kingdom profiles with cross-cohort validation, we identified conserved alterations in T2D, characterized by reduced bacterial and viral diversity and increased fungal and archaeal diversity. A cross-kingdom panel of 33 microbial markers derived from these models achieved robust diagnostic performance (AUR-OC=0.82), outperforming single-kingdom models. Notably, Saccharomyces cerevisiae was consistently depleted in T2D and inversely correlated with glycemic indices. In mice, oral S. cerevisiae supplementation improved glucose tolerance and insulin sensitivity while reducing the abundance of Eggerthella lenta and Klebsiella pneumoniae, bacterial taxa previously linked to adverse metabolic and inflammatory phenotypes. Together, our findings highlight the diagnostic value and mechanistic relevance of multi-kingdom microbial signatures in T2D and position S. cerevisiae as a potential fungal probiotic candidate for metabolic intervention.}, }
@article {pmid42364169, year = {2026}, author = {Pan, P and Zhou, NY}, title = {Metabolic interactions enable aerobic degradation of the environmental pollutant BDE-47.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag163}, pmid = {42364169}, issn = {1751-7370}, abstract = {As a prevalent congener of polybrominated diphenyl ethers (PBDEs), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) poses significant environmental and health risks due to its persistence and bioaccumulation. However, the limited understanding of the microbial degradation mechanism of BDE-47 has hindered the development of effective bioremediation strategies. Here, we decipher an aerobic catabolic pathway of BDE-47 mediated by metabolic relay within a synthetic consortium composed of two environmental isolates, Rhizorhabdus wittichii YL-JM2C and Cupriavidus necator JMP134. Bioaugmentation with this consortium achieved complete removal of BDE-47 in real wastewater samples. The molecular basis underlying this cooperative degradation was elucidated through the heterologous expression and functional characterization of key enzymes involved. Namely, the dioxygenase TcsAaAb from strain YL-JM2C catalyzed the initial conversion of BDE-47 into 2,4-dibromophenol (2,4-DBP) and 3,5-dibromocatechol (3,5-DBC). As a dead-end intermediate in strain YL-JM2C, the former (2,4-DBP) was subsequently transformed into the latter (3,5-DBC) by the hydroxylase TfdB from strain JMP134. The resulting 3,5-DBC was catabolized through the downstream ortho-cleavage pathway present in both strains. These key enzymes for BDE-47 degradation coexist across diverse environments, including soil, seawater, and marine sediments. Global marine metagenomic profiling revealed a significant enrichment of these catabolic signatures in the Mariana Trench, implying that microorganisms in the hadal zone possess the genetic potential for PBDE catabolism. This study unveils previously unrecognized aerobic catabolic mechanisms for BDE-47 within natural ecosystems, offering promising bioremediation strategies for PBDE-contaminated environments.}, }
@article {pmid42364365, year = {2026}, author = {Manning, VA and Moore, PA and Medina, AR and Trippe, KM}, title = {Genome-resolved metagenomics of an acid-tolerant nitrifying biofilm suggests cooperative nitrogen cycling at low pH.}, journal = {The Science of the total environment}, volume = {1046}, number = {}, pages = {181954}, doi = {10.1016/j.scitotenv.2026.181954}, pmid = {42364365}, issn = {1879-1026}, abstract = {Ammonia emissions from animal feeding operations are a major source of nitrogen loss and environmental pollution. Nitrifying bacteria used within ammonia scrubbers offers a promising strategy to recover nitrogen for fertilizer; however, the acidic environment within air scrubbers generally inhibits nitrification and sustained nitrification at low pH remains poorly understood. Here, we present a genome-resolved analysis of an acid-tolerant nitrifying community (ATNC) enriched from a laboratory bioreactor operating at pH values between 4 and 4.6 that was previously shown to support nitrification. Long-read metagenomic sequencing yielded 12 high-quality metagenome-assembled genomes accounting for 94.7% of community abundance, including four phylogenetically distinct Nitrospira representing both comammox and canonical nitrite-oxidizing lineages, alongside heterotrophic species of Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and a filamentous Ktedonobacterales strain. Genomic reconstruction suggested niche partitioning in nitrogen cycling, with comammox Nitrospira encoding the capacity for complete nitrification and Rhodanobacteraceae harboring genes associated with denitrification. Acid tolerance and biofilm persistence were associated with diverse ion-transport systems, alternative respiratory complexes, extracellular polymeric substance biosynthesis, and expanded repertoires of secreted proteases and carbohydrate-active enzymes that facilitate matrix turnover and carbon scavenging. Within the biofilm, Chloroflexi likely contribute structural scaffolding, while heterotrophs appear to be adapted for extracellular organic matter turnover and to act as metabolic partners. Together, these findings suggest that metabolic cooperation, functional redundancy, and biofilm-mediated resource sharing may support nitrification under acidic conditions. This work provides genome-resolved insight into the microbial processes potentially underpinning nitrification-enhanced ammonia capture and identifies candidate genomic features relevant to optimizing nitrogen recovery while minimizing denitrification-driven losses in engineered systems.}, }
@article {pmid42364424, year = {2026}, author = {Chambers, LM and Spakowicz, D and Chalif, J and O'Connor, R and Kistenfeger, Q and Mehra, Y and Mohssen, M and Abdeen, C and Haight, P and Nagel, C and Neff, R and Cohn, D and Copeland, LJ and Backes, F and Cosgrove, C and Hays, J and Dravillas, C and McLaughlin, E and O'Malley, D}, title = {PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy.}, journal = {Gynecologic oncology}, volume = {211}, number = {}, pages = {74-78}, doi = {10.1016/j.ygyno.2026.06.016}, pmid = {42364424}, issn = {1095-6859}, abstract = {BACKGROUND: PRO-PLATINUM evaluates whether a 5-strain probiotic formulation can favorably modulate the gut microbiome during platinum-based chemotherapy in ovarian cancer (OC), while assessing feasibility, safety, and translational correlates of response and toxicity.<br><br>PATIENTS AND METHODS: PRO-PLATINUM is an IRB-approved, randomized, double-blind, placebo-controlled trial enrolling 124 patients with stage II-IV or platinum-sensitive recurrent high-grade OC receiving platinum-based chemotherapy. The study opened to enrollment in February 2026. Participants are randomized 1:1 to a 5-strain probiotic (WBF-038) or placebo, stratified by newly diagnosed advanced versus recurrent disease. The intervention contains inulin and five microbial strains: Akkermansia muciniphila, Anaerobutyricum hallii, Clostridium beijerinckii, Clostridium butyricum, and Bifidobacterium infantis, and is administered orally twice daily beginning within seven days of cycle 1 and continuing through seven days after the completion of cycle 6. Eligible patients must have ECOG performance status 0-2, adequate organ function, and no major probiotic-related contraindications. Stool, blood, and vaginal samples are collected at baseline, cycle 3, and cycle 6; tumor tissue is collected at surgery when available. The primary endpoint is change in gut microbiome composition by whole-genome metagenomic sequencing. Secondary endpoints include intervention adherence, biospecimen feasibility, recurrence-free survival, and overall survival. Exploratory endpoints include toxicity, postoperative infections, stool consistency, diet, medication and antibiotic exposure, quality of life, symptom burden, serum metabolomic and immune profiling, vaginal and tumor microbiome composition, and associations between microbial features and clinical outcomes.<br><br>CONCLUSIONS: PRO-PLATINUM will evaluate treatment feasibility and safety and generate prospective translational data to inform future microbiome-directed strategies to improve treatment tolerance, quality of life, and outcomes in OC patients.}, }
@article {pmid42364687, year = {2026}, author = {Sun, J and Han, X and Sun, X and Qin, H and Yang, D and Shangguan, M and Lu, J and Li, H and Li, Y and Bao, M}, title = {Geochemical and Microbial Functional Responses of Surface Soil to Simulated Low-Concentration CO2 Leakage from Geological Storage.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125132}, doi = {10.1016/j.envres.2026.125132}, pmid = {42364687}, issn = {1096-0953}, abstract = {Geological CO2 storage may pose environmental risks if leaked CO2 migrates into near-surface soils. To evaluate early surface-soil responses to low-concentration CO2 exposure, a 42-day aerated soil microcosm experiment was conducted using a control group and two CO2 treatment levels of 2,000 and 10,000 ppm. Soil physicochemical properties, dissolved cations, metal fractions, enzyme activities, bacterial community composition, and metagenomic functional profiles were analyzed. Sustained CO2 exposure increased electrical conductivity and HCO3[-] concentrations, whereas soil pH remained within a narrow weakly alkaline range. Sequential extraction showed limited redistribution of selected metals among operationally defined fractions, but no evidence of extensive metal mobilization was observed. Among microbial indicators, FDA hydrolase activity responded significantly to CO2 exposure, whereas microbial community structure, alpha diversity, and overall KEGG and CAZy functional profiles remained largely stable. Representative carbon- and nitrogen-cycling genes were influenced mainly by incubation time rather than CO2 concentration. Under the tested short-term, low-concentration, aerated microcosm conditions, the soil system exhibited considerable buffering capacity and resistance to CO2 exposure. The observed effects were mainly expressed as minor changes in soil solution chemistry and selected functional indicators rather than pronounced geochemical deterioration or microbial community restructuring. These findings provide experimental evidence and insights into the geochemical buffering capacity and microbial response mechanisms of surface soil systems under potential leakage scenarios of underground CO2 storage. The findings offer scientific references for environmental risk assessment of CO2 geological sequestration and the selection and interpretation of sensitive monitoring indicators.}, }
@article {pmid42364737, year = {2026}, author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M}, title = {The Lung Microbiome in Hematopoietic Stem Cell Transplantation: Immune Interactions, Clinical Consequences, and Emerging Interventions.}, journal = {Respiratory medicine}, volume = {}, number = {}, pages = {109004}, doi = {10.1016/j.rmed.2026.109004}, pmid = {42364737}, issn = {1532-3064}, abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.}, }
@article {pmid42364789, year = {2026}, author = {DiSilvestro, AN and Wesolowski, LT and Williams, BD and Warren, LK and Athrey, G and White-Springer, SH}, title = {Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses.}, journal = {Journal of equine veterinary science}, volume = {}, number = {}, pages = {106071}, doi = {10.1016/j.jevs.2026.106071}, pmid = {42364789}, issn = {0737-0806}, abstract = {BACKGROUND: Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation.<br><br>AIMS/OBJECTIVES: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate.<br><br>METHODS: Quarter Horses (mean&#xb1;SD 16&#xb1;1mo; 337&#xb1;30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators were quantified on d0, d21, and surrounding a 2-h submaximal exercise test (SET) on d22.<br><br>RESULTS: On d21, CON horses had greater Lactobacillaceae (&#x223c;5.7% vs. &#x223c;2.4% in STARCH), while STARCH had greater Lachnospiraceae (&#x223c;38% vs. &#x223c;32% in CON) but diet alone did not impact inflammatory markers. On d22, CRP increased at 24h post-SET in all horses (P<0.0001). By 48h, CRP returned to pre-SET in STARCH but remained elevated in CON (P=0.0005), resulting in greater CRP in CON than STARCH at 48h (P=0.02). TNF&#x3b1; increased from pre-SET to 1h in STARCH horses (P=0.02), then returned to pre by 6h. In CON horses, TNF&#x3b1; increased at 24h (P=0.04) and remained elevated at 48h (P=0.0005). Throughout the SET, CON had greater IL-10 than STARCH horses (P=0.005). SAA, IL-4, IL-8, and vascular endothelial growth factor (VEGF)-A were differentially impacted by the SET but were unaffected by diet.<br><br>CONCLUSION: Contrary to our hypothesis, fiber-fed horses appeared to elicit a more robust acute inflammatory response to exercise than starch-fed horses despite an altered gastrointestinal microbiome.}, }
@article {pmid42364824, year = {2026}, author = {Zhang, H and Xie, G and Jiang, L and Li, M and Ding, J and Mei, C and Xiong, X}, title = {Effects of different function-oriented hydrochars on anaerobic digestion of hydrothermal wastewater: Focusing on microbial community function and organic degradation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135266}, doi = {10.1016/j.biortech.2026.135266}, pmid = {42364824}, issn = {1873-2976}, abstract = {To elucidate the coupling relationships among hydrochar characteristics, microbial responses, and organic matter removal during anaerobic digestion of hydrothermal treatment wastewater (HTTWW-AD), raw hydrochar (HC), alkali-modified hydrochar (AHC), and iron-modified hydrochar (IHC) were prepared. Excessive microbial anabolic metabolism and limited hydrolysis-acidification efficiency were identified as the main causes of the low methane yield in HTTWW-AD. HC, AHC, and IHC increased methane yield by 115.97%, 148.25%, and 135.42%, respectively, and the methane content also increased by 9.86% - 12.50%. Metagenomic analysis revealed that microorganisms in the control (CK) system were under higher stress, whereas hydrochar addition promoted the enrichment of hydrolytic and acidogenic bacteria (HAB) and alleviated microbial stress. AHC further enriched Methanothrix and Methanobacterium, thereby enhancing both acetoclastic and hydrogenotrophic methanogenesis. The enhanced reductive methanogenesis was likely associated with its high electron-donating capacity (EDC). IHC enriched exoelectrogenic HAB, suggesting that Fe/N-related active sites may facilitate extracellular electron transfer. Gas chromatography-mass spectrometry analysis showed that HC favored the removal of ketones, N-containing heterocycles, and alcohols, whereas AHC was more effective for acids, N-containing heterocycles, and alcohols. IHC promoted the removal of diverse organic compounds, particularly ketones, phenols, and esters. These differences were associated with the enrichment of potential degraders (Hydrogenophaga, Sphaerochaeta, Mesotoga, Bacteroides, and Paludibacter), possible adsorption at surface-active sites, and Fe(III)/Fe(II)-cycle-mediated redox activation. Overall, hydrochars effectively promoted hydrolysis-acidification during HTTWW-AD. Hydrochars enriched with electron-donating functional groups favored methanogenic conversion, whereas Fe/N-related active sites were more beneficial for the removal of recalcitrant organic compounds.}, }
@article {pmid41073888, year = {2025}, author = {Michel, A and Leoz, M and Nesi, N and Petat, H and Ar Gouilh, M and Charbonnier Le Clezio, C and Marguet, C and Hassel, C and Plantier, JC}, title = {Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {908}, pmid = {41073888}, issn = {1471-2164}, mesh = {*Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Fungi/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification ; *Respiratory System/microbiology ; *RNA/isolation &amp; purification ; }, abstract = {BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits—one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)—to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p < 0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.}, }
@article {pmid42350828, year = {2026}, author = {Botta, A and Messina, C}, title = {Hantavirus infection: Neurologic manifestations should not be overlooked.}, journal = {Journal of neurovirology}, volume = {32}, number = {4}, pages = {}, pmid = {42350828}, issn = {1538-2443}, mesh = {Humans ; *Orthohantavirus/pathogenicity ; *Hemorrhagic Fever with Renal Syndrome/virology/immunology/diagnostic imaging/complications/pathology ; *Hantavirus Infections/virology/complications ; Blood-Brain Barrier/virology/immunology/diagnostic imaging ; *Hantavirus Pulmonary Syndrome/virology/immunology/diagnostic imaging ; }, abstract = {Hantavirus infection is primarily associated with hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with predominant renal and pulmonary involvement. However, neurological manifestations affecting both the central nervous system (CNS) and peripheral nervous system (PNS) are increasingly recognized. We conducted a narrative review of the literature to summarize the current evidence regarding hantavirus-associated neurological involvement. Reported CNS manifestations included encephalitis, encephalopathy, seizures, meningitis, neurocognitive alterations, posterior reversible encephalopathy syndrome, transverse myelitis, and cerebral hemorrhage. PNS involvement appeared less frequent and included Guillain-Barré syndrome, cranial nerve palsies, neuropathic pain, and sensory disturbances. Neuroimaging findings were heterogeneous, while cerebrospinal fluid analysis often demonstrated nonspecific inflammatory changes. Advanced molecular techniques such as metagenomic next-generation sequencing may improve diagnostic sensitivity, particularly in immunocompromised patients. Current evidence suggests that neurological involvement may result from endothelial dysfunction, neuroinflammation, immune-mediated injury, blood-brain barrier disruption, and, in selected cases, direct viral neuroinvasion. Greater clinical awareness is needed to improve recognition of neurological complications during hantavirus infection. Further prospective studies are required to better define the epidemiology, pathogenesis, and optimal diagnostic approaches of hantavirus-associated neurological disease.}, }
@article {pmid42351266, year = {2026}, author = {Chen, T and Xiao, J and Li, S and Peng, R and Xu, Y and Zhuang, Y and Zhao, X and Sha, M and Wang, J and Ma, J and Wang, W and Gao, J and Ma, M and Li, S and Cao, Z and Liu, S}, title = {Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02446-1}, pmid = {42351266}, issn = {2049-2618}, abstract = {BACKGROUND: Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.<br><br>RESULTS: Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84&#xa0;days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.<br><br>CONCLUSIONS: In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.}, }
@article {pmid42351291, year = {2026}, author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y}, title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02448-z}, pmid = {42351291}, issn = {2049-2618}, abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.<br><br>RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.<br><br>CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.}, }
@article {pmid42351509, year = {2026}, author = {Wang, M}, title = {Nanopore Sequencing in Mycobacterial Diagnostics: Clinical and Laboratory Roles of mNGS and tNGS.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/diagnostics16121850}, pmid = {42351509}, issn = {2075-4418}, support = {No. 20220919Y060//Hangzhou Science and Technology Commission/ ; }, abstract = {Background/Objectives: Nanopore sequencing is increasingly used in mycobacterial diagnostics, where clinical microbiologists and diagnostic laboratories must decide when broad metagenomic next-generation sequencing (mNGS) or focused targeted next-generation sequencing (tNGS) is most appropriate. This review examined reported clinical and laboratory roles of nanopore mNGS and tNGS in tuberculosis (TB) and nontuberculous mycobacterial (NTM) settings. Methods: Targeted searches of PubMed/MEDLINE, Embase, Web of Science Core Collection, and Scopus were refreshed on 4 April 2026. Thirty-five records spanning original clinical studies, evidence syntheses, and guideline-context documents were included. Results: Nanopore mNGS is most useful for broad organism detection and diagnostic rescue in unresolved pulmonary and extrapulmonary presentations, particularly when first-line testing is negative, discordant, low-yield, or when mixed infection is suspected. Nanopore tNGS appears better aligned with predefined TB confirmation and resistance-focused workflows because targeted regions allow more standardized interpretation. Agreement is strongest for rifampicin- and isoniazid-related resistance targets. In NTM settings, evidence is stronger for detection and species identification than for disease-level diagnosis. Common implementation constraints include pre-analytical variation, contamination control, host-background interference, inconsistent bioinformatics, and limited workforce capacity. Conclusions: A practical tiered approach is supported in which mNGS is positioned mainly for diagnostic rescue and discovery, whereas tNGS is considered for predefined workflows requiring standardized target interrogation and resistance-associated mutation reporting under local validation and quality systems.}, }
@article {pmid42351718, year = {2026}, author = {Tîrziu, AT and Romanescu, M and Ciordas, PD and Mercea, N and Munteanu, M and Horhat, FG and Chis, AR and Preda, MA}, title = {Metagenomic Profiling of the Gut Microbiome in Age-Related Macular Degeneration-A Pilot Study.}, journal = {Biomedicines}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/biomedicines14061290}, pmid = {42351718}, issn = {2227-9059}, support = {CNFIS-FDI-2024-F-0451//Consiliul National pentru Finantarea Invatamantului Superior/ ; }, abstract = {Background/Objectives: Age-related macular degeneration (AMD) is a multifactorial retinal disease involving inflammatory, metabolic, and genetic factors. Increasing evidence suggests that the gut microbiome may contribute to systemic pathways involved in retinal homeostasis. This exploratory pilot study investigated gut microbiome alterations in AMD patients and controls using long-read whole-genome sequencing. Methods: Bacterial DNA was extracted from fecal samples and analyzed using Oxford Nanopore sequencing, followed by taxonomic profiling, alpha and beta diversity analyses, and differential abundance testing. Results: AMD patients showed significantly reduced microbial diversity, reflected by lower richness, Shannon and Simpson indices. Species-level beta diversity analyses revealed significant differences in microbial community composition, particularly with Bray-Curtis metrics, alongside increased inter-individual microbial heterogeneity in AMD samples. Differential abundance analyses identified the depletion of several potentially beneficial commensal taxa, including Faecalibacterium prausnitzii and Parabacteriodes distasonis, whereas Staphylococcus aureus was enriched in AMD patients. Comparisons between wet and dry subtypes showed no significant differences in alpha or beta diversity. Conclusions: Overall, the findings support the presence of gut microbial dysbiosis in AMD characterized by reduced diversity, abundance-driven community shifts, and increased microbiome heterogeneity. Given the small cohort size, cross-sectional design and lack of functional analysis, these results should be considered preliminary and hypothesis-generating.}, }
@article {pmid42351858, year = {2026}, author = {Chen, X and Yuan, H and Li, X}, title = {Methane Yield, Substrate Conversion, Microbial Community Structure and Metabolic Pathways During Anaerobic Digestion of Natural Cellulosic Biomass.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/bioengineering13060613}, pmid = {42351858}, issn = {2306-5354}, abstract = {Three natural celluloses (softwood pulp, straw grass pulp, and degreased cotton) were used for anaerobic digestion tests to research methane yield, substrate conversion and microbial community structure, and further supplemented and clarified the metabolic pathway mechanisms of anaerobic digestion of cellulosic biomass. The results showed that natural cellulose could be significantly degraded and converted into methane by anaerobic microorganisms. The cumulative specific methane yields of wood pulp fiber (F1), straw pulp fiber (F2), and degreased cotton fiber (F3) were 373.57 ± 10.70 mL/g VS, 349.15 ± 13.20 mL/g VS and 346.16 ± 1.60 mL/g VS, respectively. The corresponding biodegradability values were 93.97%, 85.95% and 84.32%. Although the fermentation cycles in F1, F2, and F3 were identical (T95 was 12 days), the three groups exhibited distinct biogas production patterns. Metagenomic analysis indicated that F1 and F2 were dominated by the acetoclastic methanogenesis pathway, while the proportion of the hydrogenotrophic methanogenesis pathway increased in F3. Meanwhile, the cell motility pathway category was significantly enriched in F3. These results supplement the existing research on the anaerobic digestion of natural cellulose and provide theoretical support for the efficient anaerobic bioconversion of natural cellulosic biomass.}, }
@article {pmid42352020, year = {2026}, author = {Zhang, BY and Wang, YQ and Yang, R and Zhang, Y and Jiang, DZ and Ji, LH and Mao, YF and Tang, B and Zhang, XM}, title = {Gut Microbiota-Mediated Histidine Deficiency Drives Testicular Ferroptosis Induced by Bisphenol F Exposure.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antiox15060714}, pmid = {42352020}, issn = {2076-3921}, support = {No. 32573319 and No. 32172803//National Natural Science Foundation of China/ ; }, abstract = {Bisphenol F (BPF), a widespread environmental contaminant and a major substitute for the restricted bisphenol A (BPA), has raised increasing concerns regarding its potential male reproductive health risks, yet its underlying mechanisms remain poorly understood. This study investigates the mechanisms underlying BPF-induced testicular damage, focusing on the interplay among gut microbiota (GM) dysbiosis, histidine metabolism disruption, and ferroptosis. Using a mouse model exposed to BPF (50, 100, and 200 mg/kg/day) for 28 days, we observed significant testicular pathology, including seminiferous tubule atrophy, vacuolation, and blood-testis barrier (BTB) impairment. Metagenomic and metabolomic analyses revealed GM dysbiosis and suppressed intestinal histidine metabolism, accompanied by decreased abundance of beneficial taxa (e.g., Bacteroides, Ligilactobacillus) and increased potential pathobionts (e.g., Akkermansia, Mucispirillum). BPF exposure was associated with reduced testicular histidine levels and decreased expression of the histidine transporter-related marker LAT1, suggesting impaired histidine availability and a possible alteration in LAT1/CD98-mediated transport; however, direct inhibition of LAT1/CD98 transport activity was not experimentally demonstrated. BPF exposure was accompanied by ferroptosis-related alterations in the testes, including mitochondrial damage, iron accumulation, lipid peroxidation, and downregulation of the xCT-GSH-GPX4 antioxidant axis. In vitro experiments using mouse Sertoli cells (mSCs) confirmed BPF-induced ferroptosis, which was mitigated by the exogenous histidine supplementation. Histidine administration in vivo ameliorated testicular damage, restored BTB integrity, and reversed ferroptotic markers. Our findings support a working model in which a GM-histidine-testis axis may contribute to BPF-induced reproductive toxicity, while further functional studies are required to establish direct causality and transporter-level mechanisms.}, }
@article {pmid42352268, year = {2026}, author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE}, title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/biom16060801}, pmid = {42352268}, issn = {2218-273X}, mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; }, abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.}, }
@article {pmid42352384, year = {2026}, author = {Brown, JL and Mahadevan, P and Middlebrooks, M}, title = {Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea Slug Elysia papillosa.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/biom16060918}, pmid = {42352384}, issn = {2218-273X}, support = {OURI//University of Tampa/ ; }, mesh = {Animals ; *Gastropoda/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Phylogeny ; }, abstract = {Certain sacoglossan sea slugs, often known as "solar-powered sea slugs", are a group of marine gastropods that have the unique ability to photosynthesize by stealing functional chloroplasts from algae. The sacoglossan Elysia papillosa can maintain functional chloroplasts for up to two weeks after feeding. The microbiome of these slugs may play a crucial role in their metabolism, immunity, development, but more importantly their photosynthesis. Shotgun metagenomic sequencing was conducted on four samples of E. papillosa in order to characterize their microbiome. Sequences were classified and relative abundance was quantified with Centrifuger and functional data was examined using SqueezeMeta. Bacteria were analyzed by taxonomic groups and hypothesized function to the sea slug was determined with literature analysis. All samples were dominated by phyla Actinomycetota, Bacillota, Patescibacteriota, and Pseudomonadota. The presence of the phyla Bacteroidota and Bacillota was notable in all samples, which contain species known to produce enzymes that break down polysaccharides. It is possible that these bacteria could assist in degradation of the polysaccharide xylan found in the cell walls of Penicillus, the algal food source of E. papillosa. One species that was found in all samples was Cutibacterium acnes which has been shown to be an important component of the gut microbiota in other marine invertebrates and may provide the host with vitamin B12 and other beneficial nutrients. Many of these bacteria may be opportunistic rather than commensal. As a result, more research is required to describe the interactions between the slug and its microbiome, but this preliminary report provides a valuable starting point for identifying the microbiome make-up to further understanding of these relationships.}, }
@article {pmid42353029, year = {2026}, author = {Xu, HJ and Liu, QL and Zhang, YF and Cuan, SN and Jia, Z and Qiao, D}, title = {Metagenomic Insights into Gut Microbiota Alterations Following Dendrobium huoshanense Water Extract Intervention in Streptozotocin-Induced Type 1 Diabetic Rats.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125308}, pmid = {42353029}, issn = {1422-0067}, support = {no//the platform of the Traditional Chinese Medicine Institute of Anhui Dabie Mountain/ ; }, mesh = {Animals ; *Dendrobium/chemistry ; Rats ; *Plant Extracts/pharmacology/chemistry ; *Diabetes Mellitus, Experimental/drug therapy/microbiology ; *Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenomics/methods ; *Hypoglycemic Agents/pharmacology ; Rats, Sprague-Dawley ; Streptozocin ; Water/chemistry ; Metagenome ; }, abstract = {Dendrobium huoshanense water extract (DHWE) exhibits hypoglycemic effects in streptozotocin-induced type 1 diabetic (STZ-T1D) rats. However, its regulatory impact on the gut microbiota of T1D rats remains largely unclear. In this study, metagenomic sequencing was employed to characterize alterations in the gut microbiota of STZ-T1D rats following DHWE intervention, aiming to explore associations between DHWE-mediated gut microbial changes and T1D-related phenotypes. The results showed that 1300 mg/kg·BW/day DHWE did not significantly affect gut microbial α-diversity (p > 0.05), but drove the β-diversity structure toward that of normal rats. Meanwhile, DHWE significantly reduced the Bacteroidota/Bacillota ratio (p < 0.05), Megamonas (p < 0.01), Megamonas funiformis (p < 0.01), and notably increased the relative abundances of Adlercreutzia (p < 0.01), Adlercreutzia equolifaciens (p < 0.01) in STZ-T1D rats. Furthermore, functional annotation revealed that DHWE enriched multiple metabolic pathways, including streptomycin biosynthesis, ansamycins biosynthesis, galactose metabolism, ether lipid metabolism, and caprolactam degradation. Collectively, these findings demonstrate that DHWE reshapes gut microbiota composition and function in STZ-T1D rats, offering new clues regarding how gut microbial changes may contribute to the modulatory effects of Dendrobium huoshanense in T1D conditions.}, }
@article {pmid42353070, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Koralnik, IJ}, title = {Cross-Compartment Virome Profiling in Human Immunodeficiency Virus Infection and Substance Use Disorder Reveals Brain-CSF-Periphery Discordance and Hepatitis B Virus in Central Nervous System.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125349}, pmid = {42353070}, issn = {1422-0067}, mesh = {Humans ; *Brain/virology ; *HIV Infections/virology/cerebrospinal fluid/complications ; *Substance-Related Disorders/virology/cerebrospinal fluid/complications ; *Virome ; *Hepatitis B virus/genetics/isolation &amp; purification ; Female ; *Central Nervous System/virology ; Male ; *Hepatitis B/virology/cerebrospinal fluid ; Viral Load ; Adult ; }, abstract = {The diversity and abundance of the brain virome is an active field of investigation. However, how the brain virome relates to the presence of viruses outside of the nervous system remains unclear. The rationale for this study is that analyses across multiple biologically linked compartments within the same individuals provide an important opportunity to evaluate virome discordance and viral burden. To characterize viral prevalence and burden across anatomical compartments, we applied the targeted viral enrichment method ViroFind to matched postmortem brain (n = 66), cerebrospinal fluid (CSF; n = 24), and peripheral samples (spleen, peripheral blood mononuclear cells, and lymph nodes; n = 66) from individuals with and without human immunodeficiency virus (HIV) infection and substance use disorder (SUD) in the National NeuroAIDS Tissue Consortium. We detected nucleic acids from 27 viruses representing 12 taxa. Several viruses, including adenovirus, torque teno virus, Epstein-Barr virus, human herpesvirus 6 and 7, cytomegalovirus, parvovirus, and JC polyomavirus, showed significant inter-compartment differences in prevalence or burden. CSF exhibited lower overall viral diversity than brain or peripheral samples, whereas peripheral samples showed the highest viral burden. CNS viral detection was more likely when the same virus was also detected in the periphery. We also detected HBV and HCV in CNS samples despite them not being classically regarded as neurotropic. Broader virome profiling showed greater peripheral viral burden and diversity in HIV-positive than HIV-negative individuals, whereas SUD was not associated with overall viral burden differences. These findings highlight important cross-compartment differences in viral detection, including occurrence of occult HBV infection within the CNS, and support the value of CNS-periphery comparisons in virome studies. These findings can contribute to improved diagnosis and management of viral infections.}, }
@article {pmid42353346, year = {2026}, author = {Wang, Y and Han, Y and Wang, C and Wang, Z and Guan, Z and Li, N and Pan, J}, title = {Microbial Contamination, Degradation Characteristics of Dominant Bacteria on the Hull of the Nanhai No. 1 Shipwreck.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125631}, pmid = {42353346}, issn = {1422-0067}, mesh = {*Wood/microbiology/metabolism ; *Bacteria/isolation &amp; purification/genetics/classification/metabolism ; Biodegradation, Environmental ; Anti-Bacterial Agents/pharmacology ; }, abstract = {To clarify the microbial contamination and wood degradation risk of the Nanhai No. 1 shipwreck hull and verify on-site antibacterial agent effectiveness, microbial samples were collected and analyzed via SEM, metagenomic sequencing, bacterial isolation, enzyme activity detection, and antibacterial experiments. The results showed that Actinomycetota was the dominant phylum, and Brachybacterium, Microbacterium, and Brevibacterium were the dominant genera. Seven bacterial strains were isolated and purified, among which Brevibacterium sp. (NH.SH-B6) had the strongest wood degradation ability, possessing cellulase, LiP, MnP, and Lac activities. When cultured with hull wood as the sole carbon source, LiP was the dominant degrading enzyme of NH.SH-B6, and its maximum enzyme activity was achieved under the optimal conditions of pH = 7, 10% NaCl, 1000 mg/L FeSO4, and no PEG400 added. 50 mg/mL cinnamaldehyde and 0.5% isothiazolinone K100 had good inhibitory effects on the isolated bacteria, and bacterial proliferation was due to incomplete antibacterial agent spraying. This study clarifies the microbial degradation risk of the Nanhai No. 1 shipwreck hull and provides a scientific basis for optimizing the on-site protection strategy of the shipwreck.}, }
@article {pmid42353397, year = {2026}, author = {Walther, B and Bouilloux, F and Vayer, P and Douablin, A and Walther, F}, title = {An Ecological Framework for Interpreting the Canine Gut Microbiome.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121787}, pmid = {42353397}, issn = {2076-2615}, abstract = {The intestinal microbiome is increasingly recognized as an important determinant of canine gastrointestinal health. However, interpreting microbiome sequencing data remains challenging because most analytical approaches rely on taxonomic descriptions, alpha diversity indices, or dysbiosis indices derived generally from a limited number of microbial ecological interpretation targets. While shotgun metagenomic approaches increasingly allow the identification of microbial communities, such analyses remain costly and are not yet widely accessible in routine veterinary settings. The objective of this study was to develop an integrative interpretation framework based on widely accessible biomarkers combining fecal calprotectin and 16S rRNA gene sequencing data. These data enabled the generation of complementary ecological dimensions of gut microbiome organization: biological inflammation assessed through fecal calprotectin, microbiological inflammatory pressure estimated through a Microbiological Inflammatory Score (MIS), and microbiome stability measured by a Microbiome Resilience Score (MRS) derived from alpha diversity, functional balance, and dominance structure. Fecal microbiome profiles obtained by 16S rRNA gene sequencing were analyzed in a real-life cohort of privately owned dogs. Alpha diversity, taxonomic weighting, abundance-dependent dominance rules, beta diversity based on Bray-Curtis dissimilarity, distance to a reference microbiome core, and a 16S-derived dysbiosis score were integrated into a multidimensional interpretation model. Strong ecological associations were observed between resilience, microbial diversity, and dysbiosis-related metrics. Microbiome resilience strongly correlated with Shannon diversity (Spearman ρ = 0.98, p < 0.001), while the reconstructed 16S-derived dysbiosis score showed a more moderate positive correlation with MIS (Spearman ρ = 0.41, p = 0.004), supporting the partially independent ecological dimensions captured by the framework. The results revealed a continuum ranging from stable microbiomes to inflammatory dysbiosis. Most dogs clustered near a reference microbiome core characterized by low microbiological inflammatory pressure and high resilience, whereas a subset of microbiomes showed elevated MIS values, reduced resilience, increased compositional distance from the reference core, and higher dysbiosis index values. These findings support the value of a multidimensional experimental framework integrating inflammation, dysbiosis, and resilience to improve interpretation of canine microbiome profiles under real-life conditions.}, }
@article {pmid42353476, year = {2026}, author = {Kiani, A and Jurgens, G and Gonzalez-Ortiz, G and Walk, CL and Rinttilä, T}, title = {Investigation of the Effect of TiO2 as a Dietary Marker on Broiler Intestinal Fermentation: Combination of Ex Vivo Simulation and In Vivo Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121867}, pmid = {42353476}, issn = {2076-2615}, abstract = {The impact of dietary inert digestibility markers on gut microbiota and intestinal fermentation remains poorly understood. This study investigated the effects of dietary titanium dioxide (TiO2) supplementation at 4 kg/t feed, representing a typical dose used in animal nutrition studies, on fermentation dynamics and microbial composition in broiler chickens using combined ex vivo and in vivo approaches. Ex vivo fermentations were conducted using ileal and caecal microbiota and substrates collected from 32-day-old broiler chickens. Titanium dioxide (TiO2) was supplemented directly to the fermentations, and gas production and short-chain fatty acid (SCFA) profiles were used as the main outcome measures. In parallel, 392 broiler chickens were fed diets with or without TiO2 for 32 days, and ileal and caecal digesta were analysed for fermentation end-products and microbial composition using shotgun metagenomic sequencing. A second ex vivo experiment was performed using microbiota adapted to dietary TiO2. In the first ex vivo model, TiO2 reduced gas production and acetic acid concentration in the ileum (p < 0.05), whereas in the caecum it increased gas production, total eubacterial counts, and branched-chain fatty acids (BCFAs) (p < 0.05). In vivo, TiO2 did not affect growth performance or organ development but significantly increased isobutyric acid and total BCFA concentrations in the caecum (p < 0.05). Metagenomic analysis revealed increased caecal alpha diversity (Shannon index) and enrichment of taxa associated with amino acid metabolism, including Massilicoli timonensis, Blautia merdavium, Rubneribacter badeniensis, and Mediterraneibacter caccavium. The second ex vivo experiment showed similar trends, with increased gas and BCFA production. Collectively, these findings indicate that TiO2 can modulate intestinal fermentation and microbial composition in a segment-specific manner, suggesting that dietary markers may not be biologically inert.}, }
@article {pmid42353508, year = {2026}, author = {Shi, K and Zhou, X and Li, K and Dai, J and Shen, Y and Wu, Z and Zhang, X and Yu, Q and Chen, S}, title = {Multi-Omics Analysis Reveals the Gut-Mediated Mechanism Underlying the Seasonal Non-Laying Phenotype in Zhedong White Geese (Anser cygnoides domesticus).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121899}, pmid = {42353508}, issn = {2076-2615}, abstract = {As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E2, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut-reproductive axis and supplies promising biomarkers to improve the laying performance of geese.}, }
@article {pmid42353537, year = {2026}, author = {Liu, Y and Zhang, G and Gao, H and Fang, M and Jiang, L and Kong, Y and Liu, Q and Wang, P and Zhang, S and Li, Y}, title = {Metavirome Analysis of Viruses Carried by Dairy Cows in Shaanxi, Gansu and Ningxia, China.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121928}, pmid = {42353537}, issn = {2076-2615}, support = {32130104//National Natural Science Foundation of China/ ; 2023BCF01038, 2024BBF02017//the Ningxia Hui Autonomous Region Key R&amp;D Projects/ ; }, abstract = {Dairy cows are economically significant ruminants in China, and the dairy industry is closely linked to food safety and the agricultural economy. However, various factors such as pathogenic microorganisms often lead to frequent diseases in dairy cows. Furthermore, as potential hosts for diverse viruses, dairy cows can harbor zoonotic pathogens, which pose a threat to public health. The Shaanxi-Gansu-Ningxia region boasts abundant natural resources and extensive pastures. It is a major animal husbandry base in Northwest China, and dairy farming plays a significant role in the local economy. However, research on dairy cow virus diversity in this region remains limited; epidemic prevention and control capabilities are constrained, and the risk of disease outbreaks is elevated. In this study, 790 dairy cow samples were collected from 13 large-scale farms and free-range households in the Shaanxi-Gansu-Ningxia region from 2021 to 2023. Sample types consisted of nasal and anal swabs. Six viral metagenomic libraries were constructed and analyzed using high-throughput sequencing and bioinformatics methods, leading to the identification of 51 viral families. These comprised 16 positive-sense single-stranded RNA virus families, one Retroviridae family, four double-stranded RNA virus families, 21 double-stranded DNA virus families, and nine single-stranded DNA virus families. Among these, RNA viruses were represented by families such as Astroviridae, Coronaviridae, Caliciviridae, Picornaviridae, and Picobirnaviridae; DNA viruses were primarily detected in Circoviridae, Papillomaviridae, Genomoviridae, and Smacoviridae. Alpha diversity analysis revealed no significant differences in viral diversity and abundance among the three regions (p > 0.05); however, significant differences were observed in the read counts and proportions of RNA and DNA viruses across the provinces. Phylogenetic analysis further indicated that viruses carried by dairy cows exhibit considerable genetic diversity and pose potential cross-species transmission risks. This study established a reference database for the dairy cow virome in the Shaanxi-Gansu-Ningxia region, elucidated the phylogenetic relationships of key viruses, and provided a scientific basis for future monitoring and prevention of dairy cow viruses.}, }
@article {pmid42353547, year = {2026}, author = {Liu, L and Narrowe, AB and Firrman, J and Mahalak, KK and Chetty, VJ and Lemons, JMS and Baudot, A and Van den Abbeele, P}, title = {Perfluorooctanoic Acid (PFOA) Alters the Structure of the Gut Microbial Community and Colonoid Transcription.}, journal = {Current issues in molecular biology}, volume = {48}, number = {6}, pages = {}, doi = {10.3390/cimb48060542}, pmid = {42353547}, issn = {1467-3045}, support = {8072-41000-108-00-D//United States Department of Agriculture/ ; }, abstract = {Perfluorooctanoic acid (PFOA) is an environmentally persistent chemical that enters the gastrointestinal tract (GIT) via the food chain, posing a harmful, long-term threat to human health. In response to this challenge, research on the PFOA-GIT interaction is thriving. Currently, studies on the effect of PFOA on the epithelial cells of the GIT and those on its influence on the microbial community are often implemented separately, and less attention has been paid to the combinational effects of the chemical, the gut microbiome and metabolome. In the present study, we co-cultured fecal samples from healthy adults aged 25-70 in the ex vivo SIFR[®] simulator, adding PFOA at 10 mg/L to represent the accumulated effects of long-term exposure. The results obtained from bacterial cell counting by flow cytometry and shotgun metagenomic sequencing revealed that PFOA was broadly disruptive to the microbiome and that Pseudomonadota emerged as the dominant phylum by replacing Bacteriodota and Bacillota, including key members of short-chain fatty acid-producing groups. Bacterial culture media with and without PFOA were collected and used in human colonoid cell culture for TEER and transcription measurement. It was shown that the PFOA-impacted microbial culture had stronger effects on the cell's protective functions, in terms of tissue junction tightening, mucin biosynthesis, and immune response, than either untreated bacterial culture or PFOA alone. The results point out the possibility that the combination of PFOA and PFOA-impacted bacterial metabolites more strongly induces a change in epithelial cells' protective function than either one alone.}, }
@article {pmid42353629, year = {2026}, author = {Iorizzo, M}, title = {Microbial α-L-Rhamnosidases: Regioselective Biocatalysts for Flavonoid Biotransformation and Nutraceutical Applications.}, journal = {Current issues in molecular biology}, volume = {48}, number = {6}, pages = {}, doi = {10.3390/cimb48060625}, pmid = {42353629}, issn = {1467-3045}, abstract = {Microbial α-L-rhamnosidases are increasingly recognised as selective biocatalysts in food biotechnology, nutraceutical production, and health-related applications. These glycoside hydrolases catalyse the hydrolysis of terminal alpha-L-rhamnose residues from flavonoids, terpenoids, saponins, and other glycosylated natural products, thereby modulating sensory properties, solubility, intestinal absorption, and biological activity. While their traditional uses include debittering citrus juice and enhancing wine aroma, recent evidence demonstrates their wider value in selective flavonoid biotransformation, production of rare mono-glycosylated derivatives, probiotic fermentations, and microbiome-associated metabolism. This review summarises microbial sources, catalytic mechanisms, CAZy classification, substrate specificity, structure-function relationships, analytical methods, industrial process engineering, and emerging applications in functional foods and targeted nutraceutical applications. Particular attention is given to the distinction between alpha-(1→2)- and alpha-(1→6)-linked substrates, the production of isoquercitrin and prunin, recombinant enzyme platforms, immobilised biocatalysts, and potential future opportunities arising from metagenomics, synthetic biology, and AI-assisted protein engineering.}, }
@article {pmid42353668, year = {2026}, author = {Kerek, &#xc1; and Husz, LH and Szarka, E and Tornyos, G&#xc1; and Jerzsele, &#xc1;}, title = {Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antibiotics15060544}, pmid = {42353668}, issn = {2079-6382}, support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; }, abstract = {Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6')-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome-mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings.}, }
@article {pmid42353692, year = {2026}, author = {Elton, L and Lutimba, S and Mateos, AD and Frosini, SM and Jepson, R and Williams, A and Ali, S and Heaphy, J and Pang, V and Commins, L and O'Brien, C and Yetiş, &#xd6; and Caine, E and Ward, I and Muzslay, M and Yui, S and Karia, K and Shore, E and Rofael, S and Mack, D and Atkinson, C and McHugh, TD and Wey, EQ}, title = {Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antibiotics15060568}, pmid = {42353692}, issn = {2079-6382}, support = {N/A//Royal Free London NHS Foundation Trust/ ; }, abstract = {Background: Human hospitals and veterinary centres are hotspots for resistant microbes and plasmids, and metagenomic sequencing offers an agnostic insight into microbiomes, resistomes, and mobilomes, informing strategies for reducing AMR spread. Methods: Environmental samples, including wastewater and surface swabs, were taken from a tertiary human hospital ward (36 samples) and a companion animal veterinary hospital (48 samples) in London. Whole DNA was extracted and metagenomic sequencing undertaken using Oxford Nanopore Technologies' MinION. Data were analyzed for microbiomes, resistomes and mobilomes and compared. Results: Microbial diversity analyses highlight higher richness across human hospital (HH) environmental samples, but more evenness in veterinary hospital (VH) environmental samples. Diversity showed distinct microbial communities in the HH and VH samples. There were significantly more total antimicrobial resistance gene (ARG) types (p < 0.0001) in the environmental HH samples compared with the environmental VH samples. There was a significantly higher mean number of Enterobacteriales plasmid types (p ≤ 0.0001) in the HH samples. There were significantly more total Gram-Positive plasmid types (p ≤ 0.0001) in the VH samples. Discussion: This research highlights the presence of human and animal pathogens, ARGs and mobile genetic elements in clinical environments, underscoring the importance of multisectoral surveillance. Integrating taxonomic, resistome, and mobilome analyses provides a better understanding of the potential for AMR dissemination at the human-animal-environment interface. This provides insights relevant for the development of targeted surveillance and mitigation strategies within a OH framework.}, }
@article {pmid42353998, year = {2026}, author = {Margasoiu, I and Pînzariu, AC and Manole, LM and Spoială, EL and Păduraru, G and Ghiga, G and Popa, IP and Șerban, DN and Șerban, IL and Trandafir, LM}, title = {Gut Microbiome Responses to Nutritional and Lifestyle Interventions in Pediatric Obesity: A Systematic Review Toward Precision Nutrition.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/children13060828}, pmid = {42353998}, issn = {2227-9067}, support = {SMIS code 351058//Grigore T. Popa University of Medicine and Pharmacy/ ; }, abstract = {Background: Childhood obesity is increasingly associated with gut microbiome dysbiosis. This systematic review (PROSPERO CRD420251131354) evaluates evidence from studies published between 2020 and 2026 assessing how nutritional and lifestyle interventions influence gut microbiota in children with obesity. Methods: A systematic search of PubMed, EMBASE and EBSCO identified 21 interventional studies involving children aged 5-18 years with obesity, with the last search conducted in April 2026. Interventions comprised prebiotics, probiotics, synbiotics, postbiotics, high-fiber diets, calorie-restricted dietary approaches, and lifestyle modifications such as physical activity. Microbiome outcomes were analyzed using 16S rRNA sequencing, quantitative real-time polymerase chain reaction (qPCR), or metagenomics. Risk of bias was evaluated using the RoB 2 and ROBINS-I (version 2) tools. Due to substantial heterogeneity in study design, participant characteristics, intervention types, and analytical methods, a meta-analysis was not feasible. Results: Across 21 studies, nutritional interventions included measurable but heterogeneous alterations in gut microbiome composition. Inulin supplementation was associated with a significant increase in alpha diversity and with higher relative abundances of Bifidobacterium, Blautia, Megasphaera, Subdoligranulum, and Eubacterium coprostanoligenes. Synbiotic supplementation increased Prevotella and Dialister and reduced the Firmicutes/Bacteroidetes ratio. High-fiber dietary interventions increased Faecalibacterium, Bifidobacterium, and Clostridium, while reducing Bacteroides, and were associated with shifts in metabolic pathways related to carbohydrate, lipid, and nucleotide metabolism. Calorie-restricted diets and combined diet-exercise interventions increased beneficial taxa such as Akkermansia muciniphila, improved microbial diversity, and correlated with favorable metabolic and anthropometric outcomes. Overall, nutritional and lifestyle interventions in pediatric obesity were associated with taxon-specific and context-dependent microbiome changes, rather than uniform restructuring. Conclusions: Nutritional interventions can modulate gut microbiota diversity, composition, and predicted function in pediatric obesity; however, the observed effects vary substantially across studies. The limited number of trials, small sample sizes, and methodological heterogeneity underscore the need for larger, standardized studies to better define clinical and therapeutic implications.}, }
@article {pmid42354149, year = {2026}, author = {Bai, F and Cai, C and Zhang, T and Xu, L and Liu, Y and Liu, R and Ma, Z and Jiang, M and Gao, J and Zhang, J and Yu, X and Tang, T and Chen, J and Yao, S}, title = {Comparative Analysis of Microbial Community Structure and Functional Traits of Baijiu Daqu Across Diverse Geographical Regions in China.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/foods15122182}, pmid = {42354149}, issn = {2304-8158}, support = {YQY25-SW-210//China National Research Institute of Food and Fermentation/ ; ZQ2023JC-GC03//Science and Technology Innovation Program of Sinolight Corporation/ ; }, abstract = {Daqu is a key starter used in Baijiu production, and its microbial composition and associated metabolic functions play critical roles in fermentation performance and flavor development. This work aimed to reveal how Daqu-making temperature regulates microbial community divergence and subsequent metabolite formation via multi-omics analysis so as to provide theoretical guidance for Daqu quality control. In this study, physicochemical analysis, metagenomic sequencing, and metabolomic profiling were combined to investigate the microbial community structure, functional differentiation, and metabolite characteristics of nine Daqu samples collected from six major Baijiu-producing regions in China. The temperature during Daqu preparation was found to be a primary factor driving microbial community assembly and functional specialization. Medium-temperature Daqu exhibited higher saccharifying activity (up to 867 U) and greater microbial diversity with the enrichment of amino acid metabolism-related pathways, indicating enhanced protein degradation and amino acid utilization for the formation of flavor precursors. In contrast, high-temperature Daqu showed stronger capacities for carbohydrate degradation and conversion, particularly in starch and sucrose metabolism, which were closely associated with the enrichment of thermotolerant fungi and bacteria. LEfSe analysis identified 47 distinct microbial biomarkers (LDA score > 3.0), which could differentiate between medium- and high-temperature Daqu. Redundancy analysis indicated that environmental factors (moisture and acidity) together with functional properties (fermentation, esterification, liquefaction, and saccharification) act as key drivers of microbial functional patterns. Metabolomic analysis further revealed that medium-temperature Daqu had higher abundances of esters and fatty acids, whereas high-temperature Daqu had higher proportions of alcohols and ketones. Taken together, these results provide a multi-omics perspective on temperature-driven microbial functional differentiation in Daqu and offer a scientific basis for quality-oriented regulation and process optimization in Baijiu production.}, }
@article {pmid42354792, year = {2026}, author = {Pan, Z and Bao, J and Liu, X and Ge, G and Zhao, M}, title = {Metagenomic Insights into Regional Differences in the Rhizosphere Microbial Communities of Stellera chamaejasme L. in Inner Mongolia.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061167}, pmid = {42354792}, issn = {2076-2607}, support = {CARS-34//China Agriculture Research System/ ; }, abstract = {Rhizosphere microorganisms are important components of grassland ecosystems, but the rhizosphere microbiome of the poisonous and medicinal plant Stellera chamaejasme L. remains poorly characterized. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition, community structure, differentially enriched taxa, and KEGG-based functional potential of rhizosphere microbial communities associated with S. chamaejasme from three typical steppe regions in Inner Mongolia. Acidobacteria, Proteobacteria, and Actinobacteria were the dominant phyla, while Sphingomonas, Bradyrhizobium, and Streptomyces were among the dominant genera. Genus-level profiles and ordination analysis showed region-associated community patterns, and rarefaction curves indicated that sequencing depth was sufficient to capture most detectable taxa. LEfSe analysis identified region-associated differentially enriched taxa, including Sphingomonas-, Bradyrhizobium/Nitrospira-, and Streptomyces/Solirubrobacter-associated taxa. KEGG annotation suggested broadly similar major functional categories across regions, with some differences in the relative abundance of metabolic pathways. These results provide baseline metagenomic information on S. chamaejasme rhizosphere communities. Because of the limited replication and lack of soil physicochemical measurements, ecological mechanisms should be tested in future studies.}, }
@article {pmid42354802, year = {2026}, author = {Hao, D and Yu, X and Sun, X and Cheng, D and Ding, H and Wang, Y and Li, Y and Geng, Z and Xu, G}, title = {Thermophilic Microbial Inoculant Promotes Lignocellulose Degradation During Green Waste Composting.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061177}, pmid = {42354802}, issn = {2076-2607}, support = {PTYX202514//Fundamental Research Funds for the Central Universities/ ; Liao[2025]TG03//China Central Financial Forestry and Grassland Science and Technology Promotion Demonstration Project/ ; }, abstract = {Thermophilic microbial inoculant (CI) has been demonstrated to optimize the green waste composting (GWC) process. The pathways through which it enhances lignocellulose degradation remain unclear. This study evaluated composting performance under four treatments: CI, effective microorganisms (EM), Phanerochaete chrysosporium (WF), and natural composting (CK). To elucidate the biological differences between efficient lignocellulose-degrading systems and CK, metagenomic analyses were conducted on CI and CK based on lignocellulose degradation rates. The results indicated that CI inoculation did not negatively affect the compost heating process and produced a nitrogen-rich, safe, and mature compost product. Compared to other treatments, CI increased the lignocellulose degradation rate by 3.66% to 31.8%. Metagenomic analysis revealed that CI inoculation enriched genes encoding glycoside hydrolases (GHs), glycosyl transferases (GTs), carbohydrate esterases (CEs), and carbohydrate-binding modules (CBMs) across multiple composting phases, positively impacting dominant carbohydrate-active enzyme (CAZyme) families including AA3, CE1, and CE7. CI inoculation also elevated the relative abundance of lignocellulose-degrading microorganisms (0.70~2.73%), simplified microbial network structure, and strengthened microbial cooperation. Within the microbial network, Chryseolinea, Protaetiibacter, and unclassified_f__Burkholderiaceae were identified as core taxa involved in lignocellulose degradation. Redundancy analysis (RDA) identified temperature as the primary factor influencing biological factors, with CI improving composting efficiency by optimizing the microenvironment. Collectively, this work provides a novel strategy for microbial inoculant application in composting and offers new perspectives for identifying core taxa, contributing to advancing composting efficiency.}, }
@article {pmid42354818, year = {2026}, author = {Yang, Z and Xv, W and Cai, Y and Gu, H and Feng, Y}, title = {Long-Term Application of Fermented Fertilizer Attenuates the Accumulation of Antibiotic Resistance Genes in Aquaculture Sediment.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061193}, pmid = {42354818}, issn = {2076-2607}, abstract = {Aquaculture sediments are increasingly recognized as important reservoirs of antibiotic resistance genes (ARGs). Although thermophilic fermentation is widely used to reduce ARGs and pathogens in manure, most biosafety assessments stop at the fertilizer product itself, leaving unresolved whether these benefits persist after application to aquaculture sediments. Here, we compared inorganic fertilizer (IF), raw manure (RM), and fermented fertilizer (FF) to test whether fermentation confers sustained biosafety benefits in aquaculture pond sediments. After a 6-month co-culture period, sediment samples were analyzed using shotgun metagenomic sequencing, ARG and mobile genetic element (MGE) profiling, antibiotic residue determination, and network analyses. Long-term fertilization significantly altered sediment physicochemical properties, microbial community composition, and resistome structure. Among the three groups, the RM exhibited the highest total ARG abundance and the greatest number of unique ARG subtypes, with significant enrichment of multidrug resistance genes as well as pathogen-, disease-, and host-associated mobile genetic elements (MGEs). In contrast, the FF group showed the lowest total ARG abundance and fewest unique ARG subtypes, along with suppression of pathogen-associated MGEs, indicating that FF can effectively reduce the risk of ARG dissemination. However, the potential impact of residual antibiotics still warrants attention. Redundancy analysis showed that TC and TN primarily explained bacteriome and resistome variation under RM, whereas pH, EC, AP, and AK were more strongly associated with FF. Co-occurrence analysis further suggested that fertilizer-driven microbial community shifts may regulate ARG persistence and potential cross-ecosystem dissemination. Overall, fermented fertilizer attenuated, but did not eliminate, manure-derived resistance risks in aquaculture sediments. These findings support fermented fertilizer as a safer management option than raw manure and highlight the need for integrated risk assessment combining ARGs, MGEs, microbial hosts, and antibiotic residues.}, }
@article {pmid42354826, year = {2026}, author = {O'Donald, SN and Patel, F and Keen, P and Hanson, LA and Cunningham, F and Lawrence, ML and Tekedar, HC}, title = {Hi-C Metagenome Deconvolution of Double-Crested Cormorant (Nannopterum auritum) Fecal Samples Demonstrates Feasibility of Linking Microbial Genomes, AMR Genes, and Mobile Elements in Avian Microbiomes.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061198}, pmid = {42354826}, issn = {2076-2607}, support = {N/A//New York Institute of Technology/ ; }, abstract = {The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene-host associations and provide a framework for future studies of microbial connectivity in One Health contexts.}, }
@article {pmid42354835, year = {2026}, author = {Mohammed, MZ and Linhares, DCL and Zeller, MA and Silva, GS and Rademacher, C and Peterson, C and Trevisan, G}, title = {Genetic Characterization of PRRSV Diversity and Detection of Other Pathogens in Live Virus Inoculation Material Used in Breeding Herd Stabilization Programs.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061207}, pmid = {42354835}, issn = {2076-2607}, support = {GR-028677//American Association of Swine Veterinarians Foundation/ ; IPPA 23-120//Iowa Pork Producers Association/ ; }, abstract = {Live virus inoculation (LVI) is widely used for porcine reproductive and respiratory syndrome virus (PRRSV) stabilization, yet preparation practices and pathogen composition remain poorly characterized. This study aimed to evaluate variability in LVI preparation, quantify PRRSV genomic load, and detect additional swine pathogens. A survey was conducted to document LVI preparation methods, and samples were analyzed using reverse-transcription quantitative PCR (RT-qPCR) for PRRSV quantification and next-generation sequencing for PRRSV and the metagenomic characterization of additional pathogens. Among 61 LVI samples, substantial variability was observed in preparation practices and viral composition, with 31 distinct PRRSV variants identified and seven samples containing multiple strains. PRRSV RNA concentrations ranged from 10[1.69] to 2.52 × 10[8] copies/mL. Metagenomic analysis detected a complete or near-complete genome for PRRSV, porcine parvovirus, and porcine circovirus type 2. Genome fragments of porcine sapovirus, porcine rotavirus, porcine astrovirus, and bacterial genetic material from Salmonella spp., Pseudomonas spp., Streptococcus spp., and Escherichia coli were also detected. These findings highlight substantial heterogeneity in LVI materials and encourage the use of next-generation sequencing to verify LVI PRRSV composition and screen for co-existing pathogens, reinforcing the need for standardized preparation protocols and further investigation into optimal viral dosing for effective immunization.}, }
@article {pmid42354848, year = {2026}, author = {Gou, F and Zhao, Q and Han, Y and Sun, Y and Ding, W and Chen, J and Jin, S}, title = {Effects of Dietary Concentrate-to-Roughage Ratio on Rumen Microbiota, Functional Profiles, and Fermentation Characteristics in Yak.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061223}, pmid = {42354848}, issn = {2076-2607}, support = {2024-NK-109//Qinghai Provincial Science and Technology Department/ ; }, abstract = {This study investigated the effects of different concentrate-to-roughage ratios on the rumen microbial community, functional potential, and fermentation characteristics in yak. Forty Qinghai Plateau-type yaks (8-9 months, 68.725 ± 18.973 kg) were randomly assigned to four dietary groups with concentrate-to-roughage ratios of 80:20 (C80), 65:35 (C65), 50:50 (C50), and 35:65 (C35). After a 15-day adaptation period, animals were fed for 105 days. Rumen contents were analyzed using metagenomic sequencing combined with fermentation parameter measurements. High-concentrate diets (C80 and C65) were associated with increased relative abundance of starch-degrading and propionate-producing bacteria, such as Prevotella and Succiniclasticum, whereas low-concentrate diets (C50 and C35) were associated with higher abundance of cellulolytic bacteria, including Ruminococcus and Fibrobacter. Functional analysis indicated increased relative abundance of genes involved in glycolysis (ko00010), propanoate metabolism (ko00640), and energy-related pathways in high-concentrate groups, while fiber degradation and methane-related pathways were relatively higher in low-concentrate groups. Rumen fermentation parameters showed a significant decrease in pH with increasing concentrate level (p = 0.001), and NH3-N concentrations differed among treatments (p = 0.036). Dietary concentrate-to-roughage ratio significantly influences rumen microbial composition, functional potential, and fermentation characteristics in yak. A moderate concentrate level (approximately 65:35) may contribute to a more balanced rumen microbial and fermentation profile under the conditions of this study.}, }
@article {pmid42354871, year = {2026}, author = {Qiu, Q and Sun, X and Li, H and Zhou, D and Huo, H}, title = {Plastic Degradation Potential and Metagenomic Analysis of an Enriched Gut Microbial Consortium from Tenebrio molitor.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061246}, pmid = {42354871}, issn = {2076-2607}, support = {52230003//National Natural Science Foundation of China/ ; }, abstract = {Plastic pollution has become an increasingly severe global environmental issue, highlighting the urgent need for efficient and sustainable biodegradation strategies. In this study, an enriched gut microbial consortium, NE-01 derived from Tenebrio molitor, exhibited significant degradation activity toward polystyrene (PS), polyethylene (PE), and polyethylene terephthalate (PET). Metagenomic sequencing revealed that Pseudomonas and Proteobacteria were the dominant taxa, maintaining high community diversity and providing a microbial foundation for the degradation of plastics and other complex organic compounds. Functional annotation and metabolic pathway analysis indicated that xenobiotic biodegradation and metabolism occupied a large proportion of the metabolic network, suggesting the consortium's potential for degrading exogenous pollutants. Several key genes associated with the degradation of aromatic and halogenated compounds, such as benzoate, toluene, styrene, and bisphenol A, were identified. Metabolic reconstruction further suggested possible degradation pathways for PS, PE, PET, and the plasticizer di(2-ethylhexyl) phthalate (DEHP). This study preliminarily demonstrated that the T. molitor gut-derived microbial consortium harbors multiple plastic-degrading genes and provides a theoretical basis for developing green, microbe-based strategies for plastic degradation.}, }
@article {pmid42354876, year = {2026}, author = {Yue, Y and Jiang, Y and Zhang, Y and Xiao, T and Hao, H and Wang, Q and Tong, Z and Zhang, J and Chen, H}, title = {Duration of Spent Mushroom Substrate Return Affects Microbial Assembly and Nitrogen Metabolism to Promote Functional Stabilization in Rice-Mushroom Crop Rotation Systems.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061251}, pmid = {42354876}, issn = {2076-2607}, support = {T2024310//Shanghai Agricultural Science and Technology Innovation Project/ ; 24YF273800//Shanghai Sailing Program/ ; 202509/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Spent mushroom substrate (SMS) return is a vital strategy for agricultural waste recycling and soil fertility improvement, yet its ecological impacts of duration remain poorly understood. This study employed metagenomic sequencing to explore soil fertility, microbial dynamics, and nitrogen cycling across different SMS return durations (0, 1, and 3 years) within rice-mushroom crop rotation systems. Soil nutrients (organic matter, total nitrogen, total phosphorus) initially decreased and then increased throughout the rice growth cycle. The one-year return (y1) induced early nutrient depletion, whereas the three-year return (y3) significantly enhanced late-stage nutrient accumulation. With increasing duration, bacterial and archaeal assembly shifted from stochastic toward deterministic processes, while fungal diversity and stochasticity decreased continuously. Co-occurrence network analysis demonstrated that SMS return increased network complexity and intercommunity competition. This transition was accompanied by a functional shift in keystone taxa from those responsive to exogenous organic matter in y1 to those mediating nitrogen fixation, anammox, and sulfur metabolism in y3. Nitrogen cycling in y1 increased potential N2O emission risks through nirS upregulation and nosZ downregulation, whereas y3 mitigated inorganic nitrogen loss by upregulating gene abundances of ammonia assimilation, nitrification, and DNRA genes. Notably, the structure of nitrogen-cycling genes fluctuated in y1 but was resilient to y0 levels in y3. These findings demonstrated that while initial SMS return triggered ecological fluctuations and environmental risks, continuous return (y3) achieved functional stability by reshaping microbial niches. This study highlights the importance of SMS return duration in balancing soil fertility enhancement with environmental risk mitigation in sustainable paddy ecosystems.}, }
@article {pmid42354906, year = {2026}, author = {Cao, YF and Wang, YR and Zheng, PX and Wang, XC and Xu, L and Sun, C}, title = {Multi-Omics Reveals the Impact of Domestic Wastewater Input on the Dissolved Organic Carbon Pool and Microbial Community in the Qiantang River Estuary.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061282}, pmid = {42354906}, issn = {2076-2607}, support = {32370006//National Natural Science Foundation of China/ ; Y24C010009//Zhejiang Provincial Natural Science Foundation/ ; }, abstract = {Estuarine ecosystems face intense anthropogenic pressures, yet systematic research on how domestic wastewater influences the dissolved organic carbon (DOC) pool via microbial community regulation remains limited. In this study, we conducted a microcosm experiment simulating wastewater input into the Qiantang River and integrated multi-omics (16S rRNA sequencing, metagenomics, metatranscriptomics, and FT-ICR MS) to elucidate the mechanism. Results showed that: (1) Wastewater input increased initial DOC and changed its degradation pattern: slower decay but higher removal. (2) Compared to the control, the wastewater-amended group exhibited a decreased fluorescence intensity contribution of carboxyl-rich alicyclic molecule (CRAM)-like compounds, indicating reduced chemical stability of recalcitrant DOC (RDOC). (3) Wastewater drove directional microbial succession from catabolic-dominant taxa (e.g., Comamonas, Citrobacter) to anabolic-dominant taxa (e.g., Reyranella), shifting metabolism from pollutant degradation to endogenous synthesis, thereby lowering the system's efficiency in forming stable RDOC. (4) Multi-omics revealed a "stimulation-balance" functional response: early activation of xenobiotic degradation and signal transduction (day 2), followed by a shift to anabolic metabolism (day 28). This functional transition, driven by microbial succession, ultimately reduced RDOC stability. Our findings reveal that wastewater reshapes the microbial carbon pump, providing a theoretical basis for assessing estuarine carbon sink responses to pollution control measures.}, }
@article {pmid42354916, year = {2026}, author = {Zhang, X and Lu, C and Lu, L and Meng, L and Liu, Y and Ma, B}, title = {Metagenome-Assembled Genomes Support the Proposal of Candidatus Flavobacterium genomatis from the Northeast Black Soil Ecosystem.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061292}, pmid = {42354916}, issn = {2076-2607}, support = {2024YFD1501800//National Key R&amp;D Program of China/ ; 2024ZD1000603//National Key Science and Technology Special Project for Deep Earth Research/ ; 42277283//National Natural Science Foundation of China/ ; 2024C03131//Key R&amp;D Program of Zhejiang Province/ ; 2024Z267//Key R&amp;D Program of Ningbo/ ; GZC20251786//National Program for Funding Postdoctoral Researchers/ ; }, abstract = {Soils are critical microbial habitats that support terrestrial ecosystem functioning and harbor numerous uncultured and functionally uncharacterized microbial groups. The black soil region in northeast China is a key agricultural ecosystem globally, yet the classification and functional understanding of its crucial microbial groups remain underexplored. In this study, we identified three high-completeness metagenome-assembled genomes (MAGs) from the Global Mollisols Genomic Atlas (GMGA). Phylogenetic and comparative genomic analyses identified these genomes as representing a novel evolutionary branch within the genus Flavobacterium, classified under the phylum Bacteroidota. Their novel taxonomic position is further supported by average nucleotide identity (ANI) and average amino acid identity (AAI) thresholds, demonstrating significant divergence from all known reference genomes. Functional annotation indicated that this species possesses strong plant polysaccharide degradation potential and a chemoheterotrophic lifestyle, together with environmental stress tolerance and a specialized nitrogen metabolic network adapted to agricultural inputs, thereby conferring a metabolic advantage in black soil environments characterized by high organic matter input and marked seasonal fluctuations. In addition, global distribution analysis showed that this lineage is widely distributed across diverse ecosystems and is significantly enriched in soil habitats, particularly in environments with fluctuating carbon sources and high organic matter inputs. The new species is most abundant in temperate soils, with the northeast black soil region of China emerging as a key hotspot. Based on these findings, and because no pure culture is currently available, we propose Candidatus Flavobacterium genomatis based on genome-resolved metagenomic evidence and in alignment with the International Code of Nomenclature of Prokaryotes rules for uncultivated prokaryotes. Our results expand the known species diversity of the genus Flavobacterium and suggest potential ecological roles of uncultured black-soil microbes in carbon and nitrogen cycling, including possible involvement in N2O reduction under suitable environmental conditions.}, }
@article {pmid42354965, year = {2026}, author = {He, Z and Wang, B and Jin, D and Tian, M and Gong, L}, title = {Effects of Rice Straw Incorporation on Paddy Soil Microbiome and Metabolome Throughout the Crop Growth Period.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061341}, pmid = {42354965}, issn = {2076-2607}, support = {2024BS1002;2026CY3515;2025XKJS8528//Liaoning Academy of Agricultural Sciences/ ; 2025JH2; 101300068//Liaoning Province Applied Basic Research Program/ ; }, abstract = {Rice straw incorporation is a paddy soil management practice that can reduce environmental pollution, mitigate soil degradation, and minimize nutrient loss. In this study, temporal shifts in soil microbial communities and metabolic profiles were investigated across three key rice growth stages-pre-planting (BS), tillering (TI), and harvest (HA)-to elucidate the ecological effects of straw incorporation. The Shannon diversity and Pielou evenness indices were significantly higher under straw incorporation than under the control at the BS and TI stages, but significantly lower at the HA stage. Straw incorporation also increased the relative abundance of key bacterial taxa, including Polaromonas sp. AER18D145, Sphingomonas sediminicola, and Thiobacillus denitrificans. Functional annotation indicated that the microbial community was mainly associated with amino acid biosynthesis and glycolysis. Metabolomic analysis revealed significant changes in steroids and their derivatives, terpenoid lipids, and carboxylic acids and their derivatives. Three metabolites-3-hexa-isoprenyl-4,5-dihydroxybenzoic acid, LysoPE (16:1(9Z)/0:0), and stachyose-differed significantly across all stages, suggesting their potential as metabolic indicators of straw incorporation. KEGG enrichment analysis identified significant alterations in arachidonic acid, purine, galactose, and pyrimidine metabolism. Redundancy analysis further revealed positive associations of LysoPE (16:1(9Z)/0:0) and stachyose with Brevundimonas sp. Root608 and Polaromonas sp. AER18D145.}, }
@article {pmid42354967, year = {2026}, author = {Romero-Ricardo, L and López, Y and Lopez-Mejia, Y and García, A and Contreras-Martínez, H and Galeano, K and Gastelbondo, B and Fragoso, P and Paternina, L and Arrieta, G and Mattar, S}, title = {Metagenomic Analysis Reveals Viral Diversity in Phlebotomine Sand Flies from Caribbean Region in Colombia.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061343}, pmid = {42354967}, issn = {2076-2607}, support = {BPIN 2020000100322//Ministry of Science, Technology and Innovation/ ; }, abstract = {Phlebotomine sand flies are dipterans that transmit leishmaniasis, bartonellosis, and arboviruses of public health importance. Colombia is a tropical country with high annual incidences of arboviruses, such as dengue and, more recently, yellow fever, all of which have similar symptoms. This study characterized the viruses circulating in phlebotomine sand flies in two departments in the Colombian Caribbean. Between August 2023 and December 2024, a descriptive study was conducted in the Departments of Córdoba and Cesar in Colombia. Four municipalities were selected per department, and four insect captures were performed using CDC light traps. Specimens were taxonomically identified and organized into groups according to species and study area, and total RNA was extracted for NGS analysis. Short sequences were quality-assessed, assembled using MEGAHIT to obtain contigs, and classified using DIAMOND-MEGAN6 to select viral genomic sequences for phylogenetic analysis. Thirteen viral families were identified, including a virus from the family Rhabdoviridae in Pi. evansi in the department of Cesar and another from the family Dicistroviridae in Lutzomyia gomezi in both departments. Two genome segments of the family Phenuiviridae were found in Lutzomyia gomezi in the department of Córdoba, Colombia. Sand flies harbor a diverse range of viral families, some of which are previously undescribed, and can be studied to determine their taxonomy and assess their potential to infect vertebrate cells or their interactions with medically important pathogens such as Leishmania spp.}, }
@article {pmid42354972, year = {2026}, author = {Diakoumopoulou, D and Slavko, A and Papadimitriou, K and Karoussis, IK and Nikolaou, C and Chatzipanagiotou, S and Ioannidis, A}, title = {Subgingival Microbiota Shifts Following Diode Laser-Activated Indocyanine Green Treatment in Periodontitis: A Pilot 16S rDNA Study.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061347}, pmid = {42354972}, issn = {2076-2607}, support = {485/03-07-2023/OPN: 9&#x3a1;5&#x399;46&#x3a8;8&#x39d;2-83&#x3a6;//National and Kapodistrian University of Athens/ ; }, abstract = {Periodontal disease is driven by a dysbiotic subgingival microbiota enriched in anaerobic pathogens, and novel antimicrobial strategies are needed to complement conventional therapy. This pilot study assessed changes in the subgingival microbiota following diode laser-activated indocyanine green-based treatment (EmunDo) using 16S rDNA amplicon sequencing of paired samples collected before and after therapy. Microbiome analysis revealed compositional shifts across all taxonomic levels, with reductions in disease-associated genera including Porphyromonas, Treponema, Fretibacterium, and Prevotella, and relative increases in taxa more commonly associated with periodontal health, such as Streptococcus, Actinomyces, and Haemophilus. Functional prediction further suggested treatment-associated variation in metabolic categories. Overall microbial richness was preserved between groups. These findings suggest that EmunDo treatment was associated with a restructuring of the subgingival microbiota toward a less dysbiotic profile, warranting further investigation in larger controlled studies using higher-resolution approaches such as shotgun metagenomics.}, }
@article {pmid42354979, year = {2026}, author = {de Sousa, LC and Caeiro, AJ and de Carvalho, CCCR}, title = {Screening of Marine Bacteria for Lipase Activity and Application as Whole-Cell Biocatalysts.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061355}, pmid = {42354979}, issn = {2076-2607}, support = {no. 101000327, project FuturEnzyme//European Union/ ; UID/04565/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Several strategies can be employed for the identification of novel microbial lipases. Despite the increasing importance of metagenomics in bioprospecting, significant limitations in the expression of recombinant proteins, and lipases in particular, remain. Culture-based bioprospecting approaches are, therefore, still valuable. In this work, a collection of bacterial isolates, mainly of marine origin, was screened for lipase activity through a culture-based approach. Screening for lipolytic bacteria was performed in solid media containing olive oil emulsions and rhodamine B. Positive isolates were subsequently grown in liquid media, to confirm lipase production. Significant hydrolytic activity towards the triglyceride substrates tributyrin and triolein could be observed with the biomass produced, although no lipase activity could be detected in the culture supernatants. Six isolates presenting high activity were characterized as whole-cell biocatalysts, and all were found to be active at temperatures ranging between 25 and 65 °C, and at pH values between 6 and 10.5. Genomic analyses of two of these Gram-negative lipase-producing isolates revealed the presence of several hypothetical genes encoding for lipolytic enzymes, including outer cell-bound enzymes, predicted through the application of machine-learning tools. These natural isolates, containing cell-associated lipases, may therefore be of special interest for application as whole-cell biocatalysts.}, }
@article {pmid42355557, year = {2026}, author = {Ang, MY and Chen, L and Song, L and Lipovich, L and Choo, SW}, title = {Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/life16061032}, pmid = {42355557}, issn = {2075-1729}, support = {5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; }, abstract = {Large language models (LLMs) are increasingly adopted in life-science research for scientific writing, coding, literature synthesis, workflow troubleshooting, and preliminary data interpretation. In microbial genomics and bioinformatics, their appeal is clear because researchers routinely integrate genome annotations, antimicrobial resistance profiles, virulence determinants, taxonomic assignments, microbiome outputs, workflow scripts, and primary literature. Yet this domain also highlights major risks, including hallucinated biological claims, inaccurate citations, irreproducible code, unsupported genotype-to-phenotype inference, and inappropriate clinical or public health framing. This narrative review examines responsible LLM use in microbial genomics as a representative life-science setting where interpretation depends on database provenance, validated workflows, expert assessment, and reproducible evidence chains. It considers applications in genome annotation, antimicrobial resistance interpretation, virulence analysis, microbiome and metagenomics workflows, coding support, and scientific writing. The review further presents MicrobeGuardGPT as a conceptual reliability framework for assessing LLM-assisted microbial genomics outputs before scientific, clinical, or public health use. By connecting task domains, evidence verification, expert validation, and reliability classification, the framework supports risk-aware LLM integration in bioinformatics. Responsible implementation will require domain-specific benchmarks, curated database linkage, transparent reporting, reproducible workflows, human oversight, and governance standards tailored to biological interpretation across research, diagnostic, surveillance, outbreak-response, educational, and translational contexts.}, }
@article {pmid42355602, year = {2026}, author = {Schroeder, TH and Eliwi Alsaffan, M and Stäudle, H and Dervishi, A}, title = {Influence of Ongoing Antibiotic Therapy on the Detection of Pathogenic Microorganisms Using Metagenomic Next-Generation Sequencing and Blood Culture in ICU Patients.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124434}, pmid = {42355602}, issn = {2077-0383}, abstract = {Background: Blood cultures often yield negative results in critically ill patients, particularly after antimicrobial therapy has started. Plasma metagenomic next-generation sequencing enables culture-independent pathogen detection, but its diagnostic performance relative to blood cultures, especially under ongoing antibiotic exposure in ICU populations, remains unclear. Methods: In this retrospective single-center study, we analyzed adult ICU patients who underwent plasma metagenomic next-generation sequencing testing with paired contemporaneous blood culture between March 2023 and September 2024. Patients were classified according to antibiotic exposure at the time of sampling, and the diagnostic yield and performance of metagenomic next-generation sequencing and blood culture were compared overall and stratified by duration of antibiotic exposure. Results: A total of 393 paired metagenomic next-generation sequencing-blood culture samples from 302 ICU patients were analyzed. Blood culture positivity was significantly lower in patients receiving antibiotics at the time of sampling (10.4% vs. 30.4%), whereas metagenomic next-generation sequencing positivity for bacteria remained stable (52.6% vs. 50.8%). With increasing antibiotic exposure, blood culture yield declined sharply, while metagenomic next-generation sequencing detection showed minimal variation. Overall, the concordance of metagenomic next-generation sequencing compared with blood culture as a comparator was 75.3%, with a negative predictive value of 88.0%. Across all subgroups, metagenomic next-generation sequencing demonstrated a higher diagnostic yield than blood culture, with the greatest relative advantage in antibiotic-treated patients. Conclusions: In critically ill patients receiving antimicrobial therapy, blood culture diagnostic yield is markedly reduced, whereas plasma metagenomic next-generation sequencing maintains pathogen detection across varying durations of antibiotic exposure. Metagenomic next-generation sequencing represents a valuable complementary diagnostic tool alongside blood cultures in pretreated ICU patients.}, }
@article {pmid42355677, year = {2026}, author = {He, C and Zou, H and Jiang, Z and Zhou, Y and Ying, B}, title = {Metagenomic Next-Generation Sequencing for Pulmonary Tuberculosis Diagnosis and Infection Risk Factor Analysis in AECOPD Patients: A Single-Center Retrospective Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124507}, pmid = {42355677}, issn = {2077-0383}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; ZYGD23036//1. 3. 5 project for disciplines of excellence from West China Hospital of Sichuan University/ ; 2024YFFK0225//Science and Technology Department of Sichuan Province/ ; }, abstract = {Background: Pulmonary tuberculosis (TB) is a significant trigger of acute exacerbations of chronic obstructive pulmonary disease (AECOPD), so its timely and accurate diagnosis is essential. Also, the risk factors for TB occurrence in this population remain unclear. This study aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) for TB diagnosis in AECOPD patients, as well as to identify the associated risk factors. Methods: A retrospective observational cohort of 659 AECOPD patients with suspected pulmonary infection was enrolled. The microbial cell-free nucleic acids in bronchoalveolar lavage fluid samples were extracted and subjected to mNGS detection. The clinical data for each patient were collected from the hospital information system. The statistical analyses were performed with SPSS version 25.0. Results: A total of 170 cases, included for final analyses, were categorized into TB (n = 41), bacterial infection (n = 73), and non-infective control (n = 56) groups. Among these groups, the TB group had the highest intensive care unit (ICU) admission rate (46.34%) and longest median hospital stay (19.50 days) (p < 0.01). For TB diagnosis, mNGS demonstrated a greater sensitivity (86.00%), a lower specificity (93.30%), and a higher area under the curve (AUC, 0.877) than TB-DNA detection (70.21%, 100%, 0.848, respectively) and Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay (63.83%, 100.00%, 0.870, respectively). Notably, mNGS identified the bacterial or viral co-infections in 18.00% of TB cases. Furthermore, the stringently mapped read number determined by mNGS showed a positive correlation with ICU admission rate (r = 0.76) and in-hospital mortality (r = 0.77). The lower body mass index (BMI) and reduced natural killer (NK) cell count were identified as the independent risk factors in the TB group (both p < 0.05). Conclusions: For the diagnosis of pulmonary TB in AECOPD patients, mNGS demonstrated comparable performance to TB-DNA detection and Xpert MTB/RIF assay, and also mNGS identified co-infections. In addition, a lower BMI and reduced NK cell count were identified as the independent risk factors for TB occurrence in this cohort.}, }
@article {pmid42355923, year = {2026}, author = {Mammadov, RA and Roest, HP and Fuhler, GM and Su, J and Visseren, T and Janssen, HLA and Porte, RJ and Murad, SD and Hansen, BE and van der Laan, LJW and Peppelenbosch, MP}, title = {Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124755}, pmid = {42355923}, issn = {2077-0383}, abstract = {Background/Objectives: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut-liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host-microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan-Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam-Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation.}, }
@article {pmid42357036, year = {2026}, author = {Osipov, DO and Rozhkova, AM and Volkov, PV and Zorov, IN and Sinitsyna, OA and Trofimchuk, ES and Moskvina, MA and Grokhovskaya, TE and Yaroslavov, AA and Sinitsyn, AP}, title = {Changes in Mechanical Properties and Structure of PET Films Treated with Metagenome-Derived LCC[ICCG] PETase Heterologously Expressed in Penicillium verruculosum.}, journal = {Polymers}, volume = {18}, number = {12}, pages = {}, doi = {10.3390/polym18121510}, pmid = {42357036}, issn = {2073-4360}, support = {126030218233-1//The Ministry of Education and Science of the Russian Federation/ ; }, abstract = {This study examines the nature of enzymatic degradation of polyethylene terephthalate (PET) films mediated by a novel recombinant LCC[ICCG] PETase enzyme preparation based on P. verruculosum fungus. The investigation was conducted using amorphous PET samples and PET samples with varying degrees of crystallinity as substrates for PETase-catalyzed hydrolysis under different temperature and pH conditions. Mechanical testing revealed that enzymatic treatment reduced the yield stress by 20-25%, tensile strength by approximately twofold, and elongation at break by 5-10 times, while the deformation mechanism remained unchanged. Enzymatic degradation under acidic conditions was ineffective, whereas increasing the pH to 9-10 markedly accelerated PET degradation and the associated deterioration of mechanical properties. Thermal analysis (TGA, DSC) and microscopy (optical and scanning electron microscopy) demonstrated that degradation was localized at the polymer surface, leading to the formation of cavities, cracks, and submicron-sized pores rather than bulk material disintegration. An inverse correlation was observed between PET crystallinity and susceptibility to enzymatic degradation: samples with crystallinity below 13% could be almost completely degraded, whereas samples with crystallinity above 30% exhibited little or no measurable weight loss over the same period. Low-crystallinity PET underwent rapid degradation accompanied by a transient increase in crystallinity, while highly crystalline PET primarily accumulated surface defects that nevertheless caused a substantial loss of mechanical strength. Consequently, the experimental data obtained in this study provide useful information for understanding PET degradation and for future studies on enzymatic PET recycling. The systematization of feedstock characteristics and the elucidated patterns of enzymatic degradation will enable optimization of pretreatment, enzymatic hydrolysis, and monomer recovery process parameters, thereby facilitating the eventual production of secondary raw materials.}, }
@article {pmid42357147, year = {2026}, author = {Chen, X and Hou, C and Yu, H and Xie, J}, title = {Enhanced Yield of GmJAG1-Edited Soybeans Accompanied by Improved Function of the Rhizosphere Microbiome.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/plants15121828}, pmid = {42357147}, issn = {2223-7747}, support = {2023YFF1001600//National Key R&amp;D Program of China/ ; }, abstract = {In the present study, we investigated how soybean yield is enhanced upon editing of the gene GmJAG1 and the consequent influence on the structure and function of the rhizosphere microbiome. Field trials revealed that gene-edited (GE) soybeans had a 55.22% increase in yield without concomitant changes in root length. Metagenomic sequencing of the rhizosphere soil microbiome showed that, compared with the corresponding non-edited line (CK), the alpha diversity of the GE groups remained unaltered, whereas beta diversity differed significantly at the soybean reproductive (R2) stage. Notably, the rhizosphere microbiome of GE soybeans at the R2 stage exhibited enrichment of functional pathways related to transport, amino acid biosynthesis, and central metabolism. These findings suggest that GmJAG1 editing may shape the functional profile of the rhizosphere microbiome, which could potentially contribute to yield gains. This work offers a novel microbiological perspective for understanding the mechanisms by which yield may be improved in GE crops.}, }
@article {pmid42357170, year = {2026}, author = {Wang, P and Yin, D and Fu, G and Yi, X and Guo, Z}, title = {Nitrogen Input Alters Root Exudation of Kandelia obovata and Nitrogen Cycling in Constructed Mangrove Wetlands.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/plants15121851}, pmid = {42357170}, issn = {2223-7747}, support = {32271704//National Natural Science Foundation of China/ ; 2022A1515010562//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20230808105410020//The Shenzhen Science and Technology Project/ ; }, abstract = {The role of mangrove root exudates in mediating the nitrogen cycle, particularly under high dissolved inorganic nitrogen (DIN) input, in coastal ecosystems remains unclear. This research investigated variation in the root exudates, and nitrogen transformation and output, in constructed mangrove wetlands planted with Kandelia obovata under high, moderate, and low nitrogen-input levels (PCWs-H, PCWs-M, and PCWs-L, respectively). PCWs-H promoted increased root density and biomass accumulation, enhancing soil nitrogen sequestration, whereas PCWs-L induced greater specific root length, specific root surface area, and number of root tips. These changes directly influenced denitrification efficiency. Hydroxymethoxyphenylcarboxylic acid-O-sulfate and Arg-Ser released in root exudates under PCWs-H might act as potential denitrification inhibitors, thereby suppressing denitrifiers and impairing dissolved nitrogen purification. Elevated nitrogen loading predominantly limited denitrification, resulting in relative NO3[-]-N removal rates of PCWs-H < PCWs-M < PCWs-L (p < 0.05). Compared with PCWs-H and PCWs-L, the enhanced soil organic nitrogen storage under PCWs-M was associated with flavonoids in root exudates. Metagenomic analysis showed that denitrification was the dominant nitrogen removal pathway. Nitrogen loading influenced the effects of root exudates on the microbial community. Under PCWs-H, triterpenoids promoted norBC and nirK/S abundance but depressed amoABC abundance. Sterols and flavonoids in exudates under PCWs-L depressed nosZ abundance, instead activating dissimilatory nitrate reduction to ammonium. Compared with PCWs-H and PCWs-L, N2O emissions were minimal under PCWs-M. This study revealed that mangrove root exudates mediate the nitrogen cycle in mangrove wetlands, providing a theoretical basis for local authorities to manage DIN inputs and mitigate N2O emissions.}, }
@article {pmid42357267, year = {2026}, author = {Dumitru, CN and Dumitru, AO and Goroftei, L and Niculet, E and Ignat, MD and Baroiu, L and Nechita, A and Balan, G}, title = {Pharmacomicrobiomics of Non-Antibiotic Drugs: Mechanisms and Clinical Consequences of Gut Microbiota Alterations.}, journal = {Pharmaceutics}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/pharmaceutics18060651}, pmid = {42357267}, issn = {1999-4923}, support = {NA//"Dunarea de Jos" University of Galati/ ; }, abstract = {Background: The gut microbiota constitutes a metabolically active "second genome" that profoundly modulates drug pharmacokinetics, pharmacodynamics, and adverse reaction profiles. Beyond antibiotics, widely prescribed non-antibiotic pharmacotherapies exert clinically relevant pharmacomicrobiomic effects with implications for therapeutic optimisation and pharmacovigilance. Methods: This narrative review, conducted following PRISMA 2020 reporting principles (without PROSPERO pre-registration), searched PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library (January 2015-December 2024) for evidence on proton pump inhibitors (PPIs), metformin, NSAIDs, statins, SGLT2 inhibitors, and oral iron. Evidence tables included clinical human studies with molecular microbiota characterisation (16S rRNA or shotgun metagenomics), ≥20 participants, and a control arm; preclinical data informed mechanistic synthesis. Results: Of 68 eligible studies, 20 met criteria for the evidence tables. PPIs significantly remodelled gut microbiota composition with enrichment of oral-origin taxa ("oralisation of the gut"), associating with Clostridioides difficile infection and SIBO. Metformin enriched Akkermansia muciniphila and butyrate producers, contributing causally to glycaemic efficacy. NSAIDs compromised barrier integrity, with synergistic dysbiosis under PPI co-prescription. Statins correlated with reduced prevalence of the dysbiotic Bact2 enterotype. SGLT2 inhibitor data remained discordant. Oral iron consistently enriched Enterobacteriaceae at the expense of beneficial commensals.}, }
@article {pmid42357653, year = {2026}, author = {Sholes, SL and Norton, S and Gonzalez, A and Gaspar, JM}, title = {MGtree: A Fast and Flexible Alignment-Based Metagenomics Pipeline.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060643}, pmid = {42357653}, issn = {1999-4915}, support = {n/a//Merck &amp; Co., Inc., Rahway, NJ, USA (United States)/ ; }, mesh = {*Metagenomics/methods ; Phylogeny ; Humans ; Norovirus/genetics/classification ; Genotype ; *Sequence Alignment/methods ; Computational Biology/methods ; Genome, Viral ; *Software ; Papillomaviridae/genetics/classification ; Human Papillomavirus Viruses/genetics/classification ; }, abstract = {Metagenomics analysis is a critical tool in identifying and typing viral samples to aid surveillance, clinical, epidemiological, and other workflows. Despite advances in sequencing technology and analysis pipelines, there are still limitations that lead to reduced taxonomic resolution or false positives from highly recombinant or challenging samples. Here we describe MGtree, a novel metagenomics pipeline that utilizes a combination of full-length read alignments and phylogenetic analysis to classify samples of interest. We demonstrate that MGtree accurately genotypes viral samples from challenging norovirus and HPV datasets. MGtree outperforms the popular metagenomics programs Kraken2 and Centrifuge, and it succeeds with low-input samples where de novo assembly fails. MGtree's correct assignments across highly mutant and coinfected samples highlights its ability to resolve viral genotypes and its potential to improve classification precision in complex samples.}, }
@article {pmid42357654, year = {2026}, author = {Paoli, JE and Trovão, NS and Odoom, T and Mohktar, Q and Buabeng, KB and Adu, B and Tasiame, W and Anderson, B and Tawiah-Yingar, DNY and Subramaniam, K and von Fricken, ME and Mensah, GI and Mietzsch, M and McKenna, R and Johnson, SAM and Mavian, CN}, title = {One Health Genomic Surveillance at Human-Animal Interfaces in Rural Ghana Reveals Underreported Viruses of Zoonotic and Economic Concern.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060644}, pmid = {42357654}, issn = {1999-4915}, support = {N/A//University of Florida/ ; }, abstract = {Under a One Health framework, viruses of veterinary and zoonotic importance pose significant threats to animal and human health, food security, and livelihoods, particularly in regions with intense human-animal interactions. In West Africa, despite recent advances in surveillance programs, important gaps remain in understanding viral diversity and cross-species transmission at wildlife-livestock interfaces. We conducted metagenomic surveillance to characterize viruses circulating across livestock, domestic animals, and wildlife in rural Ghana in 165 animals sampled across five regions. Viral RNA from serum and tissue samples was sequenced with the Illumina platform, and genomes were de novo assembled with MEGAHIT. Phylogenetic relationships were reconstructed using Bayesian approaches. We report the first genomic sequences of porcine parvovirus 3, canine parvovirus, rotavirus A genotype R16, and bovine hepacivirus subtype B from Ghana in over a decade. Phylogenetic analyses revealed intercontinental linkages between Africa and Europe for parvoviruses, persistence of hepacivirus lineages, and evidence of cross-species transmission for rotavirus. Notably, detection in apparently healthy animals highlights underrecognized circulation, gaps in vaccination effectiveness, trade-related biosecurity vulnerabilities, and the role of wildlife in viral maintenance and transmission. Our findings reveal dynamic viral diversity and connectivity across animal populations and ecological interfaces, emphasizing the fluid and interconnected nature of pathogen circulation within One Health systems. By integrating metagenomics and phylogenetics, this study provides a scalable framework for enhancing surveillance capacity, enabling the early detection of emerging threats and informing targeted strategies to mitigate zoonotic and economically important viral diseases in West Africa.}, }
@article {pmid42357666, year = {2026}, author = {Lai, T and Liu, F and Li, G and Hua, L}, title = {ViroBioTree: A Tree-Structured Biological Evidence Retrieval Framework for Viral Protein Function Annotation.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060656}, pmid = {42357666}, issn = {1999-4915}, support = {Grant No. 2026GXNSFAA00640099//Natural Science Foundation of Guangxi province/ ; Guike AD25069086//the Science and Technology Project of Guangxi/ ; }, mesh = {*Viral Proteins/genetics/metabolism ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Humans ; Open Reading Frames ; SARS-CoV-2/genetics ; Genome, Viral ; *Software ; }, abstract = {Accurate viral protein function annotation is essential for genomic surveillance, yet conventional retrieval-augmented generation (RAG) pipelines often fragment biological evidence into fixed-length text chunks, disrupting relationships among ORFs, annotations, structural domains, sequence motifs, residue mappings, and model-derived attention evidence. We propose ViroBioTree, a tree-structured biological evidence retrieval framework for downstream viral protein evidence review rather than a new primary annotation classifier. Built as an evidence organization layer on ViralMultiNet-derived ORF-level predictions and annotations, ViroBioTree converts sequence, annotation, structure, and attention evidence into typed biological nodes and traceable edges, then performs deterministic multi-channel recall, evidence-aware reranking, balanced TopK selection, rule-based verification, and node-cited report generation. In a demo benchmark, ViroBioTree achieved its strongest deterministic proxy performance on structure-explanation tasks, with Precision@K = 1.0, Recall@K = 1.0, and diversity = 0.52; these values reflect expected node-type and tag agreement rather than independent biological correctness. A bounded full-scale SARS-CoV-2 index contained 39,800 ORF rows, 80,000 attention records, 199,418 nodes, and 495,886 edges. In a stratified full20k diagnostic evaluation, ViroBioTree showed task-dependent advantages over LlamaIndex vector retrieval for conflict detection, evidence retrieval, and structure explanation, while LlamaIndex remained competitive or stronger for annotation-rich function annotation. A cross-family Influenza A Virus (IAV) diagnostic audit showed that the schema can represent IAV evidence namespaces while explicitly exposing missing formal ORF inputs, missing attention evidence, and unavailable residue/PDB assertions. Supplementary robustness, external sanity-check, diversity-risk, expert-evaluation, domain-tool positioning, and cross-family audit analyses supported traceability, report quality, and conservative evidence handling, but also showed that stable Precision@K under query perturbation does not necessarily imply stable retrieved evidence sets. ViroBioTree operates offline and deterministically, but does not address raw-read assembly, base calling, primary ORF prediction, or wet-lab validation. Its results should be interpreted as proxy and expert-reviewed evidence for traceable viral protein evidence retrieval and report generation rather than as direct validation of biological function annotation.}, }
@article {pmid42357739, year = {2026}, author = {Xue, T and Zhang, B and Wang, Z and Ma, Y and Shen, Q and Ding, J and Yang, X}, title = {Rapid Metagenomic Detection of Brucella abortus During a Two-Case Bovine Abortion Investigation in Inner Mongolia, China.}, journal = {Veterinary sciences}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/vetsci13060541}, pmid = {42357739}, issn = {2306-7381}, abstract = {Abortion in cattle entails substantial economic loss, and rapid identification of abortigenic pathogens is critical for timely on-farm response and reduction in human exposure risk. In 2024, two Holstein cows from a small farm in Inner Mongolia aborted in close succession without an obvious cause. Vulvar swabs from both cows, one afterbirth sample, and whole blood from one aborted fetus were collected. Shotgun metagenomic sequencing was performed, followed by host-read removal, taxonomic profiling with Kraken2, de novo assembly of Brucella-aligned reads, and whole-genome comparison. Serological tests, Gram-stained smears, and Brucella genus- and species-specific qPCR assays were used as orthogonal verification. Putative resistance and virulence determinants were screened against CARD and VFDB. Brucella reads were detected in all samples, with the highest relative abundance in the 138-afterbirth (96%). qPCR assays detected Brucella DNA and B. abortus-specific signals in all four samples. A draft Brucella genome was assembled from the 138-afterbirth sample and was phylogenetically placed within B. abortus, showing relatedness to previously circulating Chinese lineages. Cows 138 and 198 were RBT-positive with SAT titres of 1:100 (++). No acquired Brucella resistance genes were identified in CARD. Within 72 h of sample receipt, B. abortus was reported to the farm and local authorities and emergency biosecurity measures were implemented. This field investigation shows that metagenomic sequencing, when combined with conventional serology, microscopy, and targeted qPCR, can support rapid etiological investigation when culture is delayed, hazardous, or biosafety level 3 facilities are unavailable.}, }
@article {pmid42357757, year = {2026}, author = {Ma, L and Qu, J and Li, X and Liu, Y}, title = {Ecological Reassembly of the Milk Microbiome and Its Associated Resistome During the Dry Period in Dairy Cows.}, journal = {Veterinary sciences}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/vetsci13060559}, pmid = {42357757}, issn = {2306-7381}, support = {2023YFD1800100//National Key Research and Development Program of China/ ; No. IFR-06//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {The aim of this study was to characterize the coordinated dynamics of the mammary microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the dry period, calving, and early lactation. The mammary microbiome undergoes substantial ecological changes across these stages, yet the coordinated dynamics of microbial composition, ARGs, and MGEs remain poorly understood. Here, shotgun metagenomic sequencing was performed on mammary secretion samples collected before dry-off (BM), immediately after calving (ACM), and one month postpartum (AM). The mammary microbiome exhibited a clear "exposure-bottleneck-reassembly" trajectory. BM was characterized by high microbial diversity and the enrichment of environmentally associated taxa, whereas ACM displayed a pronounced immunological bottleneck with markedly reduced microbial diversity and network complexity. During AM, microbial communities partially recovered but remained distinct from the BM state, indicating persistent ecological restructuring after calving. ARGs and MGEs showed parallel dynamics, with broad resistome and mobilome diversity in BM, a sharp contraction in ACM, and a selective re-expansion in AM. Network analysis further revealed maximal ecological complexity in BM, increased ARGs/MGEs connectivity in ACM, and partial stabilization in AM. These findings demonstrate that host physiological transitions, together with dry cow therapy (DCT), drive the coordinated remodeling of the mammary microbiome, resistome, and mobilome across the dry period.}, }
@article {pmid42358061, year = {2026}, author = {Morvil, N and Goh, WGW and Zheng, C and Sutjipto, S and Ng, DHL and Zambon, M}, title = {Navigating the Future of Respiratory Infections: Key Insights From International Congress in Singapore, 17-20 September 2025.}, journal = {Influenza and other respiratory viruses}, volume = {20}, number = {7}, pages = {e70276}, doi = {10.1111/irv.70276}, pmid = {42358061}, issn = {1750-2659}, mesh = {Humans ; Singapore ; *Respiratory Tract Infections/prevention &amp; control/diagnosis/epidemiology/drug therapy/therapy/virology ; Antiviral Agents/therapeutic use ; Animals ; }, abstract = {BACKGROUND: The 8th International Society for Respiratory Viruses (ISRV) Antiviral Group Conference, held jointly with the 3rd International Meeting on Respiratory Pathogens in Singapore (17-20 September 2025), examined evolving approaches to prevention and management of respiratory infections. This report summarizes the major themes and perspectives that emerged across the meeting.<br><br>METHODS: We reviewed plenary sessions, thematic symposia and panel discussions and synthesized recurring concepts relevant to clinical practice and preparedness. Discussions were organized into key domains, including therapeutics, host response, vaccination, surveillance, diagnostics and research infrastructure.<br><br>RESULTS: Presentations highlighted the development of long-acting and broadly active antivirals, interest in combination therapy and early treatment, and increasing recognition that inflammatory host responses contribute substantially to disease severity. Advances in vaccines targeting conserved viral components and long-acting monoclonal antibodies were discussed, along with the growing role of adaptive platform trials and harmonized clinical endpoints. A recurring theme was the transition from pathogen-centred management to a broader framework incorporating host responses. Speakers also emphasized integrated surveillance using genomic sequencing, metagenomics and rapid point-of-care diagnostics within a One Health framework addressing zoonotic spillover.<br><br>CONCLUSIONS: The meeting illustrated how clinical care, translational science and public health preparedness are becoming increasingly interconnected. Sustained investment in surveillance systems, clinical trial platforms and access to therapeutics will be necessary to translate scientific progress into routine care and to strengthen readiness for future epidemics and pandemics.}, }
@article {pmid42358249, year = {2026}, author = {He, L and Huang, Y and Li, H and Zhu, B and Zhang, Z and Wu, J and Zhou, S and Zhan, Q and Wu, K and Wu, F}, title = {Novel insights into gut microbiota alterations in major depressive disorder with suicidal ideation: a metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1843301}, pmid = {42358249}, issn = {1664-302X}, abstract = {INTRODUCTION: Suicidal ideation in major depressive disorder (MDD) is common, yet its biological mechanisms and biomarkers remain unclear. The gut microbiota, a key component of the gut-brain axis, has been implicated, but current evidence is limited.<br><br>METHODS: We analyzed fecal samples from 141 participants, including 52 healthy controls (HCs) and 89 first-episode, drug-na&#xef;ve MDD patients, further classified into suicidal ideation (SI, n = 57) and non-suicidal ideation (NSI, n = 32) groups using the Beck Scale for Suicide Ideation (BSSI). Shotgun metagenomic sequencing with HUMAnN3-based taxonomic and functional profiling was performed. Microbial diversity, differential abundance, and partial correlation analyses with suicidal ideation severity were conducted to identify key microbial taxa associated with suicidal ideation. For functional difference analysis, MaAsLin2 was employed across four levels: KEGG Orthology (KO), KEGG pathways, CAZy, and MetaCyc pathways. Mediation analysis was used to assess potential mediating effects between suicidal ideation and key microbial taxa after adjustment for age, sex, education, and BMI.<br><br>RESULTS: No significant differences were observed in overall microbial diversity. Bacteroides cellulosilyticus was enriched in HCs and showed a significant negative association with suicidal ideation severity. Functionally, compared with the NSI group, patients with suicidal ideation exhibited reduced microbial capacities related to peptidoglycan biosynthesis. Mediation analysis further indicated that B. cellulosilyticus may modulate suicidal ideation through pathways involved in carbohydrate transport and metabolism, vitamin K2 biosynthesis, and DNA repair.<br><br>CONCLUSION: Bacteroides cellulosilyticus may act as a potentially protective microbial species, negatively regulating suicidal ideation, possibly by enhancing carbohydrate metabolism and short-chain fatty acid production. Notably, this species has received limited attention in the context of psychiatric disorders, highlighting its potential as a novel microbial target. These findings provide new microbiome-based insights into suicidal ideation in MDD.}, }
@article {pmid42358254, year = {2026}, author = {Duan, G and Kong, L and Duan, S and Nie, S and Gu, W}, title = {Research progress on emerging and important Tick-Borne pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1866307}, pmid = {42358254}, issn = {1664-302X}, abstract = {Ticks are important vector arthropods, which can carry and transmit a variety of pathogenic microorganisms, and pose a serious threat to global public health. This study reviews the research progress of the main and emerging tick-borne pathogens, such as Lyme disease related Borrelia, Rickettsia, Babesia, Thrombocytopenia Syndrome Virus (SFTSV), Tick-borne Encephalitis Virus (TBEV), Alongshan virus (ALSV), etc., focuses on their genomic diversity, pathogenicity, transmission and immune escape, co- infection. In addition, the application of new detection technology [Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), metagenomic next-generation sequencing (mNGS), microfluidics] in Tick-Borne pathogens is summarized.It highlights current research limitations, including delayed vaccine development and inadequate surveillance systems. Finally, future research directions are prospected, providing theoretical references for the prevention and control of tick-borne diseases.}, }
@article {pmid42358269, year = {2026}, author = {Hou, Z and Shi, M and Gou, S and Liao, D and Hu, C and Zhang, Q and Zhang, X and He, L and Ba, Y and Zhang, Y and Li, Y and Zhou, K and Wang, H and Song, L}, title = {Relative contributions of vegetation and soil properties to microbial community structure and function in alpine and subalpine meadows of the southeastern Tibetan Plateau.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1847498}, pmid = {42358269}, issn = {1664-302X}, abstract = {INTRODUCTION: Ongoing climate warming is expected to promote the upward expansion of subalpine meadows and the gradual replacement of alpine meadows on the southeastern margin of the Tibetan Plateau. However, the mechanisms by which these vegetation transitions reshape belowground microbial taxonomic composition and metabolic functional potential remain poorly understood.<br><br>METHODS: We investigated soil microbial community structure and functional potential in alpine meadow (AM) and subalpine meadow (SM) ecosystems in the Napahai Basin by integrating vegetation surveys, soil chemical analyses, enzyme activity assays, and metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Altitudinal differences in hydrothermal conditions were associated with pronounced divergence in plant community composition and soil nutrient status between the two meadow types. Although microbial &#x3b1;-diversity did not differ significantly, &#x3b2;-diversity analyses revealed distinct taxonomic and functional differentiation. Functional annotations based on CAZymes and KEGG indicated that variation in microbial functional potential was closely associated with coordinated changes in carbon, nitrogen, and phosphorus availability, suggesting that microbial metabolic strategies shifted along the environmental gradient. Random forest and partial least squares path modelling further showed that plant community composition exerted a stronger direct influence on microbial functional configuration than soil-mediated indirect effects. These findings highlight the prominent role of vegetation in shaping microbial functional potential and underscore the sensitivity of belowground ecological processes to vegetation transitions along environmental gradients in high-elevation meadow ecosystems.}, }
@article {pmid42358428, year = {2026}, author = {Chen, Y and Tian, D and Bai, Y and Xu, J and Liu, S and Wang, Y and Li, X}, title = {Case Report: Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease: the key diagnostic role of metagenomic high-throughput sequencing.}, journal = {Frontiers in medical technology}, volume = {8}, number = {}, pages = {1801483}, pmid = {42358428}, issn = {2673-3129}, abstract = {BACKGROUND: Listeria monocytogenes is an opportunistic foodborne pathogen that causes severe invasive infections, such as meningitis, primarily in immunocompromised individuals, the elderly, and pregnant women. Diagnosis is often challenging due to nonspecific early symptoms.<br><br>CASE DESCRIPTION: A 67-year-old male with a history of chronic obstructive pulmonary disease (COPD) presented with a 4-day history of persistent high-grade fever and altered mental status. Initial empirical antibiotic therapy (meropenem) proved ineffective.Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) definitively identified L.monocytogenes. The patient was diagnosed with "Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease". Patients with pathogenic bacterial infections completed a 21-day course of ampicillin and sulbactam sodium and a 14-day course of gentamicin, resulting in a rapid improvement in clinical symptoms and biochemical parameters.<br><br>CONCLUSION: This case underscores the critical role of mNGS in the aetiological diagnosis of central nervous system infections, especially when conventional methods are inconclusive. It highlights the need for a high index of suspicion for listeriosis in elderly patients with comorbidities presenting with unexplained fever and neurological decline.}, }
@article {pmid42358480, year = {2026}, author = {Flores, GD and Damon, ZF and Ford, M and Gancz, NN and Savoca, PW and Esfand, SM and Chu, KA and Querdasi, FR and McCann, CF and Westman, JG and Labus, JS and Clewett, D and Parr, AC and Hsiao, EY and Jacobs, J and Silvers, J and Callaghan, BL}, title = {A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {55}, number = {}, pages = {101275}, pmid = {42358480}, issn = {2666-3546}, abstract = {Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12-15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.}, }
@article {pmid42358948, year = {2026}, author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G}, title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1849216}, pmid = {42358948}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; }, abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.<br><br>METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.<br><br>RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.<br><br>CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.}, }
@article {pmid42359020, year = {2026}, author = {Wei, BH and Da, HJ}, title = {Purulent Pericarditis Caused by Polymicrobial Periodontal Pathogens (Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis): A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {598156}, pmid = {42359020}, issn = {1178-6973}, abstract = {BACKGROUND: Purulent pericarditis is a rare, life-threatening infection, most commonly caused by bacteria such as Staphylococcus aureus. We report an exceptional case of hematogenously disseminated infection probably originating from the oral cavity, highlighting a novel pathogen profile.<br><br>CASE PRESENTATION: We report a 66-year-old male with no history of periodontal disease or oral procedures presented with purulent pericarditis and a concomitant subphrenic abscess. Metagenomic next-generation sequencing (mNGS) of pericardial fluid revealed a polymicrobial infection with three periodontal pathogens: Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis. The patient was treated with pericardiocentesis, targeted antibiotics, and organ support, resulting in clinical stabilization.<br><br>CONCLUSION: This case provides clinical evidence that a consortium of periodontal pathogens can disseminate hematogenously to cause severe metastatic infections in sterile sites, even in individuals without overt oral disease. It underscores the need to consider occult oral origins in infections of unknown source and illustrates the value of comprehensive molecular diagnostics in identifying fastidious organisms, although it remains undetermined whether both conditions were secondary to the same source.}, }
@article {pmid42359168, year = {2026}, author = {Mundt, B and Kant, R and Grzybek, M}, title = {Viral pathogens in urban rats: A one health systematic review of global surveillance evidence.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101468}, pmid = {42359168}, issn = {2352-7714}, abstract = {BACKGROUND: Commensal rats (Rattus norvegicus and Rattus rattus) thrive in urban environments worldwide, where they live near humans and may act as reservoirs for viral pathogens of public health relevance. Although rats are increasingly recognised as sentinels of urban environmental health, the diversity and distribution of viral infections circulating in urban rat populations remain incompletely characterised within a One Health framework.<br><br>OBJECTIVES: This systematic review synthesises global evidence on viral pathogens detected in urban rats, focusing on rat hepatitis E virus/Rocahepevirus ratti and human-associated hepatitis E virus/Paslahepevirus balayani where distinguishable, Seoul virus (SEOV), SARS-CoV-2, and additional viral taxa identified through targeted surveillance or, in rare cases, metagenomic approaches.<br><br>METHODS: Following PRISMA 2020 guidelines, five electronic databases were searched for primary studies reporting viral detection in urban Rattus spp. Eligible studies underwent screening, structured data extraction and quality appraisal. Viral prevalence was summarised descriptively by pathogen and geographic region.<br><br>RESULTS: A total of 70 studies met the inclusion criteria, spanning Europe, Asia, North America, South America and the Caribbean. HEV and SEOV were the most frequently reported viruses, with prevalence varying widely between regions. HEV prevalence ranged from low levels in parts of Europe and Asia to high levels in North America. SEOV was detected across all regions, with particularly high prevalence in parts of Asia and the Americas. SARS-CoV-2 was not detected in European rats but was reported at low to moderate prevalence in the Americas. Numerous additional viral pathogens were identified.<br><br>CONCLUSIONS: Urban rats globally harbour diverse viral communities, including pathogens with zoonotic potential. Surveillance remains uneven and methodologically heterogeneous. Integrating rat biomonitoring into coordinated One Health surveillance systems is critical to strengthen early warning capacity and mitigate zoonotic risk.}, }
@article {pmid42359352, year = {2026}, author = {Lyu, C and Zhou, Q and Xiao, X and Bai, X and Pu, Y and Zhu, H and Zhao, M and Meng, J and Lyu, H}, title = {Metagenomics next-generation sequencing of plasma combined with blood cells for improving the prognosis of early infection in patients with hematologic disorders: a real-world cohort study in northern China.}, journal = {Frontiers in molecular biosciences}, volume = {13}, number = {}, pages = {1662559}, pmid = {42359352}, issn = {2296-889X}, abstract = {INTRODUCTION: Infection is a leading cause of death in hematologic disorder patients. While plasma metagenomic next-generation sequencing (mNGS) is widely used, no studies have explored the clinical value of whole blood mNGS, combining plasma and blood cells, in these patients.<br><br>METHODS: We retrospectively analyzed the results of whole blood mNGS testing from 231 blood samples of hematological disorders patients with suspected infections. The diagnostic performance of whole blood mNGS and its clinical impacts on treatment were assessed based on the final clinical diagnosis.<br><br>RESULTS: mNGS testing in both plasma and whole blood showed significantly higher pathogen detection rates than blood culture (72.29%, 77.06% vs. 21.65%, P < 0.001). The total concordance rate of whole blood mNGS was also significantly higher than that of blood culture, conventional microbial testing, and plasma mNGS when compared to the final clinical diagnosis. Of the 101 pathogens detected by whole blood mNGS, 13 were missed by plasma mNGS. As a result, whole blood mNGS demonstrated a broad pathogen detection capability, especially in patients with non-hematologic malignancies or hematopoietic stem cell transplantation. Regarding treatment, whole blood mNGS had a positive impact on 72.73% of all patients, and 75.15% patients with pulmonary infections. It helped rule out infection in a timely manner, reduce or stop unnecessary antibiotic use, and enabled 77.88% of infected patients to benefit from whole blood mNGS sequencing.<br><br>DISCUSSION: Whole blood mNGS assays, combining plasma and blood cells, significantly improved pathogen detection rates and optimized antibiotic therapy in patients with hematological diseases and pulmonary infections or bloodstream infection. This approach facilitates the early management of patients with hematologic disorders who are at risk of infection.}, }
@article {pmid42359485, year = {2026}, author = {Addy, HPK and Amedorme, D and Osei-Poku, P and Kwarteng, A}, title = {Predicted Functional Potentials of Bacterial Communities in Fermented Maize Products From Ghana, Nigeria, and Benin via 16S rRNA Amplicon Sequencing and PICRUSt2.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70272}, doi = {10.1002/mbo3.70272}, pmid = {42359485}, issn = {2045-8827}, mesh = {RNA, Ribosomal, 16S/genetics ; *Zea mays/microbiology ; *Fermented Foods/microbiology ; Ghana ; Nigeria ; Benin ; *Microbiota/genetics ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Sequence Analysis, DNA ; Phylogeny ; Lactobacillus/genetics/metabolism ; DNA, Bacterial/genetics ; }, abstract = {Fermented maize products are integral to the diets of many African communities. Despite their cultural significance and health benefits, little is known about the metabolic potential of their microbial populations. This study utilized 16S rRNA amplicon sequencing data from the NCBI to characterize the functional capabilities of microbiomes in six maize-based fermented foods. Quality assessment and taxonomic classification were performed using QIIME2 with the SILVA 138 database, while functional predictions were generated with PICRUSt2 and analyzed in R. Taxonomic profiling revealed that Firmicutes dominated all samples, reaching peak abundance in Mawe (94.9%) and S37_Fermented_Maize (91.4%). Proteobacteria were elevated in S19_Fermented_maize (up to 36.5%) and S38_Dehulled_Maize (16.0%). At the genus level, Lactobacillus was most abundant in S5_Mawe (82.2%) and S6_Mawe (79.6%), while Acetobacter peaked in S19_Fermented_maize (32.7%). Regarding functional predictions, Lactobacillus appeared to drive key KEGG Orthologs and pathways, specifically ABC transporters, transcriptional regulation, and DNA replication mechanisms. In contrast, Weissella and Streptococcus contributed notably to peptide/nickel transport, L-lactate dehydrogenase (EC 1.1.1.27), and nucleotide biosynthesis. Acetobacter was prominent in Ogi, showing a connection with site-specific methylation (EC 2.1.1.72) and phospholipid synthesis (PHOSLIPSYN-PWY). Notably, commercial Mawe samples exhibited higher predicted activities related to transposase activity (K07496), energy metabolism, and peptidoglycan maturation (PWY0-1586). These findings demonstrate that while traditional fermentation processes maintain a consistent set of metabolic functions predominantly driven by Lactobacillus, distinct variations exist depending on product type and production approach. These predicted functions provide a baseline for further experimental validation of the metabolic contributions of microbial communities in fermented maize products.}, }
@article {pmid42359789, year = {2026}, author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ}, title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2691334}, doi = {10.1080/19490976.2026.2691334}, pmid = {42359789}, issn = {1949-0984}, mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth &amp; development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth &amp; development/metabolism ; }, abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.}, }
@article {pmid42360122, year = {2026}, author = {Banerjee, P and Al-Bayer, S and Calaor, J and Weber, S and Graham, NR and Andersen, JC and Economo, EP and Kennedy, S and Krehenwinkel, H and Gillespie, RG and Roderick, GK and Rogers, HS and Puliafico, KP}, title = {Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70172}, doi = {10.1111/1755-0998.70172}, pmid = {42360122}, issn = {1755-0998}, support = {RC21-1034//Strategic Environmental Research and Development Program/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; *Biodiversity ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; }, abstract = {DNA-based methods offer a rapid and cost-effective way for detecting species occurrence and monitoring biodiversity; among them, bulk DNA metabarcoding is well-established, and recently developed environmental DNA (eDNA)-based methods offer a non-lethal alternative. With a goal to develop suitable methods for assessing insect biodiversity for understudied island ecosystems where DNA reference libraries are incomplete, we compared established bulk DNA metabarcoding methods with eDNA across three replicated terrestrial ecosystem types (degraded forest, limestone forest, and grassland) on the island of Guam. Using two mitochondrial COI primer pairs, we performed bulk DNA metabarcoding of standard entomological collection methods (Malaise traps, pan traps, and vegetation beating), and compared the assessment of biodiversity with that from different eDNA sources (flowers, leaves, tree trunks, and spider webs). In our samples, eDNA and bulk DNA metabarcoding both detected a large proportion of overall taxa (OTUs, 86.6% and 60.3%, respectively). Although bulk DNA metabarcoding detected significantly more taxa, eDNA proved to be a reasonable non-lethal alternative. As expected, because of limitations in existing reference databases for understudied systems, species-level identification was achieved for only a few OTUs. Overall, the sampling approach was the dominant driver of arthropod diversity, explaining ~17% of the observed variation, while habitat type accounted for ~4%. Thus, each sampling approach captured some unique diversity and contributed to the complementary effect of maximizing detection. For rapid biodiversity surveys of terrestrial arthropods, we recommend integrating metabarcoding approaches, and in sensitive ecosystems where specimen capture is undesirable, eDNA offers a powerful non-lethal alternative to monitor diversity and community change.}, }
@article {pmid42360286, year = {2026}, author = {Shi, Q and Chen, C and Bai, T and Zhang, S and Wu, Y and Wu, H and Luo, H and Chen, Y and Zheng, S and Meng, X and Wu, Y and Gao, J and Wang, Z and Chen, H}, title = {Protein-Free Diet Aggravates Food Allergy Response via the Consumption of Glycochenodeoxycholic Acid in a Murine Model.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c03218}, pmid = {42360286}, issn = {1520-5118}, abstract = {Amino acid-based formulas (AAFs) are increasingly consumed in infants with food allergy (FA), while the effects of their long-term consumption on FA remain poorly known. This study investigated the effects of the long-term consumption of AAFs on FA by subjecting neonatal mice to an amino acid-based diet (AAD). Long-term consumption of AAD exacerbated allergic symptoms, Th2 responses, and mast cell activation and concurrently suppressed the differentiation of CD103[+] DCs and Tregs in the MLN. Furthermore, integrated metabolomics and metagenomics analysis revealed that AAD induced intestinal microbiota dysbiosis and altered the systemic metabolome, characterized by a marked depletion of Bacteroides and glycochenodeoxycholic acid (GCDCA). Critically, oral supplementation with GCDCA effectively attenuated the FA response in AAD-fed mice. In summary, our findings suggest that long-term consumption of AAD aggravates FA via GCDCA depletion, which highlights the necessity to avoid the excessive use of AAFs and positions GCDCA supplementation as a promising therapeutic strategy for FA.}, }
@article {pmid42360299, year = {2026}, author = {Drahun, I and Chukwunta, A and Ayodele, A and Pilling, BG and van Herk, WG and Cassone, BJ}, title = {Bacteriomes, cryptic forms and evolution of a common wireworm pest species, Hypnoidus bicolor.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70054}, pmid = {42360299}, issn = {1365-2583}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Like other insects, coleopterans harbour dynamic bacteriomes that shape core aspects of their life history. The bacteriomes of several wireworm species (Coleoptera: Elateridae) have been described; however, little research has been undertaken to determine the factors that influence their structure and composition. These soil-dwelling larvae of click beetles are significant agricultural pests in the Canadian Prairies, with the most ubiquitous species, Hypnoidus bicolor, delineated into two genetically distinct clades and both sexual and parthenogenetic populations. In this study, we collected 69 H. bicolor adults and larvae from nine populations spanning three Prairie provinces and subjected them to Sanger and 16S rRNA gene sequencing to determine their clade and characterize their bacteriome, respectively. Combined with long-term surveillance, we provide compelling evidence that the parthenogenetic and sexual populations are associated with different clades. Development, sampling location and host genetics all contributed to the plasticity of H. bicolor bacteriomes. These differences are largely attributed to gut bacterial community composition of larvae, whereas, in adults, they appear driven by overall community structure as well as differences in the presence/absence of taxa and within-clade/population variance. Several notable genera emerged from our study, including Alphaproteobacteria and Rickettsiella endosymbionts that predominated in the parthenogenetic clade. Incorporation of this research into integrative pest management and reclassification of H. bicolor into a cryptic species complex is also discussed. Overall, this study advances our understanding of Elateridae bacteriomes, including factors that contribute to their richness and community composition.}, }
@article {pmid42360358, year = {2026}, author = {Meier, DV and Greve, A and de Beer, D and Abed, RMM and Woebken, D}, title = {Sulfide-oxidizing potential and hypersalinity tolerance strategies in salt-crust covered coastal microbial mats.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag166}, pmid = {42360358}, issn = {1751-7370}, abstract = {Hypersaline microbial mats are dense microbial ecosystems capable of performing nearly complete element cycling under harsh conditions including near-saturation salinity. Our previous study of salt-crust covered microbial mats showed that oxygenic photosynthesis was inhibited at salt saturation, while phototrophic sulfide oxidation persisted despite well-known sulfide-oxidizing taxa being undetectable. In this study, we analyzed metagenome-assembled genomes (MAGs) from the same mats to identify sulfide-oxidizing taxa and adaptations enabling oxygenic phototrophs to survive salt saturation. We extended the dataset by including morphologically identical mats exposed to lower salinity regimes to identify metabolic capabilities specifically selected for by saturation-level salinity. The phototrophic sulfide oxidation capability was found in nearly all cyanobacterial MAGs, in some Chloroflexota, and in abundant Rhodovibrio populations previously not known to oxidize sulfide. Furthermore, we found clear indications of Haloarchaea-like potassium-based osmoregulation in Bradymonadaceae (Myxococcota) adding another taxon to the few known potassium-accumulating bacteria. Despite lower oxygen concentrations, salt-crust covered mats showed smaller proportions of fermenters and higher proportions of aerobic microorganisms than lower salinity mats. We compared the genetic signatures of hypersalinity and desiccation tolerance in cyanobacterial MAGs from this study to genomes from desiccation-prone environments such as desert soils and small freshwater streams. Genomes of hyperhalophilic cyanobacteria were characterized by lack of certain potassium transporters and catalase genes and presence of additional osmolyte transporter subunits and sulfide-oxidation genes. We hypothesize that during salt saturation the oxidative stress for mat dwelling cyanobacteria is lowered, while the ability to oxidize sulfide provides them with energy when oxygenic photosynthesis is inhibited.}, }
@article {pmid42360629, year = {2026}, author = {Liu, KJ and Gao, Y and Yang, X and Xia, Y and Lu, C and Li, ZR and Chu, X and Huang, H and Xu, P and Shi, M and Yuan, K and Yang, H}, title = {Diagnostic Performance and Cost-Effectiveness of BALF mNGS in Older Adults with Pulmonary Infections.}, journal = {Infectious diseases and therapy}, volume = {}, number = {}, pages = {}, pmid = {42360629}, issn = {2193-8229}, support = {KQTD20200820145822023//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20240813120110015//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20230807095204008//Shenzhen Science and technology innovation Commission foundation/ ; No. LCYJ2021008//Key Program for Clinical Research at Peking University Shenzhen Hospital/ ; }, abstract = {INTRODUCTION: Pulmonary infections in elderly patients cause high morbidity and mortality. Conventional culture has low sensitivity and slow turnaround, delaying targeted therapy. Metagenomic next-generation sequencing (mNGS) is an emerging technology, but its diagnostic performance and cost-effectiveness are unclear. This study therefore aims to evaluate its diagnostic performance compared to conventional culture in older adults with pulmonary infections and to assess its cost-effectiveness.<br><br>METHODS: From March 2020 to March 2023, 522 patients (aged 55-69&#xa0;years) diagnosed with pulmonary infections were enrolled at Peking University Shenzhen Hospital. Of these, 168 patients underwent simultaneous mNGS and conventional culture testing using bronchoalveolar lavage fluid (BALF) samples, while the remaining 354 patients received culture testing alone. Pathogen detection results were compared to assess the diagnostic performance of mNGS versus traditional culture methods. Additionally, cost-effectiveness analyses of the two diagnostic strategies-as well as the impact of mNGS testing timing post-admission-were conducted in the overall cohort and across stratified subgroups.<br><br>RESULTS: Among the 168 patients who underwent both tests, mNGS identified a greater diversity and abundance of microorganisms than culture (overall detection: 89.88% vs. 26.79%; pathogen detection: 67.86% vs. 18.45%, p&#x2009;<&#x2009;0.001). mNGS testing yielded a net economic benefit of 1202.70 CNY per patient overall and 3831.15 CNY among pathogen-positive cases. Delaying mNGS testing tended to be associated with increased hospitalization length of stay (LOS) and costs, with the most pronounced difference observed around 6&#xa0;days after admission (p&#x2009;<&#x2009;0.001). Early mNGS testing (within 6&#xa0;days of admission) provided a net benefit of 6346.00 CNY.<br><br>CONCLUSIONS: BALF-based mNGS showed higher positivity rates and a broader pathogen detection spectrum compared to conventional culture methods in this study. Early implementation of mNGS shows strong potential to guide the treatment of pulmonary infections and reduce healthcare costs for elderly and aging patients.}, }
@article {pmid42361430, year = {2026}, author = {Horowitz, ML and Shrestha, A and Feng, KH and Pelton, CA and Wells, R and Allen, RF and Clauss, TM and Stokka, D and Cavin, JM and Walsh, MT and Holmes, EC and Allison, AB}, title = {Viral etiology of orogenital papillomatosis and squamous cell carcinoma in bottlenose dolphins in the southeastern United States.}, journal = {Virology}, volume = {623}, number = {}, pages = {111015}, doi = {10.1016/j.virol.2026.111015}, pmid = {42361430}, issn = {1096-0341}, abstract = {Orogenital papillomatosis and squamous cell carcinoma is an emerging yet poorly understood complex disease of bottlenose dolphins (Tursiops truncatus and T. erebennus), both in the wild and under managed care. Previous studies have indicated a potential role of papillomaviruses and/or herpesviruses in the development of oncogenesis, although unbiased metagenomic approaches to examine the disease-associated virome in biopsied lesions have not been performed. Herein, we determined the viruses present in oral and genital lesions from both wild and managed care bottlenose dolphins from the southeastern United States through deep sequencing. The sampled dolphins were infected with two closely related but phylogenetically distinct lineages of delphinid gammaherpesvirus. Multiple different papillomaviruses were also detected, including a new species and several novel types of Tursiops papillomaviruses. Delphinid gammaherpesviruses were detected more often and at higher levels than papillomaviruses in both wild and managed care dolphins, although co-infections with both viruses were common. Additionally, we demonstrate that oral and genital swabs are an effective method for detecting viral infection in dolphins with or without lesions, providing a simple, non-invasive surveillance tool and an adjunct to surgical tissue biopsies. To build diagnostic tools for further study on viral diseases of bottlenose dolphins, we immortalized primary cells from oral frenulum biopsies via retroviral transduction of the simian virus 40 large T antigen gene, which was confirmed by immunoassays and chromosomal mapping. Elucidating the etiologic agent(s) and malignant transformation process of this important disease of dolphins may ultimately lead to the development of targeted therapeutics and/or preventative recommendations.}, }
@article {pmid42361635, year = {2026}, author = {Tian, L and Lu, JN and Zhang, Y and Zhang, Q and Jiang, G and Yin, Y and Li, L and Fei, YH and Yang, Y and Ruan, Z and Guo, Y and Wang, S and Tang, YT and Chao, Y and Qiu, R}, title = {Overlooked dissemination risk of resistomes in mining soil environments.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142779}, doi = {10.1016/j.jhazmat.2026.142779}, pmid = {42361635}, issn = {1873-3336}, abstract = {Global mining significantly alters soil microbial communities and enriches antibiotic resistance genes (ARGs) via metal co-selection. However, the dissemination of mining-associated resistomes into surrounding ecosystems remains poorly understood. We conducted a national-scale metagenomic investigation of 416 soil samples to characterize the mining resistome and its dissemination potential. Mining soils were notably enriched in bacitracin resistance genes. Host analysis revealed that 60% of ARG-carrying genomes in downstream farmland were shared with mining sites, while source tracking indicated that 57% of quinolone resistance genes in farmlands likely originated from mining areas. Bipartite network analysis further supported this resistome connection from mines to agricultural soils. Using an optimized risk assessment framework, we identified 14 high-risk ARGs, 50% of which were previously unreported. These high-risk ARGs exhibited distinct latitudinal distributions, often associated with uncharacterized hosts. This study provides the first systematic, national-scale evidence of ARG dissemination from mining environments to agricultural ecosystems. By identifying overlooked high-risk ARGs, this research fills critical knowledge gaps in evaluating resistomes from extreme environments and offers essential insights for managing ARG dissemination risks.}, }
@article {pmid42361757, year = {2026}, author = {Lyu, Y and Bi, X and Tan, Y and Jiang, J and Zhang, Y and Zhou, M and Chen, G and Guo, G}, title = {SANI® process enables sustainable coking wastewater treatment: performance, microbial mechanisms and detoxification.}, journal = {Water research}, volume = {304}, number = {}, pages = {126354}, doi = {10.1016/j.watres.2026.126354}, pmid = {42361757}, issn = {1879-2448}, abstract = {Coking wastewater (CW), characterized by high organic concentration, high toxicity, and poor biodegradability, poses significant challenges for biological treatment. The sulfate reduction-autotrophic denitrification-nitrification (SANI®) process, known for its robustness in treating municipal wastewater with high salinity and low sludge production, has not yet been explored for CW treatment under high-toxicity conditions. This study established a lab-scale continuous-flow SANI system treating real CW at stepwise increasing concentrations (30 %→60 %→100 % of real CW ratio) to investigate toxic pollutants removal performance and sulfur-mediated degradation mechanisms. The SANI process achieved efficient and stable removal of carbon (COD 83.5 %, TOC 93.3 %), nitrogen (NH4[+]-N 97.5 %, TN 85.1 %), and characteristic toxic pollutants (volatile phenols >99 %, SCN[-] >99 %) during 100 % CW treatment, with effluent biotoxicity substantially reduced. 16S rRNA gene sequencing revealed functionally complementary microbial consortia: sulfur-reducing genera (Gudongella, Desulfitobacterium) dominated the anaerobic reactor; mixotrophic denitrifiers (Thauera, Comamonas) enriched in the anoxic reactor; and nitrifiers (Nitrospira) coupled with sulfur-oxidizers (Thiobacillus) prevailed in the aerobic reactor. Metagenomic analysis elucidated complete nitrogen/sulfur metabolic networks and typical toxic pollutant degradation pathways: SCN[-] degradation proceeded via the CNO pathway, while phenol degradation followed the meta-cleavage pathway after hydroxylation. This study pioneers SANI process for sulfur-rich real CW treatment, demonstrating it enables simultaneous removal of carbon, nitrogen, and toxic pollutants-offering a breakthrough low-carbon alternative for industrial wastewater.}, }
@article {pmid42361875, year = {2026}, author = {Liu, C and Che, C and Huang, P and Gao, J and Wang, S and Ji, B}, title = {Dual carbon source driven metabolic coupling shapes microalgal-bacterial granular sludge stability.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125119}, doi = {10.1016/j.envres.2026.125119}, pmid = {42361875}, issn = {1096-0953}, abstract = {Microalgal-bacterial granular sludge (MBGS) is a viable technology for wastewater treatment, yet its operational stability is often limited under single-carbon conditions due to metabolic imbalance. In this study, six dual carbon strategies were evaluated to investigate their roles in regulating system stability and pollutant removal. The results showed that carbon source composition strongly influenced reactor performance, potentially by pH buffering, thereby reshaping microenvironmental conditions and microbial community structure. Among all conditions, the acetate-glucose system achieved the highest stability, with simultaneous removal of COD (91.1%), NH4[+]-N (96.8%), and PO4[3-]-P (96.9%). Metagenomic analysis and system performance indicated that proton consumption during acetate assimilation likely offset acidification from glucose fermentation, maintaining a favorable alkaline niche (pH 10.0-10.2) that enriched functional bacteria (e.g., Thauera, 4.1%) and enabled simultaneous nitrogen and phosphorus removal. In contrast, the glycerol-glucose system induced severe acidification (pH < 4.0), which suppressed bacterial activity and shifted the community toward acid-tolerant fungi (e.g., Fusarium, 38.9%), resulting in functional deterioration. These findings suggest that pH buffering likely serves as a key regulatory parameter linking carbon metabolism to system stability. Rational pairing of carbon sources with complementary proton fluxes may provide a practical strategy to enhance MBGS robustness and offers a generalizable framework for carbon-source design in biological wastewater treatment.}, }
@article {pmid42361876, year = {2026}, author = {Chen, S and Zhang, C and Li, P and Li, S and Xing, H and Zhao, Z and Zhang, C and Zhou, D and Huo, H}, title = {Tightened Coupling of Organic Nitrogen and Organic Carbon Synthesis Governs Integrity of Soil Organic Matter in Black Soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125123}, doi = {10.1016/j.envres.2026.125123}, pmid = {42361876}, issn = {1096-0953}, abstract = {Soil organic matter (SOM) underpins fertility and carbon sequestration in black soils, yet the regulatory role of soil organic nitrogen (SON) in SOM stabilization remains poorly resolved. Herein, a total of 246 cropland black soils samples spanning three SOM gradients (10 g/kg interval) collected before spring plowing were analyzed using integrated multi-spectroscopic techniques and metagenomics to unravel chemical transformations and microbial mechanisms linking nitrogen and carbon processes. Results demonstrated that SOM accumulation drove a compositional transition from labile polysaccharides-C toward persistent alkyl-C, aromatic-C and aromatic-N containing structures. SON emerged as a dominant regulator of both SOM accumulation and stabilization by promoting aromatization and nitrogen incorporation, thereby enhancing aromaticity and structural persistence. Metagenomic evidences revealed intensified microbial coordination between soil organic carbon (SOC) and SON synthesis under high SOM conditions. On average, 64.8% microbial species encoded concurrent capacities for SOC and SON synthesis under favorable SOM enrichment status. 79.4% higher microbial network interaction and 83.3% stronger coupling intensity between SOC and SON synthesis were observed in favorable SOM enrichment status. Above improvements were attributed to coordinated upregulation of five SOC synthesis pathways and six SON synthesis pathways, with increases ranging from 21% to 57.5% and 24% to 99.8%, respectively. Overall, this study demonstrates that SON is not only a passive component but also an active driver that couples microbial carbon-nitrogen metabolism to govern SOM integrity, providing a novel biological perspective for understanding SOM integrity in black soils.}, }
@article {pmid42361879, year = {2026}, author = {Ge, Z and Wang, S and Zhang, N and Li, Y and Huang, D and Zhang, J}, title = {Habitat-dependent viral dynamics and auxiliary metabolism in ecological floating beds: implications for biogeochemical function.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125118}, doi = {10.1016/j.envres.2026.125118}, pmid = {42361879}, issn = {1096-0953}, abstract = {Ecological floating beds (EFBs), plant-substrate floating treatment systems, have been widely implemented in aquatic ecological restoration, where microbes play crucial roles in nutrient cycling and material transformation. However, the ecology of viruses in EFBs remains poorly understood. Here, prokaryotic and metagenome-derived viral communities in a full-scale EFB were analyzed over 12 months utilizing 84 samples from biofilms, plant roots, and surrounding water. Viral communities, dominantly by Caudoviricetes (96.7%), exhibited temporal and habitat-dependent responses that contrasted with their prokaryotic hosts. Deterministic processes, primarily temperature and total organic carbon, shaped viral community composition and auxiliary metabolic gene (AMG) repertoires. Temperate viruses were enriched in biofilms and roots (8.91%-13.45%) compared to water (7.75%), indicating distinct interactions with attached prokaryotes and highlighting these niches as potential metabolic hotspots. Virus-host linkage analyses connected viruses to dominant prokaryotes and revealed abundant AMGs (n = 3,703; 238 types), including genes implicated in carbon, phosphorus and sulfur transformations. Furthermore, prokaryotic C/N/P/S-cycling gene repertoires showed stronger coupling in attached habitats, whereas viruses carrying element-cycling AMGs were relatively more abundant in water. These findings provide a genome-resolved view of habitat-dependent viral community structure and auxiliary metabolic potential in EFBs, identifying attached habitats as important compartments for future validation of virus-host interactions and their possible links to restoration-related biogeochemical processes.}, }
@article {pmid42361932, year = {2026}, author = {Ying, Y and Zheng, X and Yang, J and Ye, H and Dong, Z and Ji, Y and Li, S and Tan, X and Zhang, W}, title = {Tong-Xie-Yao-Fang Ameliorates IBS-D: Potential Role of Alistipes finegoldii-associated Gut Tryptophan Indole Metabolism.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {122061}, doi = {10.1016/j.jep.2026.122061}, pmid = {42361932}, issn = {1872-7573}, abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent chronic gastrointestinal condition characterized by visceral hypersensitivity, low-grade mucosal inflammation, and impaired epithelial barrier integrity. Current therapies remain limited, highlighting the need for more alternative strategies. Tong-Xie-Yao-Fang (TXYF), a classical Chinese herbal formula, has shown clinical efficacy in IBS-D, however, the mechanisms underlying its therapeutic effects remain unclear.<br><br>AIM OF THE STUDY: This study aimed to investigate whether and how TXYF exerts therapeutic effects by modulating colonic tryptophan metabolism, with a particular focus on the gut microbiota.<br><br>MATERIALS AND METHODS: IBS-D model was induced by combining chemical irritation and wrap restraint stress in C57BL/6J mice, and multi-omics approaches were employed to identify specific microbiota and metabolites modulated by TXYF. The multi-omics findings were further verified in vivo and in vitro.<br><br>RESULTS: TXYF treatment significantly alleviated IBS-D symptoms in our model. Non-targeted metabolomics identified the tryptophan-indole pathway as a key axis modulated by TXYF, with indole-3-acetic acid (IAA) emerging as a prominent differential metabolite in colonic tissue. Western blot analysis showed that TXYF activated the aryl hydrocarbon receptor (AhR) in the colon. Integrative metagenomic and metabolomic analyses revealed a strong association between Alistipes finegoldii and colonic indole and IAA levels. Consistent with these findings, transplantation of A. finegoldii combined with tryptophan supplementation, or administration of IAA alone, recapitulated the therapeutic effects of TXYF against IBS-D. In vitro, both IAA and faecal supernatant from TXYF-treated mice protected against tumour necrosis factor-induced epithelial barrier disruption in an AhR-dependent manner.<br><br>CONCLUSION: Collectively, the present study suggests that the therapeutic efficiency of TXYF against IBS-D is closely associated with its ability to modify microbiota-derived colonic IAA production, with gut microbiota member Alistipes finegoldii playing a key role in this effect.}, }
@article {pmid42361963, year = {2026}, author = {Loc, DH and Sulesco, T and Tóth, GE and Lühken, R and Schmidt-Chanasit, J and Velavan, TP}, title = {First Mosquito-Based Molecular Evidence of Tembusu Virus in Vietnam.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108927}, doi = {10.1016/j.ijid.2026.108927}, pmid = {42361963}, issn = {1878-3511}, abstract = {BACKGROUND: Mosquito borne flavivirus diversity in Vietnam remains incompletely characterized. Tembusu virus (TMUV), an emerging flavivirus associated with ducks and other avian hosts, has been reported in poultry in Vietnam, but molecular evidence from field-caught mosquitoes has been lacking.<br><br>METHODS: We screened 10,658 mosquitoes representing four major arbovirus vector species including Aedes aegypti, Ae. albopictus, Culex quinquefaciatus, Cx. tritarniorhynchus, collected across multiple ecological settings in Vietnam. Mosquitoes were grouped into 586 pools and tested using broad range RT-PCR assays targeting flaviviruses and alphaviruses. Positive flavivirus amplicons were subjected to sequencing, and one TMUV positive pool underwent deeper sequencing and phylogenetic analysis.<br><br>RESULTS: The Cx. tritaeniorhynchus pool (25 specimens) collected in rural southern Vietnam yielded a TMUV draft genome. In the complete genome phylogeny, the Vietnamese mosquito derived sequence clustered within a distinct monophyletic clade comprising strains from China, Thailand, Taiwan, and Vietnam.<br><br>CONCLUSIONS: These findings provide the first mosquito-based molecular evidence of a TMUV related virus in Vietnam and suggest that mosquito surveillance can reveal previously unrecognized viral diversity and transmission patterns.}, }
@article {pmid42362546, year = {2026}, author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE}, title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74744-z}, pmid = {42362546}, issn = {2041-1723}, abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.}, }
@article {pmid42362550, year = {2026}, author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R}, title = {Remodelling of the gut virome after long-term fasting.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42362550}, issn = {2055-5008}, abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.}, }
@article {pmid42362787, year = {2026}, author = {Sinha, B and Khandeparker, L}, title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42362787}, issn = {1573-2959}, abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.}, }
@article {pmid41499025, year = {2026}, author = {Cunanan, DJ and Carandang, THDC and Pilapil, JD and Cunanan, DJ and Mollasgo, AG and Manalo, GNS and Co, GS and Rosch, J and Carroll, K and Notarte, KI}, title = {Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {4}, pages = {1077-1091}, pmid = {41499025}, issn = {1435-4373}, abstract = {PURPOSE: Accurate and timely diagnosis is essential to ensure effective management of bacterial pneumonia to improve patient outcomes. This study aims to evaluate the use of metagenomic nanopore sequencing in the microbiological diagnosis of pneumonia compared to standard diagnostic procedures. METHODS: A comprehensive literature search across multiple databases was performed. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy 2 (QUADAS-2) tool. Pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and area under the curve (AUC) were determined. RESULTS: Thirteen studies were included in the systematic review, with eight eligible for meta-analysis. In the microbiological diagnosis of bacterial pneumonia, the overall sensitivity of nanopore sequencing using both MinION and GridION platforms is 86.08% (95% CI 75.96–92.37) while specificity is 84.97% (95% CI 75.94–91.02). Results show a high PPV (85.13%; 95% CI 77.72–90.38) and high NPV (85.27%; 95% CI 76.79–91.01). Nanopore sequencing also has a high diagnostic value based on the computed AUC (0.922) and DOR (40.68; 95% CI 11.22–147.48). Sensitivity analyses suggest a trend toward higher diagnostic accuracy for bacterial pneumonia with the MinION device and lower accuracy with the GridION platform. We also found that accuracy is higher when the focus of diagnosis is ventilator-associated pneumonia (VAP) and when endotracheal aspirate alone is utilized as the sample type. CONCLUSIONS: Nanopore sequencing offers faster, real-time results compared to traditional culture. It also shows higher specificity than short-read metagenomic next-generation sequencing (mNGS), particularly in ventilator-associated pneumonia. Further research is warranted for subgroup analyses to optimize the use of nanopore sequencing in detecting bacterial pneumonia.}, }
@article {pmid41511674, year = {2026}, author = {Yin, Q and Mei, X and Ma, Y and Zheng, M}, title = {Central nervous system infections caused by carbapenem-resistant klebsiella pneumoniae after CAR T-cell therapy in a patient with preexisting colonization: a case report and literature review.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {5}, pages = {1491-1499}, pmid = {41511674}, issn = {1435-4373}, support = {81974005//National Natural Science Foundation of China/ ; Y-SYBLD2022MS-0055//the Beijing Xisike Clinical Oncology Research Foundation/ ; 2025AFD777//the Joint Fund for Innovation and Development of Natural 205 Science Foundation of Hubei Province/ ; }, abstract = {OBJECTIVE: To investigate the risk factors for corresponding infections following chimeric antigen receptor (CAR) T-cell infusion in Carbapenem-resistant Enterobacteriaceae (CRE) carriers and to provide insights for managing such cases. METHODS: A retrospective analysis was performed on the clinical presentation, laboratory findings, treatment, and prognosis of a patient with preexisting colonization who developed CRE intracranial infection after CAR T-cell therapy. A systematic review of the literature was conducted to explore optimal antibiotic strategies for CRE-associated central nervous system infections. RESULTS: Carbapenem-resistant Klebsiella pneumoniae was detected in perianal swabs before preconditioning chemotherapy, and the patient subsequently received high-dose corticosteroids for cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome following CAR T-cell infusion. Despite broad-spectrum coverage, recurrent fevers and convulsions ensued. Metagenomic next-generation sequencing of cerebrospinal fluid on day +14 confirmed Kbsiella pneumoniae infection, later identified as a multidrug-resistant strain. Clinical and microbiological clearance was achieved following combination therapy centered on intravenous ceftazidime-avibactam, supplemented with intrathecal polymyxin B, guided by antibiotic susceptibility testing. The patient ultimately died three months later due to lymphoma progression. CONCLUSION: Defining optimal management strategies for CRE carriers is essential to integrate infection risk mitigation into the personalized framework of CAR T-cell therapy.}, }
@article {pmid41654923, year = {2026}, author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY}, title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41654923}, issn = {1479-5876}, support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.}, }
@article {pmid41779333, year = {2026}, author = {Hu, Y and Li, A and Qiu, S and Zhu, T and Guo, J and Zhang, W and Zhao, C and Lyu, Y}, title = {Characteristics of Multispecies Bacterial Cocultures for the Removal of Ammonia, Nitrate, and Nitrite from Water.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {5}, pages = {3811-3830}, pmid = {41779333}, issn = {1559-0291}, support = {2025AFD305//Hubei Provincial Natural Science Foundation - Yichang Innovation and Development Joint Fund/ ; }, abstract = {The removal of ammonia, nitrate, and nitrite from wastewater is essential for controlling nitrogen pollution. However, the efficiency of biological nitrogen removal is often limited by the scarcity of highly active bacterial strains. In this study, a coculture system, designated YEM003, was constructed using eight nitrogen-metabolizing bacterial strains isolated from the same activated sludge. YEM003 exhibited robust nitrogen removal performance, effectively eliminating ammonia, nitrate, and nitrite from wastewater under varying oxygen conditions. Metagenomic analysis revealed enrichment of key genes involved in nitrogen metabolism and elucidated nitrogen removal pathways of YEM003. Due to the unbalanced abundance distribution of the eight strains in YEM003, the contributions of each strain to the nitrogen removal metabolism in different wastewaters differed significantly. Overall, YEM003 exhibits comprehensive and efficient biological nitrogen removal capabilities and shows strong potential for application in wastewater nitrogen removal processes.}, }
@article {pmid41803286, year = {2026}, author = {Zhu, C and Zhu, Y and Gao, H and Wang, X and Guo, Y and Sun, H and Qi, M and Zhang, B and Hu, Y}, title = {Long-Term Preservation of Humid Earthen Sites: Shelter Efficacy, Essential Oil Dynamics, and Microbial Adaptation.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41803286}, issn = {1432-0991}, support = {2023C03G1752302//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, abstract = {This study evaluates the long-term conservation of humid earthen archaeological sites using protective shelters and plant essential oil treatments at the Laohuling Dam (Liangzhu, China), a UNESCO World Heritage site. Over seven years (2017–2024), structural deterioration, biological colonization, and microbial community dynamics were monitored through field surveys, amplicon sequencing (16 S rRNA and ITS), and shotgun metagenomics. Protective shelters effectively reduced large-scale structural damage and higher-plant colonization; however, enclosed and climate-controlled conditions promoted persistent microbial biofilms in high-humidity zones. Oregano essential oil treatments rapidly eliminated visible biofilms and suppressed recolonization for approximately 6–8 months, but did not prevent long-term microbial recovery. Post-treatment communities shifted from phototrophic and biofilm-forming taxa toward fast-growing, opportunistic heterotrophs, predominantly affiliated with Pseudomonadota. Metagenomic analyses revealed a stable resistome across consecutive treatment years. The high abundance of multidrug resistance genes (e.g., adeF, β-lactam- and CAMP-associated genes) primarily reflected the dominance of Pseudomonadota-related taxa rather than evidence of resistance evolution driven by essential oil application. No significant increase in resistance gene diversity or abundance was detected. These findings demonstrate that sheltering and essential oil treatments are effective short-term conservation tools but reshape microbial succession rather than eliminating biological risks. Long-term preservation of humid earthen sites therefore requires integrated strategies combining microclimate control, low-bioreceptivity materials, and continuous microbial monitoring.}, }
@article {pmid41998050, year = {2026}, author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE}, title = {Metaproteomics uncovers the functional capacity of a soil microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47816-9}, pmid = {41998050}, issn = {2045-2322}, support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; }, abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.}, }
@article {pmid42029951, year = {2026}, author = {Kallistova, A and Savvichev, A and Toshchakov, S and Tutubalina, N and Rusanov, I and Petrova, K and Kadnikov, V and Beletsky, A and Zakharova, E and Ravin, N and Pimenov, N}, title = {Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42029951}, issn = {1432-0991}, support = {22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; }, abstract = {It is evident that climate change is causing glaciers to melt at an accelerated rate. This has a noticeable impact on the hydrological regime of high-altitude lakes, as well as the activity of microbial communities. However, the impact of climate change on microbial processes, abundance and diversity of microbial communities in high-altitude lakes remains to be elucidated. The objective of the study was to evaluate the structure, activity and metabolic capacity of microbial communities inhabiting the high-altitude Caucasus lake. Analytical and radiotracer methods were used together with 16S rRNA profiling, and metagenome analyses. Elevated concentrations of dissolved organic carbon (DOC) were observed in both the water column of the lake (12.2–19.4 mg/l) and the pore water of the sediments (6.3–15.8 mg/l). The intensity of photosynthesis in water column was very low. The bulk of phototrophs concentrated on the sediment surface where we suggest they produce organic matter due to sufficient light penetration and warming of the overlying water. The elevated DOC concentrations facilitated the activity of diverse heterotrophic microorganisms, resulting in oxygen depletion and activation of anaerobic processes in sediments. In case of an increase in the average annual temperature of the region, it is possible to predict the transformation of the lake into a eutrophic meromictic reservoir with constantly anoxic water layers, where sulfate reduction and methanogenesis would assume a pivotal role.}, }
@article {pmid42047869, year = {2026}, author = {Gloanec, N and Huré, M and Bailly, L and Petit, &#xc9; and Loutelier-Bourhis, C and Goux, D and Coëffier, M and Ribet, D}, title = {Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42047869}, issn = {1432-0991}, support = {SUMONING ANR-22-CE14-0064-01//Agence Nationale de la Recherche/ ; Labex SynOrg ANR-11-LABX-0029//Agence Nationale de la Recherche/ ; ANR-18-EURE-0020 XL CHEM//Agence Nationale de la Recherche (FR)/ ; }, abstract = {Isolating bacteria from the human gut microbiota and analyzing their phenotypes is essential for complementing the data obtained by metagenomics and for characterizing the functions of these microorganisms in human physiology. In this study, we isolated bacteria from the gut microbiota of healthy individuals and identified an uncharacterized bacterial strain that we designated HC1M1C21T. Phylogenetic analyses based on 16S rRNA and whole genome sequences indicated that this strain belongs to the family Lachnospiraceae. The closest relative of strain HC1M1C21T is Pilosibacter fragilis CSJ-4T (97.0% 16S rRNA gene sequence identity). P. fragilis was initially classified in the family Clostridiaceae. Based on our phylogenetic analyses, we propose to transfer the genus Pilosibacter from the family Clostridiaceae to the family Lachnospiraceae. HC1M1C21T has a DNA G + C content of 48.7%. This strain is anaerobic, Gram-stain-positive, non-motile and non-spore-forming. HC1M1C21T cells appear as single rods or chained rods with tapered ends. Optimal growth was observed at 37°C, at pH between 5.7 and 7.0 and at salinity below 10 g/L. HC1M1C21T is a potent butyrate producer. On the basis of these data, HC1M1C21T represents a novel species from the genus Pilosibacter, for which the name Pilosibacter rotomagensis sp. nov. is proposed. The type strain of P. rotomagensis is HC1M1C21T (= DSM 119410T=LMG 33828T).}, }
@article {pmid42062386, year = {2026}, author = {Szklenarik, G and Dora, D and Szincsak, S and Acquah, CK and Biswas, A and Horváth, M and Galffy, G and Lohinai, Z}, title = {The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47296-x}, pmid = {42062386}, issn = {2045-2322}, abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic disorder affecting host–microbiome interactions beyond the airways. Although bacterial alterations in COPD have been documented, the gut mycobiome and its ecological integration with bacterial communities remain unexplored. In this study, we profiled the gut mycobiome of 61 non-small-cell lung cancer (NSCLC) patients stratified by COPD severity using ITS2 sequencing and analyzed 47 overlapping patients with available metagenomic data to construct cross-kingdom bacterial–fungal networks. Alpha diversity, assessed by Shannon, Simpson, and Chao1 indices, did not differ significantly between patients with and without severe COPD. Partial least squares discriminant analysis (PLS-DA) revealed partial separation of the two groups, with COPD severity explaining 6% of overall compositional variance (R[2]=0.06, p = 0.058). COPD-severe patients exhibited a significantly reduced Ascomycota/Basidiomycota ratio (p = 0.039) and lower relative abundance of Mucoromycota. Analysis of compositions of microbiomes (ANCOM) identified Myrothecium and Lasiodiplodia crassispora enriched in severe COPD, while Helotiales_unclassified and Phallus atrovolvatus were more abundant in non-severe cases. Fungal co-occurrence networks demonstrated reduced connectivity and modularity in severe COPD compared with non-severe COPD. Cross-kingdom analyses integrating bacterial genera revealed strengthened Candida–Enterococcus/Clostridium hubs and weakened Faecalibacterium/Roseburia–yeast associations in severe disease. Keystone analysis showed increased centrality for Candida, Aspergillus, Enterococcus, and Clostridium, and decreased centrality for Akkermansia and Roseburia. A compositional balance classifier achieved high discriminatory power (AUC = 0.88) in distinguishing COPD-severe from non-severe patients. These findings indicate that COPD severity is not characterized by major diversity loss but by guild-specific compositional shifts and extensive network rewiring, favoring oxygen-tolerant, opportunistic taxa over short-chain fatty acid–associated commensals.}, }
@article {pmid42343068, year = {2026}, author = {He, G and Liu, T and Xing, J and Rao, L and Chen, S and Xie, C and Wei, G and Quan, X}, title = {In Situ Quorum Quenching Effect Induced by Negative Potential on Electro-Conductive Membranes for Membrane Fouling Control in Membrane Bioreactors.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04557}, pmid = {42343068}, issn = {1520-5851}, abstract = {Membrane fouling is a major impediment to the widespread application of membrane bioreactors (MBRs) for water treatment. In recent years, the electro-conductive membrane bioreactor (E-MBR) has demonstrated efficacy in mitigating membrane fouling. The application of a negative potential to the electro-conductive membrane promotes electrostatic repulsion, effectively displacing negatively charged extracellular polymeric substances (EPS) away from the membrane surface. However, given the established vital role of quorum sensing (QS) in membrane fouling development, the interference of the negative potential on QS-mediated EPS secretion and biofilm formation has been largely overlooked. Herein, we found that the negative potential applied to the electro-conductive membrane could effectively suppress the QS process, thereby inducing the in situ quorum quenching (QQ) effect. The application of negative potential significantly reduced the levels of the signal molecule C14-HSL as well as EPS. Metagenomic analysis indicated that the relative abundance of the "signal transduction mechanism" pathway was suppressed, and the functional genes encoding C14-HSL receptor proteins belonging to "LuxR family" was downregulated in the cake layer of E-MBR. Density functional theory calculations and molecular dynamics simulation results revealed that the application of negative potential enhanced the electrostatic repulsion between the membrane and C14-HSL and induced the conformational changes of the LuxR protein, which synergistically induced the in situ QQ effect. This study provides a novel perspective on the antifouling mechanism in E-MBR.}, }
@article {pmid42343220, year = {2026}, author = {Nichols, H and Molokin, A and Davies, CP and Maloney, JG}, title = {Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05298-9}, pmid = {42343220}, issn = {1471-2180}, support = {8042-32000-112-00-D//USDA, ARS/ ; }, abstract = {BACKGROUND: Microeukaryotic parasites of the intestinal tract are an understudied group of organisms that infect humans and many other animals. Targeted sequencing methods focused on individual loci are usually employed for detection of these parasites, making comprehensive studies of microeukaryotic parasite diversity within hosts or other systems difficult. Exploratory approaches such as shotgun metagenomic sequencing to survey the diversity of microeukaryotic parasites in new and existing datasets are not well developed.<br><br>RESULTS: Utilizing existing datasets from 12 goose fecal samples, we explored some of the benefits and challenges of using shotgun metagenome sequencing to detect microeukaryotic parasites. We demonstrated the importance of careful curation of read classification data to avoid erroneously linking pathogens to hosts or environments as unsupported classifications were common in the data and varied widely depending on analysis parameters. However, we were able to establish strong support for the presence of sequences of Eimeria and Enterocytozoon bieneusi. In addition, examination of trichomonad reads indicated that parasite reads mapping to human pathogens unlikely to colonize geese may in fact represent cryptic microeukaryotic species that are not included in existing curated databases opening new potential avenues of study.<br><br>CONCLUSIONS: Taken together these findings support the idea that exploring microeukaryotic parasite diversity within shotgun metagenomic datasets can be beneficial to our understanding of the presence and diversity of these organisms in wildlife hosts.}, }
@article {pmid42343233, year = {2026}, author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM}, title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690689}, doi = {10.1080/19490976.2026.2690689}, pmid = {42343233}, issn = {1949-0984}, mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration &amp; dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; }, abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.}, }
@article {pmid42343345, year = {2026}, author = {Huang, H and Ye, X and Gu, D and Huang, E and Yu, X and Ai, L and Deng, J and Guo, P and Liu, H and Chen, Y and Wang, R and Luo, Y and Chen, P}, title = {Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03786-0}, pmid = {42343345}, issn = {1465-993X}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2022B1111020003//2021 Guangdong Province Key Areas Research and Development Plan "Biosafety Technology" Key Project/ ; 2023P-TS46//Featured Clinical Technique of Guangzhou/ ; 0720240122//Guangdong Provincial Center for Disease Control and Prevention Supports Talent Projects/ ; }, abstract = {BACKGROUND: Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) improves pathogen detection in severe pneumonia-related sepsis, but sampling is invasive and prone to false-positive results. Blood is easier to obtain, and broad-spectrum targeted NGS (tNGS) of microbial cell-free DNA may offer a practical alternative to BALF-based testing. We evaluated the diagnostic and prognostic value of blood-based bstNGS.<br><br>METHODS: In this retrospective cohort, 122 adults with suspected severe pneumonia-related sepsis and paired BALF and blood samples underwent BALF-mNGS, blood-bstNGS and blood-mNGS. Pathogens were adjudicated using a composite clinical reference. We assessed blood-BALF concordance, compared diagnostic performance across methods, and examined whether blood-bstNGS could down-weight likely false-positive BALF-only detections and stratify prognosis.<br><br>RESULTS: BALF-mNGS identified 414 microorganisms; 51% were adjudicated as causative or possibly causative, corresponding to 85.24% of patients. Among these pathogenic microorganisms, blood-bstNGS detected 45.02%, significantly more than blood-mNGS (22.27%), and nearly all pathogens detected by blood-mNGS were also detected by blood-bstNGS. Against the clinical reference, blood-bstNGS showed higher sensitivity (63.46%) than blood-mNGS (35.58%), conventional microbiological tests (CMTs) (49.04%), and blood culture (9.62%). Organisms detected only in BALF but not in blood were less likely to be classified as causative. Patients with concordant blood-bstNGS and BALF-mNGS profiles had significantly lower 30-day and 90-day mortality.<br><br>CONCLUSIONS: In severe pneumonia-related sepsis, blood-bstNGS provides sensitive, non-invasive pathogen detection. It acts as a complementary tool rather than a replacement for BALF-mNGS, offering an important diagnostic alternative when BALF is unavailable and improving specificity and prognostic utility when used in combination.}, }
@article {pmid42343457, year = {2026}, author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X}, title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02453-2}, pmid = {42343457}, issn = {2049-2618}, abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.<br><br>RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and&#x200b; a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in&#x200b; stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.<br><br>CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.}, }
@article {pmid42343580, year = {2026}, author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and L De Souza, M and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH}, title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.6c00391}, pmid = {42343580}, issn = {1520-6025}, abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and l-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.}, }
@article {pmid42343765, year = {2026}, author = {Qiu, X and Lei, Z and Wang, J}, title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {42}, number = {5}, pages = {2103-2113}, doi = {10.13345/j.cjb.250783}, pmid = {42343765}, issn = {1872-2075}, support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; }, mesh = {*Solanum lycopersicum/growth &amp; development/drug effects ; *Plant Roots/growth &amp; development/drug effects ; *Seedlings/growth &amp; development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; }, abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.}, }
@article {pmid42343869, year = {2026}, author = {Liang, P and Zhang, X and Cai, S and Hu, Z and Dong, L}, title = {Invasive aspergillosis in autoimmune inflammatory rheumatic diseases: epidemiology, risk factors, diagnosis, management and challenges.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2685285}, doi = {10.1080/07853890.2026.2685285}, pmid = {42343869}, issn = {1365-2060}, mesh = {Humans ; *Rheumatic Diseases/immunology/complications/drug therapy/epidemiology ; Risk Factors ; *Autoimmune Diseases/immunology/complications/drug therapy/epidemiology ; Aspergillus/immunology/isolation &amp; purification ; Immunosuppressive Agents/adverse effects ; Immunocompromised Host ; *Opportunistic Infections/epidemiology/diagnosis/immunology ; Antifungal Agents/therapeutic use ; *Invasive Pulmonary Aspergillosis/epidemiology/diagnosis ; Aspergillosis/diagnosis/epidemiology ; }, abstract = {BACKGROUND: Invasive aspergillosis (IA) is a life-threatening opportunistic fungal infection caused by Aspergillus species. In recent years, IA appears to have become more frequently reported among patients with autoimmune inflammatory rheumatic diseases (AIIRD), likely reflecting the broader use of immunosuppressive therapies, with incidence in high-risk AIIRD subgroups reported to reach approximately 6.7% in selected cohorts.<br><br>OBJECTIVE: This review aims to summarize the current evidence on the epidemiology, susceptibility mechanisms, risk factors, clinical presentation, diagnosis, and management of IA in AIIRD, and to outline the clinical practical challenges in this population.<br><br>METHODS: This narrative review was informed by a structured literature search of PubMed, Embase, Web of Science, and Google Scholar for studies on IA in AIIRD published up to August 2025.<br><br>RESULTS: IA in AIIRD patients generally appears to arise from multiple interacting factors, including compromised host immunity, immunosuppressive therapy, the underlying rheumatic disease itself, comorbidities, and environmental exposures. Aspergillus infection and the resulting anti-Aspergillus immunity may also induce or exacerbate autoimmune inflammation. Invasive pulmonary aspergillosis is the most commonly reported manifestation, typically presenting with nonspecific respiratory symptoms, and disseminated infection tends to occur in the setting of profound immunosuppression. Early, integrated microbiologic testing (e.g. serum or bronchoalveolar lavage galactomannan, culture, polymerase chain reaction, and next-generation sequencing) together with serial imaging examination may facilitate earlier detection and guides care. Although robust AIIRD-specific evidence remains limited, current practice generally favour a multidisciplinary, individualized approach incorporating timely antifungal therapy and careful modulation of immunosuppression. Reported mortality remains high, ranging from 25% to 85% across AIIRD cohorts, particularly when diagnosis and treatment are delayed.<br><br>CONCLUSIONS: IA is a serious and likely under-recognized infection in AIIRD patients. Multiple determinants appear to increase infection risk, and symptoms and imaging manifestations can mimic rheumatic disease activity, potentially contributing to diagnostic delay. Current epidemiological and clinical data on AIIRD-IA remain limited, and further studies are needed to refine risk stratification, establish diagnostic criteria tailored to AIIRD patients, and inform more evidence-based management strategies.}, }
@article {pmid42343917, year = {2026}, author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T}, title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2687219}, pmid = {42343917}, issn = {2000-2297}, abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.<br><br>METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.<br><br>RESULTS: Beta diversity demonstrated significant differences between groups (p&#x2009;<&#x2009;0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.<br><br>CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.}, }
@article {pmid42343927, year = {2026}, author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD}, title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.}, journal = {Applications in plant sciences}, volume = {14}, number = {3}, pages = {e70064}, pmid = {42343927}, issn = {2168-0450}, abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.<br><br>METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.<br><br>RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.<br><br>DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.}, }
@article {pmid42343969, year = {2026}, author = {Schaerer, LG and Anderson, RS and Chan, J and De Long, SK}, title = {Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag035}, pmid = {42343969}, issn = {2633-6685}, abstract = {Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/l to an average of 12.3 g/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. Lactiplantibacillus pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.}, }
@article {pmid42343970, year = {2026}, author = {Das, R and Kumar, R and Tamang, B}, title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag032}, pmid = {42343970}, issn = {2633-6685}, abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.}, }
@article {pmid42343982, year = {2026}, author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE}, title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.}, journal = {TH open : companion journal to thrombosis and haemostasis}, volume = {10}, number = {}, pages = {a28685248}, pmid = {42343982}, issn = {2512-9465}, abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.<br><br>OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.<br><br>METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known &#x3b2;2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.<br><br>RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell &#x3b2;2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-&#x3b2;2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-&#x3b2;2GP1 monoclonal antibody than a negative control.<br><br>CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.}, }
@article {pmid42344006, year = {2026}, author = {Tepson, JA and Agyirifo, DS}, title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.}, journal = {International journal of food science}, volume = {2026}, number = {}, pages = {6618960}, pmid = {42344006}, issn = {2314-5765}, abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.}, }
@article {pmid42344497, year = {2026}, author = {Yu, W and Yang, P and Ding, M and Guo, L and Liu, Y and Zhou, D and Gu, C}, title = {Acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with post-tuberculosis chronic pulmonary aspergillosis: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1828229}, pmid = {42344497}, issn = {2296-858X}, abstract = {This report describes a 59-year-old woman with a history of malignancy and post-tuberculosis lung disease complicated by chronic cavitary pulmonary aspergillosis. She was admitted with worsening hemoptysis and underwent bronchial artery embolization. However, she subsequently developed massive post-procedural hemoptysis, requiring mechanical ventilation. Sputum metagenomic next-generation sequencing detected SARS-CoV-2 and bacterial pathogens, prompting Paxlovid treatment for COVID-19 pneumonia. While her respiratory symptoms improved, epigastric pain developed. Based on elevated serum amylase/lipase and CT-confirmed peripancreatic inflammation, she was diagnosed with acute pancreatitis. One year later, pulmonary tuberculosis and liver metastasis recurred. This case highlights acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with multiple competing risk factors. Further, this case underscores the diagnostic complexity of structural lung disease with overlapping infections such as COVID-19 and stresses on the need for long-term surveillance.}, }
@article {pmid42344668, year = {2026}, author = {Huang, F and Zhang, Z and Zhao, Y and Ye, S and Gan, M and Li, X and Zhang, Y and Chen, L and Zhang, Y and Chen, L and Wang, T and Huang, J and Zhang, X}, title = {Altitude-Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics.}, journal = {Evolutionary applications}, volume = {19}, number = {6}, pages = {e70285}, pmid = {42344668}, issn = {1752-4571}, abstract = {High-altitude environments expose mammals and their gut symbionts to multifaceted stressors-hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short-chain fatty acid (SCFA)-producing bacteria-centered on Flavonifractor plautii, Intestinimonas butyriciproducens, and Enterococcus faecium-that formed antagonistic co-occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high-altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch-specific regulation of the tryptophan-kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety-validated isolates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings provide an actionable framework for altitude-informed facility siting, fecal microbiota transplantation (FMT) donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome-associated disease pressure in captivity.}, }
@article {pmid42344740, year = {2026}, author = {Zhang, X and Huo, H and Hu, L and Yang, F and Hu, X and Deng, Y and Feng, C and Wang, H and Huo, J}, title = {Dietary Lonicera japonica supplementation modulates cecal gut microbial composition and metabolomic profiles in weaned piglets.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1804735}, pmid = {42344740}, issn = {2297-1769}, abstract = {Weaning is a critical developmental stage in piglets and is often associated with intestinal dysbiosis, metabolic disturbances, and impaired gut barrier function. Phytogenic feed additives have emerged as promising natural alternatives to antibiotics for improving gut health. Lonicera japonica, a traditional medicinal and edible plant rich in bioactive compounds, exhibits well-documented antimicrobial, antioxidant, and immunomodulatory properties; however, its effects on the gut microbiota-metabolite axis in weaned piglets remain poorly understood. In this study, weaned piglets were fed either a basal diet (control group) or a Lonicera japonica-supplemented diet (experimental group). Cecal contents were collected for metagenomic sequencing to characterize gut microbial composition and for untargeted LC-MS-based metabolomic profiling. Functional pathway enrichment and microbe-metabolite correlation network analyses were conducted to elucidate potential mechanisms. Lonicera japonica supplementation significantly improved evenness in terms of microbial species richness and reshaped microbial community structure, characterized by the enrichment of beneficial taxa, including Firmicutes and Eubacterium coprostanoligenes, and a concomitant reduction in opportunistic pathogens such as Proteobacteria and Escherichia coli. KEGG pathway analysis revealed the upregulation of microbial pathways related to translation, replication, and energy metabolism, alongside the downregulation of stress-response-associated pathways. Metabolomic profiling demonstrated distinct metabolic signatures between groups, with elevated levels of unsaturated fatty acids, amino acid derivatives, and organic acids, and reduced bile acid intermediates in the Lonicera japonica-treated piglets. Correlation network analysis further revealed strong positive correlations between SCFA-producing bacteria and beneficial metabolites, underscoring a reinforced microbiota-metabolite axis. Collectively, these findings indicate that Lonicera japonica supplementation promotes a healthier and more stable gut ecosystem in weaned piglets through coordinated modulation of microbial composition, functional potential, and metabolic outputs. This study provides novel insights into microbiota-metabolite interactions underlying phytogenic interventions and supports the use of Lonicera japonica as a natural feed additive to enhance intestinal health and resilience during weaning.}, }
@article {pmid42344904, year = {2026}, author = {Guo, R and Chen, Q and Kong, L and Huang, A and Li, Y and Li, C}, title = {Anti-NMDAR and anti-MOG antibody double-positive encephalitis temporally associated with cytomegalovirus detection in cerebrospinal fluid: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1805851}, pmid = {42344904}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Cytomegalovirus/immunology/genetics ; *Cytomegalovirus Infections/immunology/diagnosis/drug therapy/cerebrospinal fluid/complications ; *Autoantibodies/cerebrospinal fluid/blood ; *Receptors, N-Methyl-D-Aspartate/immunology ; Antiviral Agents/therapeutic use ; DNA, Viral/cerebrospinal fluid ; Myelin-Oligodendrocyte Glycoprotein ; }, abstract = {The co-occurrence of MOG and NMDAR antibodies has been reported in a limited number of cases and is termed the overlapping syndrome (MNOS). Viral coinfections have been identified in a subset of patients with MNOS. Herein, we report the first case of MNOS with concomitant cytomegalovirus (CMV) infection detected in cerebrospinal fluid, a finding that helps to further explore the relationship between viral infection and MNOS. A previously healthy 49-year-old man developed fever and behavioral abnormalities following prodromal symptoms. Metagenomic next-generation sequencing (NGS) of the CSF identified CMV DNA with high confidence (specific reads: 362; relative abundance: 85.97%). Serology was positive for CMV IgG but negative for IgM; serum CMV-DNA detected by real-time PCR was negative. Positivity for anti-NMDAR antibodies and anti-MOG antibodies in the CSF, whereas only anti-MOG antibodies were detected in the serum. The patient's condition gradually improved after treatment with antiviral agents, corticosteroids, and intravenous immunoglobulin. The main limitations of this report include the lack of detection of CMV-DNA in CSF by real-time PCR, as well as the absence of dynamic assessment of serum/CSF CMV IgG/IgM, anti-NMDAR, and MOG antibody titers. Clinical vigilance for coexisting autoimmune encephalitis should be heightened following viral infections.}, }
@article {pmid42345796, year = {2026}, author = {Mancini, P and Brandtner, D and Cordeschi, G and Iaconelli, M and Mastrantonio, V and La Rosa, G and Porretta, D}, title = {Exploratory Metaviromic Analysis of the Sea-Rock Pool Mosquito Aedes mariae and the Water of Its Breeding Habitat.}, journal = {Biology}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/biology15120940}, pmid = {42345796}, issn = {2079-7737}, abstract = {The mosquito-associated virome may modulate host biology and influence vector competence, highlighting the importance of understanding its composition. Here, a metagenomic analysis was conducted to characterize the virome of the sea-rock pool mosquito Aedes mariae across sexes and developmental stages, together with water from its sea-rock pool breeding site in San Felice Circeo (Italy). A total of 51 viral taxa were identified, including viruses associated with bacteria and archaea (39%), plants, algae, fungi, and protists (35%), vertebrates (8%), and invertebrates (18%), including insect-specific viruses such as Mesoniviridae, Baculoviridae, Nudiviridae, Iridoviridae and Totiviridae. Twenty-five percent of the taxa were shared across samples, suggesting acquisition from breeding-site water and persistence across stages during development. Interestingly, the need for host genome filtering highlights the potential sequence similarity between viral and mosquito genomes, which may reflect the presence of endogenous viral elements or historical virus-host interactions. These findings represent the first characterization of the virome of Aedes mariae and highlight the role of aquatic breeding sites in shaping mosquito virome. Finally, we argue the importance of adequate sequencing depth and host genome filtering to capture the diversity of the mosquito virome.}, }
@article {pmid42345825, year = {2026}, author = {Zhakypbek, Y and Toktar, M and Kossalbayev, BD and Yang, Q and Shi, Q and Tursbekov, S and Belkozhayev, AM and Abseyt, AS and Kezembayeva, G and Kamarkhan, T}, title = {Soil Bacterial Community Structure and Functional Potential in the Caspian Drylands of Western Kazakhstan.}, journal = {Biology}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/biology15120969}, pmid = {42345825}, issn = {2079-7737}, support = {BR24993218//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3-V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies.}, }
@article {pmid42346014, year = {2026}, author = {Domingues, R and Pires, JCM}, title = {Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.}, journal = {Biotech (Basel (Switzerland))}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/biotech15020042}, pmid = {42346014}, issn = {2673-6284}, support = {UID/00511/2025 and UID/PRR/00511/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; LA/P/0045/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Understanding biological communities is essential for elucidating ecosystem structure and function. Metabarcoding based on ribosomal RNA (rRNA) genes, particularly 16S and 23S, is widely used to characterise bacterial and microalgal communities. However, analysing high-throughput sequencing data generated by platforms such as the Illumina MiSeq remains challenging due to fragmented bioinformatics tools, complex parameterisation, and limited accessibility for non-specialist users. In this study, a comprehensive and user-friendly bioinformatics pipeline is proposed for the analysis of 16S and 23S paired-end metabarcoding data. The workflow integrates all critical processing steps, including read merging, primer and adapter trimming, quality filtering, dereplication, chimaera removal, and clustering into Operational Taxonomic Units (OTUs). Taxonomic assignment is performed using curated reference databases, namely EZBioCloud for bacterial communities and µgreen for microalgae. The pipeline was developed in Python 3.11 and incorporates validated tools such as VSEARCH and Cutadapt, ensuring robustness and computational efficiency. Additionally, modules for alpha and beta diversity analysis are included to support comprehensive ecological interpretation. The main novelty of this work lies in providing a unified, GUI-based framework that enables the standardised processing of dual-marker (16S/23S) metabarcoding data within a single environment. In its current implementation, SOMBA supports the analysis of each marker through separate but harmonised workflows, ensuring consistency in parameterisation, processing steps, and output structure. This approach provides an accessible and standardised solution that bridges the gap between raw sequencing data and reliable biological insights, supporting applications in environmental microbiology and biotechnology.}, }
@article {pmid42346116, year = {2026}, author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M}, title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.}, journal = {Cells}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/cells15121089}, pmid = {42346116}, issn = {2073-4409}, support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; }, mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; }, abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.}, }
@article {pmid42346385, year = {2026}, author = {Li, J and Xu, X and Wang, H and Gao, R and Li, B and You, X}, title = {Relationship Between Calcium and Gut Microbial Composition and Metabolic Pathways in Children with Autism.}, journal = {Metabolites}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/metabo16060405}, pmid = {42346385}, issn = {2218-1989}, support = {531100006787540685//Chinese Academy of Medical Sciences &amp; Peking Union Medical College/ ; }, abstract = {Background/Objectives: Trace elements may influence autism spectrum disorder (ASD) severity through interactions with the gut microbiota and microbial metabolic functions, but calcium-related evidence remains limited. This cross-sectional study examined associations among hair calcium, gut microbial taxa, metabolic pathways, and behavioral phenotypes in children with ASD. Methods: We analyzed 183 children with ASD who had behavioral assessments, hair calcium measurements, and fecal shotgun metagenomic sequencing data. Participants in the lowest and highest calcium quartiles were first compared to characterize group-level microbiome differences. Full-sample analyses then tested associations among continuous hair calcium, microbial taxa, metabolic pathways, and behavioral measures after covariate adjustment. Benjamini-Hochberg false discovery rate correction was applied for multiple testing. Results: Hair calcium was positively associated with CARS, ATEC-Total, ATEC-1, and ATEC-3 scores, with the strongest associations involving ATEC-1 and ATEC-3. Alpha and beta diversity did not differ significantly between calcium quartile groups, but group-based microbiome analyses identified 63 differential species and 22 differential MetaCyc pathways. Full-sample integrated analyses connected calcium-associated microbial taxa, metabolic pathways, and ASD behavioral measures. Conclusions: Hair calcium was associated with ASD behavioral severity, selected gut microbial species, and microbial metabolic pathways. These findings support an association framework connecting longer-term calcium-related mineral profiles, gut microbial functional potential, and behavioral phenotypes, providing a basis for future longitudinal and multi-omics studies.}, }
@article {pmid42346775, year = {2026}, author = {He, Z and Nie, Y and Li, C and Sun, G and Zheng, W and Liu, H and Geng, M and Tian, J and Zhang, Y}, title = {GV-971 Ameliorates Chronic Restraint Stress-Induced Depression-like Phenotypes Accompanied by Reshaping of the Microbiota-Gut-Brain Axis.}, journal = {Marine drugs}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/md24060189}, pmid = {42346775}, issn = {1660-3397}, support = {2024CXPT029, 2025CXPT011//Key R&amp;D Program of Shandong Province, China/ ; ZR2024QH615//Shandong Provincial Natural Science Foundation/ ; SYS202205//Shandong Laboratory Program/ ; }, mesh = {Animals ; *Depression/drug therapy/etiology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Brain-Gut Axis/drug effects ; *Oligosaccharides/pharmacology ; Restraint, Physical ; Disease Models, Animal ; *Antidepressive Agents/pharmacology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; Phenotype ; Hippocampus/drug effects/metabolism ; Intestinal Barrier Function ; }, abstract = {Depression is increasingly linked to microbiota-gut-brain axis dysfunction, yet current monoaminergic antidepressants show limited efficacy. This study investigated the therapeutic potential and underlying mechanisms of GV-971, a marine-derived oligosaccharide, in a chronic restraint stress (CRS) mouse model. We first established that 8 h of daily restraint for 4-8 weeks induces a stable depression-like phenotype characterized by behavioral despair and significant reduction in peripheral monoamine neurotransmitters (5-HT and norepinephrine). GV-971 treatment robustly attenuated CRS-induced depression- and anxiety-like behaviors, restored hippocampal serotonin levels, reduced elevated plasma corticosterone concentrations, and ameliorated CRS-induced adrenal cortical hyperplasia. Mechanistically, GV-971 significantly suppressed neuroinflammation by inhibiting microglial hyperactivation in the prefrontal cortex and hippocampus. Concurrently, it repaired intestinal barrier dysfunction, evidenced by reduced permeability, restored mucosal integrity, and recovered goblet cell numbers. Crucially, integrated shot-gun metagenomics and plasma metabolomics revealed that GV-971 not only reshaped microbial taxonomy but also functionally recalibrated the gut ecosystem. It enriched beneficial taxa (e.g., Bifidobacterium pseudolongum, Bacteroides uniformis) and specific metabolic pathways, leading to increased short-chain fatty acids (valeric and caproic acids) and a significant reduction in plasma levels of tryptophan-kynurenine pathway metabolites, specifically the neurotoxic compounds kynurenine and quinolinic acid. Fecal microbiota transplantation (FMT) from GV-971-treated donors partially recapitulated the antidepressant and gut-protective effects in CRS recipients, confirming a causal role for the remodeled microbiota. Collectively, GV-971 exerts antidepressant effects by coordinately remodeling the gut microbiota, normalizing tryptophan and SCFA metabolism, restoring gut barrier integrity, and dampening central neuroinflammation, supporting its potential as a novel gut-brain axis-targeted therapy for depression.}, }
@article {pmid42347203, year = {2026}, author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ}, title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060591}, pmid = {42347203}, issn = {2076-0817}, mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration &amp; dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration &amp; dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration &amp; dosage ; }, abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.}, }
@article {pmid42347234, year = {2026}, author = {Wojnarowski, K and Cholewińska, P and Zhao, D and Hasegawa, Y and Denk, D and Palić, D}, title = {Rapid Culture-Independent Detection of Fish Pathogens Using Oxford Nanopore Technologies: Case-Based Insights Across Multiple Species and Tissues.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060622}, pmid = {42347234}, issn = {2076-0817}, mesh = {Animals ; *Fish Diseases/microbiology/diagnosis ; *Bacteria/genetics/classification/isolation &amp; purification ; *Nanopore Sequencing/methods ; Fishes/microbiology ; Metagenomics/methods ; *Bacterial Infections/veterinary/diagnosis/microbiology ; }, abstract = {Rapid and accurate diagnosis of infectious diseases in aquaculture is essential for preventing major economic and ecological losses. Traditional culture-based methods focus on isolation of individual pathogens, and often are burdened with extended processing times, particularly during investigations of polymicrobial infections. Application of Oxford Nanopore Technologies (ONT) sequencing offers a rapid, culture-independent workflow for the identification of bacterial and fungal pathogens directly from fish tissues. Swab and organ samples from four cases (1: Salmo spp.; 2: Cyprinus carpio; 3: Salvelinus fontinalis; 4: Heniochus acuminatus) were analyzed using ONT long-read sequencing for metagenomic screening and bioinformatic classification. The results revealed case-, species-, and tissue-specific microbial profiles, with external tissues showing higher microbial diversity and internal organs enriched in pathogenic taxa. Dominant pathogens included Streptococcus iniae, Aeromonas hydrophila, Pseudomonas spp., and Saprolegnia parasitica, alongside opportunistic zoonotic bacteria such as Escherichia coli and Acinetobacter baumannii. We demonstrate the potential for diagnostic application of ONT sequencing in investigations and detection of multi-pathogen infections, including assessments of microbial community structure changes during disease outbreaks in aquatic species. The presented workflow enables rapid, cost-effective, and comprehensive pathogen profiling, supporting early disease surveillance and improved management in aquatic veterinary practice.}, }
@article {pmid42347240, year = {2026}, author = {Chen, J and Wang, H and Li, Y and Xiao, Y and Yan, Y and Zhang, Y and Lu, X}, title = {Scenario-Driven Rapid Testing for Top Pathogens in Pediatric Respiratory Infections: Clinical and Economic Value from Emergency Triage to Precision Anti-Infective Management in the PICU.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060628}, pmid = {42347240}, issn = {2076-0817}, support = {WJ2025Z010//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; WX23A90//Wuhan Health Commission/ ; 32270528//National Natural Science Foundation of China/ ; CX20240883//Hunan Provincial Postgraduate Research and Innovation Project/ ; }, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/drug therapy/microbiology/virology ; *Triage ; Intensive Care Units, Pediatric ; Rapid Diagnostic Tests ; Child ; Anti-Bacterial Agents/therapeutic use ; *Anti-Infective Agents/therapeutic use ; }, abstract = {Pediatric respiratory infections remain among the leading causes of emergency department visits, hospitalization and pediatric intensive care unit (PICU) admission. Although most acute respiratory infections in children are viral, clinical manifestations overlap substantially among viral, bacterial and atypical pathogens, creating diagnostic uncertainty and promoting empirical antimicrobial use. Rapid antigen tests, nucleic acid amplification tests, multiplex respiratory panels and metagenomic sequencing have expanded the ability to detect pathogens within clinically actionable timeframes. However, evidence from pediatric emergency trials indicates that rapid pathogen detection alone does not necessarily reduce antibiotic prescribing or healthcare costs. These findings suggest that the value of rapid diagnostics depends less on analytical breadth than on whether testing is applied to the right child, in the right clinical scenario and within a predefined decision pathway. This narrative review reorganizes the evidence around a scenario-driven top-pathogen framework. Top pathogens are defined as organisms that, in a specific age group, syndrome, season or care setting, have high prevalence, severe disease potential, transmissibility, treatment implications, antimicrobial resistance relevance or infection-control value. We discuss how top-pathogen testing should differ across emergency triage, inpatient ward management, severe pneumonia, PICU care, hospital-acquired pneumonia, ventilator-associated pneumonia and outbreak settings. We further examine the economic mechanisms through which rapid testing may generate value, including reduced unnecessary antibiotics, timely antiviral therapy, optimized isolation, shorter length of stay, reduced repeated testing and prevention of healthcare-associated transmission. Finally, we propose implementation principles centered on diagnostic stewardship, antimicrobial stewardship, local epidemiology and real-world cost-effectiveness evaluation. A scenario-driven top-pathogen strategy may provide a practical bridge between broad syndromic testing and precision infectious disease management in children.}, }
@article {pmid42347253, year = {2026}, author = {Yean, S and Prasetyo, DB and Chao, S and Vuth, L and Prot, M and Baidaliuk, A and Bonnet, S and Simon-Loriere, E and Boyer, S}, title = {Combining PCR and Metagenomic Approaches to Reveal Tick-Borne Pathogens in Ticks Collected from Livestock and Companion Animals in Cambodia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060641}, pmid = {42347253}, issn = {2076-0817}, mesh = {Animals ; Cambodia/epidemiology ; *Tick-Borne Diseases/veterinary/epidemiology/microbiology ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Livestock/parasitology ; Cross-Sectional Studies ; Cattle ; *Ticks/microbiology/virology/parasitology ; Dogs ; Tick Infestations/veterinary ; Bacteria/genetics/isolation &amp; purification/classification ; }, abstract = {In Cambodia, livestock production plays an important role in the national economy and food security, yet tick-borne diseases remain an underrecognized constraint on animal health and productivity. Domestic animals may also serve as reservoirs of zoonotic pathogens in this predominantly rural setting. To address the lack of baseline molecular data on tick-borne pathogens in Cambodia, we conducted a cross-sectional study of ticks collected from November 2022 to April 2023 across 24 provinces. Ticks were collected from various hosts and environments, including cats, cattle, dogs, goats, pangolins, pythons, wild pigs, and bat cave floors, representing urban, rural, farm, wildlife rescue center, and forest fringe habitats. A total of 1526 ticks belonging to nine species were pooled into 352 samples and screened using conventional PCR (cPCR) targeting Anaplasma, Ehrlichia, Babesia, and Coxiella. Additionally, a subset of Rhipicephalus microplus ticks was analyzed using metatranscriptomic next-generation sequencing (NGS). Rhipicephalus microplus ticks collected from cattle tested positive for Anaplasma marginale (1.1% of pools) and Ehrlichia minasensis (0.9% of pools), whereas Rhipicephalus linnaei ticks collected from dogs were positive for Anaplasma platys (0.3% of pools) and Babesia canis (2.0% of pools). A high prevalence of Coxiella-like endosymbionts (15.6% of pools) was found in R. microplus from both cattle and goats. Metatranscriptomic analysis also identified six tick-associated viruses in R. microplus from cattle; with Guangdong tick manly virus being the most dominant (32.5% of samples); followed by Zhangzhou Totiv tick virus 1 (15.0%), Jingmen tick virus (5.0%), and Mogiana tick virus; Rhipicephalus-associated rhabdo-like virus; and Rhipicephalus-associated flavi-like virus; each at 2.5%. These findings provide the first molecular evidence of numerous bacterial, protozoal, and viral pathogens circulating in R. microplus and R. linnaei in Cambodia. The study highlights the need for integrated One Health surveillance to better understand, prevent, and control tick-borne diseases in the region.}, }
@article {pmid42347401, year = {2026}, author = {Zheng, L and He, Y and Yan, Y and Li, Q and Zhang, L and Xing, Z and Lu, X}, title = {Characteristics, Ecological Risks, and the Impacts on Soil Carbon Cycling of PAH Pollution in the Soil of a Retired Coking Plant in Zaozhuang, Northern China.}, journal = {Toxics}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/toxics14060503}, pmid = {42347401}, issn = {2305-6304}, abstract = {During the industrial restructuring in China, numerous outdated coking enterprises were phased out. Despite the cessation of production for several years, the soil in the production area of the retired coking plant remains heavily contaminated with polycyclic aromatic hydrocarbons (PAHs), which continue to adversely affect soil health. However, research on the pollution characteristics of soil PAHs under prolonged PAH exposure and the associated changes in functional genes related to soil carbon cycling is still inadequate. This study aims to identify the pollution characteristics and ecological risks of PAHs in the coking plant and to investigate the effects of long-term PAH contamination from abandoned coking plants on the functional genes involved in soil carbon cycling. It was found that PAHs in the soil were predominantly composed of high-molecular-weight PAHs (HMW-PAHs), which constituted 65.7% to 83.4% of the total PAH content. The total concentration of PAHs in the surface soil ranged from 3.79 to 554 mg·kg[-1], with an average concentration of 147.6 mg·kg[-1]. Source analysis based on isomer ratios indicated that PAHs primarily originated from the combustion of coal and biomass. Utilizing the toxicity equivalent factor (TEF) method, we found that the PAH levels in the CA group exceeded the Serious Risk Concentration, indicating that PAH pollution poses a potential threat to the ecological environment. Metagenomic analysis revealed that the gene abundance of alpha-amylase in the CA group was significantly higher than that in the OLA group (p < 0.05), suggesting that prolonged exposure to PAHs has enhanced the starch hydrolysis capabilities of soil microorganisms. The findings of this study refine methods for assessing the risks associated with soil PAH contamination and provide a theoretical foundation for the risk management and reuse of retired coking plant sites.}, }
@article {pmid42347555, year = {2026}, author = {Jacob, SM and Akinbo, SY and Ajakaye, OG and Ekpo, UF and Omoruyi, Z and Agbana, T and Makau-Barasa, L and Aderogba, MO and Diehl, JC and Bell, D and Bayegun, AA and Okungbowa, MA and A-Enegela, J and Akinbo, FO}, title = {Molecular Identification of Schistosoma Species Associated with Atypical Urinary Eggs in Abuja (Nigeria): Evidence of Potential Zoonotic Transmission.}, journal = {Tropical medicine and infectious disease}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/tropicalmed11060170}, pmid = {42347555}, issn = {2414-6366}, abstract = {Schistosomiasis remains a major public health concern in Nigeria. We molecularly characterized Schistosoma eggs obtained from human urine to identify species and assess the presence of hybrid schistosomes in Abuja, Nigeria. Urine samples were collected from 1887 participants aged five years and above. Samples were examined for Schistosoma eggs using light microscopy. A total of 507 (26.9%) were positive for any form of Schistosoma while 91 (4.8%) had atypical Schistosoma eggs. DNA extracted from pooled ova was analyzed using metagenomic sequencing, read mapping, phylogenetic analysis, and BLASTn confirmation. Molecular analyses identified genetic signatures associated with both S. haematobium and S. bovis within pooled human urine samples, indicating the co-circulation of multiple schistosome species in the study area. Phylogenetic analyses based on trans-ITS and mitochondrial COX1 markers supported the presence of distinct nuclear and mitochondrial schistosome lineages. However, because sequencing was performed on pooled egg samples, the findings cannot distinguish between true recombinants and mixed infections involving co-circulating parental species. These findings highlight the potential complexity of schistosome transmission dynamics in endemic communities and underscore the need for enhanced molecular surveillance, especially single-parasite genomic approaches, and integrated One Health investigations to better understand schistosome transmission and its implications for control and elimination efforts in Nigeria.}, }
@article {pmid42347906, year = {2026}, author = {Liu, Y and Lin, H and Zhu, M and Chen, X and Yu, Z and Peng, D and Dong, G and Ni, Y and Fu, J}, title = {Gut microbiota dysbiosis and short-chain fatty acid alterations in pediatric new-onset type 1 diabetes with ketoacidosis.}, journal = {Journal of endocrinological investigation}, volume = {}, number = {}, pages = {}, pmid = {42347906}, issn = {1720-8386}, support = {2023C03047//Key Research and Development Program of Zhejiang Province/ ; 2021YFC2701900//Key Technologies Research and Development Program/ ; 82370863//National Natural Science Foundation of China/ ; 82502105//National Natural Science Foundation of China/ ; LKLY25H180005//Natural Science Foundation of Zhejiang Province/ ; LQN25H040005//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {PURPOSE: Diabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication in children with type 1 diabetes (T1D) and remains associated with considerable morbidity and mortality. Although gut dysbiosis has been reported in newly diagnosed T1D, the gut microbiota and microbial metabolites during DKA onset remain poorly characterized.<br><br>METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 96 newly diagnosed T1D children, including 32 presenting with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative and correlation analyses were conducted to explore differences in gut microbial composition, SCFA levels, and their association with clinical indicators of DKA severity.<br><br>RESULTS: Children with DKA exhibited distinct gut microbial compositions, with marked &#x3b2;-diversity separation from non-DKA individuals. The DKA group was characterized by an enrichment of potential pathogens and a significant depletion of SCFA-producing genera, including Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus. Correspondingly, fecal SCFA levels were significantly reduced in the DKA group. Moreover, SCFAs and their producing bacteria were strongly correlated with clinical indices of DKA severity. Mediation analysis suggested that reductions in SCFAs, particularly propionic acid and butyric acid, were associated with metabolic alterations linking SCFA-producing bacteria to DKA.<br><br>CONCLUSION: This study provides a comprehensive characterization of gut microbiota and SCFA alterations in T1D children at DKA onset. The depletion of SCFA-producing bacteria and their metabolites reflects metabolic disturbances associated with DKA, and highlights SCFAs and their producers as candidate metabolic features warranting further validation as biomarkers and therapeutic targets.}, }
@article {pmid42347915, year = {2026}, author = {Huang, CH and Lu, IC and Lin, CW and Hsieh, MT and Chiang, IH and Lai, PH and Liu, IT and Chen, JS}, title = {Gut microbiota profiles across intrinsic capacity strata in community-dwelling older adults using full-length 16S rRNA sequencing.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {42347915}, issn = {2509-2723}, support = {NSTC 112&#x2011;2314&#x2011;B&#x2011;650&#x2011;001&#x2011;MY3//National Science and Technology Council/ ; EDAHP111045//E-Da Hospital/ ; EDAHP113004//E-Da Hospital/ ; EDAHS113021//E-Da Hospital/ ; }, abstract = {Intrinsic capacity (IC), introduced by the World Health Organization, provides a multidimensional framework for evaluating functional aging across locomotion, cognition, sensory, psychological, and vitality domains. However, gut microbial features associated with IC among community-dwelling older adults remain incompletely understood. In this exploratory cross-sectional study, we enrolled 52 community-dwelling older adults and assessed gut microbiota using full-length 16S rRNA sequencing. Participants were stratified into IC quartiles, and additional analyses examined composite IC and domain-specific IC scores as continuous measures. Alpha diversity indices were not significantly associated with composite IC after false discovery rate correction, although vitality showed nominal positive associations with observed features and Chao1 richness (both rho = 0.316, P = 0.024, q = 0.288). PERMANOVA did not show statistically robust differences in beta diversity across IC quartile groups using Bray-Curtis distance (R[2] = 0.061, P = 0.060, q = 0.383), weighted UniFrac distance (R[2] = 0.083, P = 0.140, q = 0.436), or unweighted UniFrac distance (R[2] = 0.063, P = 0.211, q = 0.443). Selected bacterial taxa, including Ruminococcaceae, Lachnospiraceae, Alistipes, and Faecalibacterium, showed nominal associations with composite or domain-specific IC measures, but none remained significant after FDR correction or covariate-adjusted regression. In PICRUSt2-predicted functional analyses, several COG features related to transport systems, multidrug efflux, and site-specific recombination were positively associated with the vitality domain after false discovery rate correction. Because functional profiles were inferred from 16S rRNA sequencing rather than directly measured by shotgun metagenomics, metabolomics, or inflammatory biomarkers, these findings should be interpreted as exploratory and hypothesis-generating. This study identifies candidate microbiota and predicted functional features for future longitudinal and mechanistic studies of multidimensional functional aging.}, }
@article {pmid42348069, year = {2026}, author = {Ernst, S and Dirschka, T}, title = {The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {42348069}, issn = {2193-8210}, abstract = {The human facial skin microbiome is a complex and dynamic ecosystem that plays a central role in maintaining skin health, immune regulation, and preventing dermatological skin conditions. Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) are the most prominent bacterial species, with shifts in their relative abundance correlating with skin site, age, skin site, and health status. Exploring the facial microbiome offers exciting opportunities, though it requires careful methodological consideration. Sampling techniques vary in invasiveness and depth, which can influence the accuracy and reproducibility of microbiome profiles. While traditional cultivation methods provide valuable insights, they often miss nonculturable microbes, limiting the view of microbial diversity. Molecular approaches such as amplicon sequencing and metagenomics enable a more comprehensive understanding of microbial communities, even though they currently cannot distinguish between viable and nonviable microbes. Addressing these challenges will help unlock the full potential of facial microbiome research. A balanced facial skin microbiome is associated with healthy skin, whereas a dysbiosis of C. acnes and S. epidermidis is commonly observed in acne-prone skin and more pronounced clinically manifest acne. A comprehensive understanding of the diversity and distribution of C. acnes phylotypes, as well as distinct lineages of S. epidermidis associated with skin disorders, is crucial for developing targeted, microbiome-based cosmetic and medical treatments. Emerging strategies aim to restore microbial balance by leveraging the skin's native microbiota, including probiotic approaches. These strategies represent a promising yet still emerging approach, as current clinical evidence remains limited and further well-controlled studies are required, although they may offer benefits by enhancing microbial diversity and supporting skin barrier function.}, }
@article {pmid42348335, year = {2026}, author = {Biswa, BB and Mori, H and Toyoda, A and Fujiwara, K and Kurokawa, K and Koide, T}, title = {Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {33}, number = {3}, pages = {}, doi = {10.1093/dnares/dsag006}, pmid = {42348335}, issn = {1756-1663}, support = {JPMJSP2104//JST/ ; 19KK0177//JSPS/ ; 24K01951//JSPS/ ; //Research Organization of Information and Systems/ ; }, mesh = {Animals ; Male ; Female ; *Limosilactobacillus reuteri/isolation &amp; purification/genetics ; Mice ; Oxytocin/blood ; *Behavior, Animal ; *Gastrointestinal Microbiome ; Feces/microbiology ; Selective Breeding ; Pyruvic Acid/blood ; }, abstract = {Domestication alters animal behaviour, particularly tameness. We previously established 2 tamed mouse groups by selective breeding for active tameness-defined as the motivation to approach a human hand-from genetically heterogeneous wild-derived mouse stock, together with 2 nonselected control groups. Genetic analyses identified loci associated with active tameness, but their low heritability suggested contributions from nongenetic factors. We therefore hypothesized that the gut microbiota, which has been shown to influence brain function, contributes to behavioural changes associated with active tameness. To test this hypothesis, we conducted shotgun metagenomic analyses of faecal samples from 10 males and 10 females (80 individuals total) from the 2 tamed and 2 nonselected groups. Tamed mice exhibited markedly higher levels of active tameness, accompanied by elevated blood concentrations of oxytocin and pyruvate. While overall taxonomic and functional diversity of the gut microbiota was largely unchanged, the abundance of Limosilactobacillus reuteri was significantly increased in the tamed mice. Administration of a pyruvate-secreting L. reuteri strain to nonselected mice elevated blood oxytocin levels and enhanced active tameness, although plasma pyruvate levels were not increased. These findings suggest that L. reuteri is associated with behavioural modulation, potentially via oxytocin-related pathways, and provide mechanistic insight into microbial contributions to animal domestication.}, }
@article {pmid42348560, year = {2026}, author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S}, title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0352336}, doi = {10.1371/journal.pone.0352336}, pmid = {42348560}, issn = {1932-6203}, mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; }, abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.}, }
@article {pmid42349033, year = {2026}, author = {Cárdenas-Conejo, Y}, title = {GenomoBase: A comprehensive resource for the family Genomoviridae.}, journal = {Virology}, volume = {623}, number = {}, pages = {111018}, doi = {10.1016/j.virol.2026.111018}, pmid = {42349033}, issn = {1096-0341}, abstract = {The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run reconstructed two candidate complete circular genomovirus genomes from metagenomic reads, both below the 78% species demarcation threshold for genomoviruses. Overall, GenomoBase supports comparative analyses and taxonomically informed exploration of public metagenomes.}, }
@article {pmid42349155, year = {2026}, author = {Li, YY and Lin, L and Wen, L and Li, XY}, title = {Rapid adaptation and enrichment of salt-tolerant anammox via dosing of chemical enhancers in packed-bed biofilm reactor.}, journal = {Water research}, volume = {304}, number = {}, pages = {126343}, doi = {10.1016/j.watres.2026.126343}, pmid = {42349155}, issn = {1879-2448}, abstract = {The application of anammox-based processes for saline wastewater treatment is constrained by the scarcity of salt-tolerant seed sludge and the lengthy adaptation periods. To overcome this challenge, exogenous chemical enhancers, hydrazine (N2H4, 5 mg/L) and glycine betaine (GB, 30 mg/L), were introduced and evaluated for their roles in facilitating salt-adapted anammox biofilms enrichment from freshwater seed in packed-bed biofilm reactors. Hydrazine addition for 15 days increased the nitrogen removal rate from approximately 50 to 441.1 mg N/(L·d) within 70 days, which was substantially higher than that achieved through natural acclimation (192.2 mg N/(L·d)). When GB was subsequently supplemented for 30 days to the naturally acclimated reactor, its nitrogen removal rate rapidly increased to 1000 mg N/(L·d) within 30 days and further to 3000 mg N/(L·d) within 60 days, catching up the reactor receiving N2H4 from the outset. According to community analysis, performance recovery coincided with immediate shift from Ca. Brocadia to Ca. Kuenenia, with its relative abundance surged ∼15-fold within 20 days, highlighting the remarkable stimulatory effect of enhancers on Ca. Kuenenia's proliferation. Inferred from KEGG pathway studies, N2H4 primarily enhanced oxidative phosphorylation and ATP synthesis, providing energetic support for early recovery of the proton motive force and osmotic balance. In contrast, GB stabilized cellular osmotic conditions and membrane structures, enabling reallocation of metabolic resources toward antioxidant defense, cellular repair, and folate biosynthesis under saline stress. This alleviated the energetic burden associated with ion transport and lipid remodeling, thereby promoting sustained recovery of the anammox community.}, }
@article {pmid42349523, year = {2026}, author = {Muqaddas, K and Mahnoor,  and Hayat, O and Islam, A and Khan, R and Naz, S}, title = {Cutaneous Leishmaniasis Promotes Skin Microbial Dysbiosis and Exacerbation of Local Inflammatory Responses.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108655}, doi = {10.1016/j.micpath.2026.108655}, pmid = {42349523}, issn = {1096-1208}, abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.}, }
@article {pmid42349567, year = {2026}, author = {Wang, J and Wen, J and Zhang, X and Zhang, X and Wu, P}, title = {Sulfide-mediated anammox performance under antibiotics stress: Linking antibiotic resistance genes, functional microbes and nitrogen-sulfur metabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135244}, doi = {10.1016/j.biortech.2026.135244}, pmid = {42349567}, issn = {1873-2976}, abstract = {Anaerobic ammonium oxidation (anammox), a sustainable and energy-efficient biological nitrogen removal process, is vulnerable to antibiotic stress during stable operation, while the mechanism of functional recovery mediated by sulfides remains unclear. This study systematically analyzed the response characteristics of the anammox process under sustained high-concentration oxytetracycline (OTC) and sulfamethoxazole (SMX) exposure, and further evaluated the potential of sulfide as an exogenous regulatory factor to mitigate antibiotic stress. Results indicate that sustained high concentration OTC and SMX exposure impaired the system's nitrogen removal performance, while the removal efficiencies of ammonium and nitrite successfully recovered to 85% and 83%, respectively, following sulfide addition. Metagenomic analysis suggested that the addition of sulfide was accompanied by an increased abundance of potential genes related to sulfur and nitrogen metabolism. Moreover, sulfide may alleviate antibiotic stress by facilitating metabolic interactions related to electron transfer and increasing the potential for SMX degradation. Furthermore, under OTC and SMX stress, a 20% increase in the abundance of Brocadia sapporoensis harboring ARGs was closely associated with the addition of sulfide. This study elucidates the biological mechanisms by which sulfides mitigate antibiotic stress, providing a theoretical basis for recovery strategies of anammox under an intensified stress model.}, }
@article {pmid42349748, year = {2026}, author = {Ortega-Yago, A and Rubio, P and Ulldemolins, P and Baeza-Oliete, J and Bas, P and Bas, T}, title = {What's new in spinal instrumentation-related infections.}, journal = {Revista espanola de cirugia ortopedica y traumatologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.recot.2026.06.008}, pmid = {42349748}, issn = {1988-8856}, abstract = {Infections associated with spinal instrumentation represent one of the most complex complications in spine surgery and frequently involve biofilm-forming pathogens that compromise the effectiveness of antimicrobial therapies. Diagnosis-particularly in chronic cases-requires the use of advanced microbiological techniques, such as implant sonication, next-generation metagenomic sequencing, and prolonged culture incubation. Therapeutic strategies depend on the chronicity of the infection and the stability of the implant, ranging from surgical debridement with retention of osteosynthesis material to staged delayed re-instrumentation. Empirical antibiotic therapy should be initiated promptly and subsequently adjusted according to microbiological results. Prevention remains a fundamental pillar and includes strict perioperative optimization. Favorable outcomes rely on early detection, a multidisciplinary team approach, and individualized surgical and antimicrobial management based on accurate clinical and radiological assessment.}, }
@article {pmid42349820, year = {2026}, author = {Zhou, Y and Zhong, WJ and An, XL and Huang, FY and Guo, XY and Gao, MK and Xu, MR and Huang, X and Li, H and Zhang, B and Springael, D and Su, JQ}, title = {FThe ISChip: A High-Throughput qPCR Array for Absolute Quantification of Insertion Sequences across the One Health Continuum.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128649}, doi = {10.1016/j.envpol.2026.128649}, pmid = {42349820}, issn = {1873-6424}, abstract = {Insertion sequences (IS) are pivotal mobile genetic elements that shape bacterial genome plasticity and act as critical drivers of environmental genetic hazards by accelerating the dissemination of antimicrobial resistance. However, high-throughput, absolute quantification of IS elements across diverse environmental matrices remains a significant technical challenge, as conventional short-read metagenomics often lacks the sensitivity and resolution required for profiling low-abundance and highly repetitive targets. Here, we developed ISChip, a high-capacity qPCR array for the multiplexed absolute quantification of 183 prevalent IS elements, serving as a robust quantitative complement to metagenomics. The platform was rigorously validated using 119 primer sets, demonstrating high specificity, efficiency, and a superior absolute sensitivity (limit of quantification: 23-28 copies per reaction) compared to conventional qPCR. We applied ISChip to 69 anthropogenically impacted samples spanning 13 matrices, including air, wastewater, soil, and human/animal feces, representing a comprehensive One Health continuum. Our results revealed a distinct compartmentalization of IS communities and identified wastewater, sludge, sediments, and human feces as primary IS hotspots. Notably, we discovered a highly conserved "core IS assemblage" in human feces, suggesting a unique niche for IS-driven microbial evolution. By providing a scalable and absolute quantitative framework, this study uncovers the extreme spatial magnitude of these biological hazards, serving as a powerful tool for monitoring genetic pollution across the One Health framework.}, }
@article {pmid42350342, year = {2026}, author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T}, title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].}, journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology}, volume = {42}, number = {6}, pages = {499-510}, pmid = {42350342}, issn = {1007-8738}, abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.}, }
@article {pmid42350492, year = {2026}, author = {Dini, H and Chenghang, S and Tong, X and Yixin, L and Tianchun, P and Shunfu, H and Yanqiang, Y and Yibo, H}, title = {Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01066-9}, pmid = {42350492}, issn = {2055-5008}, support = {32370552//National Natural Science Foundation of China/ ; 32325010//National Natural Science Foundation of China/ ; 2023YFF1304800//National Key Program of Research and Development of Ministry of Science and Technology/ ; }, abstract = {The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.}, }
@article {pmid42350494, year = {2026}, author = {Beiko, RG and Tolman, J and Barawi, SS and Fares, M and Murthy, SSN and Knox, T and Mackie, CM and Grundke, I and Jeffery, NW and Stanley, RRE and Sieben, V and LaRoche, J}, title = {Automated eDNA and eRNA profiling for biodiversity monitoring in marine and freshwater ecosystems.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-58421-1}, pmid = {42350494}, issn = {2045-2322}, abstract = {Biodiversity monitoring is essential to measure the impacts of pollution, invasive species, and the longer-term effects of climate change. Automated samplers enable temporally flexible, remote collection of environmental DNA (eDNA), improving access to time-sensitive events. The Dartmouth Ocean Technologies (DOT) Preserving eDNA Sampler has proven effective in multi-month marine deployments, but further validation is needed across a broader range of habitats and water chemistries, and to establish its suitability for collection and assessment of environmental RNA (eRNA). In this study, we collected samples near the surface (1-1.5 m depth) of a brackish pond, a freshwater lake, and two marine harbours. We identified patterns of species turnover consistent with transitions among aquatic environments, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. Automated deployment in Halifax Harbour following a significant rainfall event detected nearly ten times as many probable fecal-associated bacteria by proportion at this site relative to Lunenburg Harbour. Preserved eRNA allowed the identification of taxa below the eDNA limit of detection. Our pilot study demonstrates the feasibility of using the DOT sampler for longer-term biomonitoring in a diverse range of aquatic habitats, yielding ecological insights that would not be attainable through manual sampling alone.}, }
@article {pmid42350644, year = {2026}, author = {Suissa, D and Fidelle, M and Reich, E and Pham, TN and Thomas, S and Björk, JR and Liu, P and Zhao, L and Kitaoka, K and Piard, E and Lebhar, I and Tian, AL and Thelemaque, C and Alves Costa Silva, C and Deutsch, E and Loriot, Y and Segata, N and Piccinno, G and Hospers, GAP and Maleki Vareki, S and Silverman, MS and Lenehan, JG and Bataille, V and Boulate, D and Kuznetsova, T and Weersma, RK and Messaoudene, M and Durand, S and van der Aalst, CM and de Koning, HJ and Schuler-Thurner, B and de Vries, IJM and Rafie, E and Saliby, RM and Machaalani, M and Haferkamp, S and Schilling, B and Porcari, S and Ciccarese, C and Iacovelli, R and Cremolini, C and Choueiri, TK and Elkrief, A and Kroemer, G and Heinzerling, L and Chamoto, K and Ianiro, G and Routy, B and Derosa, L and Paragios, N and Zitvogel, L}, title = {Metabolic determinants of cancer immunotherapy outcomes identified by plasma profiling.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {42350644}, issn = {1546-170X}, abstract = {Immune-checkpoint inhibitors benefit a subset of patients with advanced cancer, and the metabolic determinants of response remain unclear. Here, using targeted metabolomics and metagenomics, we profiled 4,336 plasma samples from 1,714 patients across five tumor types and 16 cohorts spanning Europe and North America, longitudinally sampled during five immune-checkpoint inhibitor-based treatment modalities, including fecal microbiota transplantation. A multimodal machine-learning framework integrating 154 metabolites with clinical variables identified five metabolites, age, body mass index and renal function as predictors of 12-month progression-free survival. The model achieved areas under the curve of 0.88 in training and 0.73 in validation cohorts of 105 and 30 patients, respectively and generalized across seven external cohorts. Histidine was a favorable prognostic feature of survival, whereas long-chain fatty acids and succinate were negatively associated with outcome. Histidine supplementation enhanced antitumor immunity in mice. Histidine-rich diets improved progression-free survival in patients lacking dysbiotic microbiome signatures associated with histidine catabolism.}, }
@article {pmid42337002, year = {2026}, author = {Guéguen, LM and Mathieu, A and Pelletier, S and Woo, A and Misra, N and Moreau, M and Perin, O and Droit, A}, title = {META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59138-x}, pmid = {42337002}, issn = {2045-2322}, abstract = {Traditional case-control metagenomic studies are constrained by their dependence on taxonomic and functional databases. Because annotation occurs before differential analysis, they are limited to known elements and keep function and taxonomy separate. Although binning strategies have emerged to reconstruct genomes and mitigate this issue, they still require an assembly step, preventing the use of all available sequencing data. Here, we introduce META-DIFF, a pipeline based on differentially abundant k-mers independently of any prior annotation. From those k-mers, it reconstructs longer sequences and provides biological context, as well as the best set of unitigs to discriminate between conditions. Across both taxonomy-centric and functionally-centric benchmarks, it showed robust performance and displayed great reproducibility. It also behaved more conservatively than did other univariate methodologies, i.e. it maintained a high precision at the expense of recall, particularly in conditions of low fold-change and limited sequencing depth. The efficacy of META-DIFF was further validated through its application to a real-world colorectal cancer dataset, which produced both confirmatory and novel results compared with those of previous publications. The pipeline is able to exploit all reads and identify differentially abundant elements, including unknown DNA, prior to annotation. With the guidelines provided, META-DIFF provides users with great exploratory power to unravel microbiome changes.}, }
@article {pmid42337243, year = {2026}, author = {Hoskinson, C and Dai, DLY and Petersen, C and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Turvey, SE}, title = {Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42337243}, issn = {2041-1723}, support = {[274CHI] and [EC1-144621]//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; [274CHI] and [EC1-144621]//AllerGen (AllerGen National Center of Excellence)/ ; [274CHI] and [EC1-144621]//Genome Canada (G&#xe9;nome Canada)/ ; }, mesh = {Humans ; *Malassezia/genetics/isolation &amp; purification/physiology ; Infant ; Feces/microbiology ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Mycobiome ; Male ; Female ; Child, Preschool ; *Food Hypersensitivity/microbiology/immunology ; Child ; Metagenome ; Metagenomics ; *Hypersensitivity/microbiology ; }, abstract = {While early-life gut bacterial microbiota maturation has been well studied and linked to childhood disease, the development of the gut mycobiome remains poorly understood. Few studies have defined fungal succession in infancy, and even fewer have integrated fungal and bacterial maturation, allowing interkingdom analysis within the same individuals. In this study, we analyzed a subset of the CHILD Study Cohort (n = 1409 participants) and generated both ITS2 amplicon and shotgun metagenomic sequencing data from infant stool samples (n = 2256 samples). We hypothesized that the infant mycobiome follows predictable developmental trajectories that influence childhood health outcomes. We found that fungi are reliable biomarkers for gut maturation, with the notable emergence of Saccharomyces and Malassezia as some of the strongest indicators across both fungi and bacteria. Fungal composition was strongly associated with infant age (R = 0.79, p < 0.001) and with the later development of both atopic dermatitis (adj. p = 0.029) and food allergy (adj. p = 0.013). Further, differences in fungal development coincided with changes in key gut immune-modulating metabolites such as butyrate and glycerol, indicating the functional importance of infant gut mycobiome maturation in early-life immune development. Together, these results highlight the early life mycobiome as a potential therapeutic target to mitigate allergic disease development.}, }
@article {pmid42337676, year = {2026}, author = {Gorji, AE and Xue, B and Yan, T and Sadkowski, T and Chen, X and Cristobal-Carballo, O and Morrison, S and Razban, V and Smith, L and Stergiadis, S and Theodoridou, K and Shirali, M}, title = {Apple pomace and hempseed cake can reduce methane intensity (CH4/DMI) and alter the rumen microbiome in dairy cows: a shotgun metagenomic approach.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42337676}, issn = {1674-9782}, support = {Project No. 21/5/01//Department of Agriculture, Environment and Rural Affairs (DAERA)/ ; }, abstract = {BACKGROUND: With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows.<br><br>METHODS: Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes.<br><br>RESULTS: Values are reported as mean&#x2009;&#xb1;&#x2009;SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7%&#x2009;&#xb1;&#x2009;2.8%, P&#x2009;=&#x2009;0.032; HC: 54.5%&#x2009;&#xb1;&#x2009;3.4%, P&#x2009;=&#x2009;0.048) compared to the Control (48.2%&#x2009;&#xb1;&#x2009;3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81&#x2009;&#xb1;&#x2009;0.06 (Control) to 0.58&#x2009;&#xb1;&#x2009;0.05 for AP (P&#x2009;=&#x2009;0.012) and 0.64&#x2009;&#xb1;&#x2009;0.05 for HC (P&#x2009;=&#x2009;0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P&#x2009;<&#x2009;0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways (P&#x2009;=&#x2009;0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P&#x2009;=&#x2009;0.0075) and methane emissions per unit of dry matter intake (CH4/DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P&#x2009;=&#x2009;0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P&#x2009;=&#x2009;0.035), alongside a significant reduction in methane intensity (CH4/DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments (P&#x2009;>&#x2009;0.05).<br><br>CONCLUSIONS: In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.}, }
@article {pmid42338488, year = {2026}, author = {Chen, B and Chen, J and Feng, Z and Lv, H and Lin, Q and Jiang, G}, title = {Gut microbiota reconstruction after liver transplantation and its association with early postoperative infections in patients with liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1845273}, pmid = {42338488}, issn = {2235-2988}, mesh = {Humans ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Retrospective Studies ; *Postoperative Complications/microbiology ; Dysbiosis/microbiology ; Male ; *Liver Failure/surgery/complications ; Probiotics/administration &amp; dosage/therapeutic use ; Middle Aged ; Metagenomics ; Feces/microbiology ; Adult ; *Bacterial Infections/microbiology/epidemiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Postoperative infection remains a major cause of morbidity after liver transplantation (LT) in patients with liver failure. Increasing evidence suggests that gut microbiota dysbiosis may contribute to infection risk, but its dynamic changes after LT are not fully understood.<br><br>METHODS: This retrospective study included 60 patients with liver failure who underwent LT and developed postoperative infection-related risk. Patients were divided into a probiotic group and a non-probiotic group. Fecal samples were collected before transplantation and on postoperative days 7, 14, 21, and 28. Metagenomic sequencing was performed to analyze gut microbial composition, diversity, and antibiotic resistance genes.<br><br>RESULTS: The probiotic group showed a significantly lower rate of postoperative bacterial infection, especially intra-abdominal infection. After LT, gut microbiota gradually recovered in both groups, but restoration was faster in the probiotic group. The non-probiotic group showed persistent dysbiosis, characterized by enrichment of opportunistic pathogens such as Enterococcus and Klebsiella, whereas beneficial genera including Bifidobacterium and Lactobacillus were more abundant in the probiotic group. Antibiotic resistance genes were also more enriched in the non-probiotic group.<br><br>CONCLUSION: Early postoperative gut microbiota reconstruction is closely associated with infectious complications after LT, and modulation of gut microbiota may help improve postoperative outcomes.}, }
@article {pmid42338489, year = {2026}, author = {Tang, C and Li, B and Chen, J and Liu, X and She, C}, title = {Causal relationship between gut microbiota and adenomyosis: metagenomics sequencing and Mendelian randomization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1772864}, pmid = {42338489}, issn = {2235-2988}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Adenomyosis/microbiology/etiology ; *Mendelian Randomization Analysis ; *Metagenomics/methods ; Middle Aged ; Adult ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in the pathogenesis of adenomyosis (AM); however, whether this association is causal and through which mechanisms it operates remain largely unknown.<br><br>METHODS: To interrogate potential causal relationships, we performed a two-sample Mendelian randomization (MR) analysis leveraging inverse-variance weighting (IVW) as the primary estimator, complemented by MR-Egger, weighted median, and weighted mode approaches, to evaluate the causal effects of gut microbial taxa and microbiota-derived metabolic pathways on AM. We further conducted mediation analyzes to delineate the role of circulating immune-cell phenotypes in this process. In parallel, in an independent clinical cohort, 22 patients with AM and 23 age-matched healthy controls recruited from the health-screening center of our institution were enrolled according to stringent inclusion and exclusion criteria (including antibiotic-use history and long-term local residency) and subjected to shotgun metagenomic sequencing. Significant differences in the types of bacterial communities were observed between the AM group and the control group. Subsequently, the results were cross-compared with those of the MR study using the Linear Discriminant Analysis Effect Size (LEfSe) method, and further verified using the ANCOM-BC method to determine the common microbial characteristics.<br><br>RESULTS: MR analysis identified ten microbial taxa and ten metabolic pathways with evidence of potential causal associations with AM. Of these, nine taxa and five pathways were associated with a reduced risk of AM, including Alistipes indistinctus (OR&#xa0;=&#xa0;0.847, 95% CI&#xa0;=&#xa0;0.754-0.951, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), Ruminococcus torques (OR&#xa0;=&#xa0;0.818, 95% CI&#xa0;=&#xa0;0.712-0.941, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), class Deltaproteobacteria (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), family Desulfovibrionaceae (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), order Desulfovibrionales (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), Parasutterella excrementihominis (OR&#xa0;=&#xa0;0.875, 95% CI&#xa0;=&#xa0;0.784-0.977, p&#xa0;=&#xa0;0.017, p~FDR~ > 0.05), Ruminococcus bromii (OR&#xa0;=&#xa0;0.836, 95% CI&#xa0;=&#xa0;0.718-0.972, p&#xa0;=&#xa0;0.020, p~FDR~ > 0.05), Bacteroides finegoldii (OR&#xa0;=&#xa0;0.919, 95% CI&#xa0;=&#xa0;0.855-0.987, p&#xa0;=&#xa0;0.020, p~FDR~ > 0.05), and the genus Parasutterella (OR&#xa0;=&#xa0;0.886, 95% CI&#xa0;=&#xa0;0.797-0.986, p&#xa0;=&#xa0;0.026, p~FDR~ > 0.05); the five protective pathways comprised dTDP-L-rhamnose biosynthesis (OR&#xa0;=&#xa0;0.819, 95% CI&#xa0;=&#xa0;0.674-0.995, p&#xa0;=&#xa0;0.045, p~FDR~ > 0.05), lactose and galactose degradation (OR&#xa0;=&#xa0;0.818, 95% CI&#xa0;=&#xa0;0.689-0.972, p&#xa0;=&#xa0;0.022, p~FDR~ > 0.05), the reductive TCA cycle (OR&#xa0;=&#xa0;0.919, 95% CI&#xa0;=&#xa0;0.851-0.993, p&#xa0;=&#xa0;0.032, p~FDR~ > 0.05), allantoin degradation to glyoxylate (OR&#xa0;=&#xa0;0.907, 95% CI&#xa0;=&#xa0;0.830-0.991, p&#xa0;=&#xa0;0.030, p~FDR~ > 0.05), and glycolysis I (from glucose-6-phosphate) (OR&#xa0;=&#xa0;0.850, 95% CI&#xa0;=&#xa0;0.747-0.967, p&#xa0;=&#xa0;0.013, p~FDR~ > 0.05).Conversely, one taxon and five pathways were associated with an increased risk of AM: the genus Lactobacillus (OR&#xa0;=&#xa0;1.083, 95% CI&#xa0;=&#xa0;1.008-1.164, p&#xa0;=&#xa0;0.030, p~FDR~ > 0.05), degradation of glucose and glucose-1-phosphate (OR&#xa0;=&#xa0;1.202, 95% CI&#xa0;=&#xa0;1.056-1.369, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), peptidoglycan biosynthesis (in Enterococcus faecium) (OR&#xa0;=&#xa0;1.138, 95% CI&#xa0;=&#xa0;1.007-1.285, p&#xa0;=&#xa0;0.039, p~FDR~ > 0.05), pyruvate fermentation to acetone (OR&#xa0;=&#xa0;1.118, 95% CI&#xa0;=&#xa0;1.001-1.248, p&#xa0;=&#xa0;0.048, p~FDR~ > 0.05), glycerol degradation to butanol (OR&#xa0;=&#xa0;1.118, 95% CI&#xa0;=&#xa0;1.011-1.237, p&#xa0;=&#xa0;0.031, p~FDR~ > 0.05), and de novo pyrimidine deoxyribonucleotide biosynthesis (OR&#xa0;=&#xa0;1.216, 95% CI&#xa0;=&#xa0;1.063-1.390, p&#xa0;=&#xa0;0.004, p~FDR~ > 0.05).Mediation analysis revealed that the immune phenotype "CD24 on CD24[+]CD27[+] B cells" mediated the pathway from Ruminococcus bromii to AM, accounting for 32.91% of the total effect (p&#xa0;=&#xa0;0.020).Shotgun metagenomic profiling of the clinical cohort demonstrated no significant differences in &#x3b1;-diversity or &#x3b2;-diversity between the AM and control groups. At the phylum level, the relative abundance of Desulfobacterota was significantly decreased in the AM group (p<&#xa0;0.05), and at the genus level, Alistipes was similarly reduced (p<&#xa0;0.05). LEfSe analysis further indicated enrichment of Escherichia and Clostridium in the AM group, whereas Desulfobacterota and Rikenellaceae were enriched in the Control group. Matching the aforementioned results with the Mendelian randomization (MR) outcomes revealed that Desulfovibrionales and Desulfovibrionaceae constituted the shared microbial taxa. This finding was subsequently re-validated and confirmed using the ANCOM-BC method.<br><br>CONCLUSIONS: Integrating genetic causal inference with clinical metagenomic validation, this study provides convergent evidence that specific gut microbial taxa, their associated metabolic pathways, and immune-cell-mediated mechanisms may be causally implicated in the development of AM. These findings offer a framework for future microbiota-targeted preventive and therapeutic strategies against AM.}, }
@article {pmid42338795, year = {2026}, author = {Chen, J and Wei, J and Liu, T and Chen, J and Yuan, Y and Zhang, F and Zhang, J}, title = {Gut microbiome dynamics in autism: a prospective nested case-control study demonstrates microbial-clinical associations following rehabilitation interventions.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1820904}, pmid = {42338795}, issn = {1662-4548}, abstract = {BACKGROUND: Children with autism spectrum disorder (ASD) commonly exhibit gut microbiota dysbiosis and metabolic abnormalities, yet the mechanisms linking these changes to clinical symptoms remain unclear.<br><br>OBJECTIVE: This study employed a nested case-control design and multi-omics approaches to evaluate the effects of rehabilitation intervention on clinical symptoms and gut microbiota in children with ASD, identify distinct microbial-metabolic signatures, and explore their mechanistic links with sleep disorders and developmental abilities.<br><br>METHODS: Within a prospectively established pediatric cohort (n&#x202f;=&#x202f;45), we implemented a nested case-control design including 26 ASD children (18 males, 8 females; mean age 61.79&#x202f;&#xb1;&#x202f;11.15&#x202f;months) and 19 age- and sex-matched healthy controls. All ASD participants received standardized rehabilitation therapy (2&#x202f;h/day, 5&#x202f;days/week for 6&#x202f;months) comprising occupational therapy and cognitive-linguistic training. Primary outcomes included comprehensive clinical assessments [Griffiths Development Scales-Chinese (GDS-C), Children's Sleep Habits Questionnaire (CSHQ), Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS)] and longitudinal multi-omics analysis (metagenomic sequencing and LC-MS-based metabolomics). Association analyses were performed with FDR correction (q&#x202f;<&#x202f;0.05).<br><br>RESULTS: Following the 6-month rehabilitation intervention, significant clinical improvements were observed in sleep quality (CSHQ total and subscores) and developmental performance (GDS-C). Multi-omics profiling revealed distinct biological signatures in ASD children compared to healthy controls, characterized by elevated Intestinibacter_bartlettii and reduced levels of ornithine and siderophore nonribosomal peptide biosynthesis. Crucially, correlation analysis demonstrated that, after FDR correction, ornithine levels were significantly positively correlated with multiple GDS-C developmental domains, while tyrosine was associated with parasomnias. These findings establish a potential mechanistic link where amino acid metabolism connects gut microbial shifts to clinical phenotypes.<br><br>CONCLUSION: This study demonstrates that rehabilitation intervention synchronously ameliorates clinical symptoms and modulates the gut-metabolic profile in ASD. The identified associations between specific metabolites (ornithine and tyrosine) and clinical outcomes suggest a metabolic mechanism underlying the gut-brain axis, highlighting the potential of these metabolites as biomarkers for therapeutic monitoring. Further large-scale studies are needed to validate these findings.}, }
@article {pmid42338857, year = {2026}, author = {Baumgartner, EE and Weltin, L and Whitten, JP and Fahey, TE and Baumgartel, PB and Farrell, JJ}, title = {An Unusual Infectious Cause of Abdominal Pain: Non-typhoidal Salmonella Aortitis Complicating an Endovascular Aortic Stent Graft.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e109509}, pmid = {42338857}, issn = {2168-8184}, abstract = {Non-typhoidal Salmonella (NTS) is a rare but life-threatening cause of infectious aortitis and mycotic aneurysm formation, predominantly affecting immunocompromised patients and those with pre-existing vascular pathology or prosthetic hardware. Diagnosis is frequently delayed due to its non-specific clinical presentation and the poor sensitivity of conventional blood cultures. A 73-year-old immunocompromised woman with a history of penetrating aortic ulcer and prior endovascular aortic stent graft placement presented with progressive abdominal pain and para-aortic soft tissue thickening encasing the infrarenal aorta. Blood cultures were negative; however, CT-guided peri-aortic tissue aspiration and metagenomic next-generation sequencing (mNGS; Karius test) identified Salmonella enterica serovar Enteritidis susceptible to ampicillin, ceftriaxone, levofloxacin, nalidixic acid, and trimethoprim/sulfamethoxazole. The most probable infection source was the patient's prolonged daily consumption of unpasteurized eggs from backyard chickens. She was treated with intravenous (IV) ceftriaxone for 30 days followed by 18 months of oral cephalexin suppression, with significant radiographic improvement at three-month follow-up. Surgical intervention was deferred given her high operative risk from metastatic malignancy and multiple comorbidities. This case is notable for its documentation of culture-negative NTS aortitis complicating an endovascular stent graft, in which mNGS was essential for pathogen identification. It further highlights the importance of eliciting detailed dietary exposure history in high-risk patients, the novel diagnostic challenge posed by concurrent autoimmune disease mimicking non-infectious vasculitis, and the feasibility of antibiotic-only management in carefully selected surgical non-candidates.}, }
@article {pmid42338881, year = {2026}, author = {Wang, H and Wang, Y and Yang, L and Feng, J and Tian, S and Chen, L and Huang, W and Liu, J and Wang, X}, title = {Correction: Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852209}, doi = {10.3389/fmicb.2026.1852209}, pmid = {42338881}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1375804.].}, }
@article {pmid42338883, year = {2026}, author = {Goktas, NT and Guven, S and Dinleyici, EC}, title = {The combination of Lactobacillus acidophilus DSMZ 26280 and Limosilactobacillus reuteri DSMZ 25441 has an impact on clinical course and gut microbiota of children with acute infectious diarrhea.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1792126}, pmid = {42338883}, issn = {1664-302X}, abstract = {INTRODUCTION: Previous studies and society guidelines have proposed probiotics as a complementary therapy for acute infectious diarrhea, which may shorten the disease course, yet strain-specific effects and microbiome correlates remain incompletely defined. We aim to evaluate the effect of a combination of Lactobacillus acidophilus and Limosilactobacillus reuteri on the duration of diarrhea and gut microbiota composition in children with acute infectious diarrhea.<br><br>PATIENT AND METHODS: In a prospective, randomized, controlled, open-label trial at a tertiary pediatric emergency department (March-August 2024), children aged 1-6 years with acute infectious diarrhea lasting less than 24 h were allocated 1:1 to standard therapy (oral rehydration &#xb1; intravenous fluids) with or without 5-day probiotic (L. acidophilus DSMZ 26280; 108 CFU) and (L. reuteri DSMZ 25441; 108 CFU). Primary outcomes were duration of diarrhea and the proportion diarrhea-free at 72 h. The secondary outcome measures included the proportion of diarrhea-free children during first 10th day of the study. A subgroup analysis for gut microbiota composition at Day 0, 10th and 30th days of the study have been performed.<br><br>RESULTS: Of 145 enrolled children, 79 in the probiotic group (34 girls, 45 boys) and 66 in the control (30 girls and 36 boys); baseline demographics were comparable. The duration of diarrhea was significantly reduced in the probiotic group compared to the control group (46.4 &#xb1; 29.6 h vs. 81.6 &#xb1; 38.5 h, p < 0.001). The percentage of diarrhea-free children was significantly larger in the probiotic group at 72 h compared to the control (86.0% vs. 33.3%, p < 0.001). Persistence of diarrhea was lower in the probiotic group at 24, 48, and 96 h (all p < 0.001) and at day 6 (2.5% vs. 15.1%; p < 0.05); by days 7-10, persistence was rare in both groups. The probiotic combination is well-tolerated, and no adverse events have been reported. Alpha diversity indices were unchanged within/between groups. Bray-Curtis and Jaccard PCoA showed no between-group separation; unweighted UniFrac revealed differences within the probiotic group (day 1 vs. day 30) and between groups at day 30 (p < 0.05). LEfSe indicated enrichment of taxa associated with recovery in the probiotic arm and control group, and there is difference between group at Day 30.<br><br>CONCLUSION: This study evaluates a specific combination of L. acidophilus DSMZ 26280 and L. reuteri DSMZ 25441 in a randomized controlled setting, adding to the growing body of strain-specific probiotic research in pediatric acute infectious diarrhea. Adding probiotics to treatment is well-tolerated and reduces the duration of diarrhea by approximately 35 h when it starts in the early hours of infection. This probiotic combination use is associated with modest phylogenetics shifts in gut microbiota composition, with enrichment of certain taxa that have been previously associated with gut homeostasis in other contexts; however, their functional and clinical significance in this setting remains unclear. Larger blinded trials are warranted to confirm durability and detailed metagenomic analysis including metabolomics.}, }
@article {pmid42338911, year = {2026}, author = {Huang, Y and Chen, F and Yu, Z and Sheng, X and Wen, S and Zhang, X and Tang, W and Huang, M}, title = {Integrated analysis of physicochemical properties, microbiome, and flavor profiles for differentiating two aroma grades of sauce-flavor Daqu.}, journal = {Food chemistry: X}, volume = {37}, number = {}, pages = {104092}, pmid = {42338911}, issn = {2590-1575}, abstract = {Aroma characteristics are critical indicators for evaluating sauce-flavor Daqu quality. This study systematically compared physicochemical properties, enzyme activities, microbiomes, and flavor profiles of first-grade (GF) and second-grade (GS) aroma Daqu. GF had higher total acidity, amino nitrogen content, acid protease activity, a lower pH, and was correlated with enrichment of bacteria potentially associated with flavor precursor production such as Kroppenstedtia guangzhouensis and Kroppenstedtia eburnea. GS showed higher liquefying/cellulase activities and pH, and was associated with dominance by hydrolytic fungi such as Paecilomyces variotii and off-odor-related Oceanobacillus. HS-SPME-GC-MS combined with VIP and OAV analyses identified 11 differential volatile compounds. Aldehydes were strongly correlated with positive aroma grading and may serve as potential indicators associated with grade differentiation, while GS accumulated dimethyl trisulfide correlating with off-odors. The findings reveal the relationships between multi-omics characteristics and aroma grade differentiation of Daqu, and provide theoretical support for Daqu quality evaluation and production regulation.}, }
@article {pmid42338938, year = {2026}, author = {Zhong, L and Xia, K and Fan, Y}, title = {Sigmoid colonic tuberculosis presenting as a colovesical fistula mimicking colorectal malignancy: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1857599}, pmid = {42338938}, issn = {2296-858X}, abstract = {BACKGROUND: Intestinal tuberculosis (ITB) most commonly involves the ileocecal region. Isolated sigmoid colonic tuberculosis complicated by a colovesical fistula is extremely rare and may closely mimic colorectal malignancy or Crohn's disease (CD).<br><br>CASE PRESENTATION: A 73-year-old man presented with subacute diarrhea, fever, and lower urinary tract symptoms. Laboratory tests showed markedly elevated inflammatory markers and anemia. Cross-sectional imaging demonstrated segmental thickening of the sigmoid colon, pericolic lymphadenopathy, multiple serous effusions, and findings consistent with a colovesical fistula, including bladder wall disruption and intravesical gas. Colonoscopy revealed a circumferential stenosing lesion with irregular ulceration, raising strong suspicion for colorectal malignancy or CD.<br><br>Initial histopathology showed only mixed inflammatory cell infiltration without granulomas or malignant cells, and empirical antimicrobial therapy failed to control the fever. Given the positive immunological testing for tuberculosis and persistent clinical suspicion, acid-fast bacilli staining and metagenomic next-generation sequencing (mNGS) were performed on colonic biopsy tissue. Acid-fast bacilli were detected, and mNGS identified Mycobacterium tuberculosis complex, confirming ITB. Standard anti-tuberculosis therapy was initiated, leading to rapid clinical improvement, complete endoscopic mucosal healing, and radiological resolution of the colovesical fistula.<br><br>CONCLUSION: This case highlights that ITB can present as an isolated tumor-like sigmoid lesion complicated by fistula formation. When routine histology is nondiagnostic, especially in the absence of granulomas, integration of imaging, immunological testing, special staining, and molecular diagnostics may be crucial for early diagnosis, avoidance of misdiagnosis, and timely targeted treatment.}, }
@article {pmid42339070, year = {2026}, author = {Happi, AN and Ogunsanya, OA and Sijuwola, AE and Saibu, FM and Akano, K and Ayinla, AO and Daodu, RO and Page, B and Olumade, TJ and Oguzie, JU and Oluniyi, PE and Adedokun, OA and Fadele, J and Nwofoke, C and Elias, OT and Ogundana, KE and Lawal, OZ and Nosamiefan, I and Okolie, J and Adelabu, A and Lombardi, K and Eller, LA and Broach, E and Prins, PA and Heeney, JL and Modjarrad, K and Njatou, TLFA and Parker, ZF and McCauley, M and Vasan, S and Parker, E and Collins, ND and Michael, NL and Happi, CT}, title = {Genomic epidemiology and evolutionary analysis of Lassa virus from small mammals suggest bidirectional viral movement across humans and animals.}, journal = {Virus evolution}, volume = {12}, number = {1}, pages = {veag032}, pmid = {42339070}, issn = {2057-1577}, abstract = {Lassa fever is a viral haemorrhagic fever that poses a persistent public health threat in several West African countries, particularly Nigeria. The scarcity of Lassa virus (LASV) sequences isolated from small mammal reservoirs limits our knowledge and understanding of LASV genomic diversity and transmission dynamics. To address this knowledge gap, we sampled 1189 small mammals, including mice, rats, and shrews, from two LASV-endemic states in southern Nigeria (Ondo and Ebonyi States) and tested them for the presence of LASV RNA using reverse transcription-quantitative polymerase chain reaction. Selected quantitative polymerase chain reaction-positive samples were subjected to whole genome sequencing and small mammal speciation through next-generation sequencing outputs. We recorded an overall polymerase chain reaction positivity rate of 61.6%, with rat species demonstrating the highest LASV prevalence. We also conducted a serosurvey of 269 small rodents using indirect Enzyme-Linked Immunosorbent Assay (ELISA) and obtained an overall anti-LASV seroprevalence of 45%. Using the Nextera XT metagenomic sequencing protocol, we produced 55 LASV partial (n = 28) and full-length genomes (n = 27) from small mammals sampled, all of which clustered within sublineage 2g. LASV sequences generated from this study suggest that LASV variation is mostly driven by location, as isolates from this study tend to cluster more closely with other isolates collected from within the same region, rather than by collection date or host. However, samples collected from Ebonyi State were more closely related to isolates collected in Ondo State than to isolates from Edo, despite a larger physical distance. Overall, the data from this study suggest free movement of the virus across states in Nigeria, among humans and various non-human taxa. The finding of LASV in additional small mammal hosts suggests that the virus reservoir is vast and may include many small mammals not well-characterized.}, }
@article {pmid42339199, year = {2026}, author = {Acosta-España, JD and Altamirano-Jara, JB and Herrera-Yela, A and Estrella, F and Palacios, S}, title = {Metagenomic identification of Acanthamoeba Rhysodes in chronic skin lesion: Case report and literature review.}, journal = {JAAD case reports}, volume = {73}, number = {}, pages = {160-164}, pmid = {42339199}, issn = {2352-5126}, }
@article {pmid42339286, year = {2026}, author = {Dang, Y and Kong, J}, title = {A double pathogen strike: COVID-19 and talaromycosis Co-infection in a patient with post-tuberculosis lung disease.}, journal = {Respiratory medicine case reports}, volume = {62}, number = {}, pages = {102450}, pmid = {42339286}, issn = {2213-0071}, abstract = {An 80-year-old woman from rural Guangxi with post-tuberculosis lung disease (PTLD) (hereinafter referred to as PTLD)presented with one month of cough and fever. One month prior, she had ingested raw rodent meat-a known exposure for Talaromyces marneffei. Chest HRCT showed bilateral tree-in-bud opacities superimposed on prior left lung destruction. Conventional microbiological tests, including acid-fast bacilli smears, were negative. A nasopharyngeal swab was positive for SARS-CoV-2 (cycle threshold 17). Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified both T. marneffei and SARS-CoV-2. Her CD4[+] count was 344/μL and HIV serology was negative. She received nirmatrelvir-ritonavir and sequential amphotericin B followed by voriconazole, with clinical and radiological improvement. This case illustrates that PTLD may serve as a local anatomical risk factor for talaromycosis even without systemic immunodeficiency.}, }
@article {pmid42339375, year = {2026}, author = {Tomasi, N and Banchi, E and Manna, V and Celussi, M}, title = {Surface sediments prokaryotic communities: five years of 16S rRNA amplicon sequencing data from the northernmost part of the Mediterranean Sea.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112971}, pmid = {42339375}, issn = {2352-3409}, abstract = {Surface sediments harbour diverse prokaryotic communities that play a key role in biogeochemical cycling and provide valuable insights when compared with water column communities, allowing for a more comprehensive understanding of marine ecosystem functioning. Specifically, this dataset presents prokaryotic community data from 16 surface sediment samples collected seasonally from June 2020 to May 2025 at the C1-LTER station (45°42'2.99″ N, 13°42'36.00″ E; DEIMS.iDhttps://deims.org/96969205-cfdf-41d8-979f-ff881ea8dc8b) in the Gulf of Trieste, located in the northeastern Adriatic Sea (Mediterranean Sea). Extracted DNA was sequenced following the 16S Metagenomic Sequencing Library Preparation protocol and run on an Illumina NovaSeq 6000 System. Raw reads were filtered and denoised with DADA2, and taxonomic assignment was performed against the Silva 138.2 99% reference database. The dataset provides useful insights into prokaryotic communities and their seasonal variability over five years. Moreover, a focus on specific taxa is provided, such as Cyanobacteriota and Archaea, highlighting patterns of community variability in the sediment. Finally, it shows seasonal stability and generally consistent taxa distribution over time, as indicated by the high proportion of shared taxa at each taxonomic level. The raw data, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1442017, include two sets of sequencing reads obtained from surface sediment samples using the Illumina MiSeq and Illumina NovaSeq 6000 sequencing platforms, for a total of 27 16S rRNA gene sequencing FASTQ files. Overall, these data provide valuable insight into the surface sediment community in the northernmost part of the Mediterranean Sea, contributing to long-term research on sediment prokaryotic communities.}, }
@article {pmid42339699, year = {2026}, author = {Patel, D and Heidenblut, M and Mau, RL and Wagner, WP and Schwartz, E and Dijkstra, P and Hungate, BA and Ceja-Navarro, JA}, title = {Protist Predation Rapidly Reshapes Soil Microbial Gene Expression Linked to Nutrient Processing, Resistance, Virulence, and Gene Mobility Traits.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18948}, pmid = {42339699}, issn = {1520-5851}, abstract = {Protists are ubiquitous soil predators that regulate bacterial communities and biogeochemical cycling, yet how their predation alters expression of nutrient-cycling genes and traits linked to antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in natural soils remains poorly understood. Here, we used a short-term soil microcosm experiment to distinguish the effects of moisture-stimulated resident protists from enhanced predation by an introduced exogenous predatory protist community. Using quantitative stable isotope probing (qSIP) and metagenomic and metatranscriptomic analyses, we tracked protist activity and microbial responses over 3 days. Enhanced predation rapidly reshaped transcriptionally active microbial communities, increasing expression of nitrogen and phosphorus cycling genes while concurrently elevating diversity and transcription of ARGs, VFs, and MGEs, including multidrug-efflux systems, motility-, biofilm-related traits, and phage-associated elements. Metagenome-assembled genome─resolved analyses showed that some resident soil populations were activated by wet-up and remained transcriptionally active under predation pressure, encoding nutrient-cycling, resistance, virulence, and mobility traits that contributed to the functional background of wetted soils. These results suggest that, even over short time periods, protist predation links soil nutrient processing with environmentally relevant resistance and genetic mobility pathways, acting as a crucial ecological driver of gene expression related to nutrient processing and microbial interaction traits during environmental change.}, }
@article {pmid42340399, year = {2026}, author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA}, title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02818-y}, pmid = {42340399}, issn = {1432-184X}, abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.}, }
@article {pmid42341025, year = {2026}, author = {Wohl, DL and Belder, PT and Mitchell, BD}, title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350558}, doi = {10.1371/journal.pone.0350558}, pmid = {42341025}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; }, abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.}, }
@article {pmid42341423, year = {2026}, author = {Zheng, J and Yao, DY and Lu, YY and Luo, SJ and Liang, XX}, title = {Diagnostic utility of metagenomic next-generation sequencing for determining the etiology of thoracolumbar spine infections.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117517}, doi = {10.1016/j.diagmicrobio.2026.117517}, pmid = {42341423}, issn = {1879-0070}, abstract = {OBJECTIVE: This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) in identifying the etiological agents of thoracolumbar spine infections and examined its clinical relevance in facilitating timely diagnosis and therapeutic decision-making.<br><br>METHODS: A total of 54 patients with suspected thoracolumbar spinal infection admitted to the Department of Spinal Orthopedics between June 1, 2022, and January 15, 2026, were enrolled. Tissue specimens from all patients underwent microbial culture, histopathological examination, and metagenomic next-generation sequencing (mNGS). Based on established clinical diagnostic criteria, patients were classified into an infection group (n = 49) and a non-infection group (n = 5). The pathogen detection rate, and diagnostic sensitivity of mNGS and conventional culture were compared using the paired &#x3c7;&#xb2; test.<br><br>RESULTS: Among the 54 patients with suspected thoracolumbar spine infection, the male-to-female ratio was 2:1. The overall positive detection rate of mNGS was 75.9% (41/54), which was significantly higher than that of microbial culture at 57.4% (31/54) (&#x3c7;&#xb2; = 4.500, p < 0.05). When clinical diagnosis served as the reference standard, mNGS demonstrated greater sensitivity for diagnosing thoracolumbar spinal infections compared to microbial culture (83.7% vs. 63.3%), and this difference reached statistical significance (&#x3c7;&#xb2; = 4.500, p < 0.05).<br><br>CONCLUSION: mNGS shows a high pathogen detection rate and superior sensitivity for diagnosing thoracolumbar spinal infection, providing valuable support for clinical diagnosis and guiding therapeutic management in suspected cases.}, }
@article {pmid42341424, year = {2026}, author = {Tsuboi, I and Inoue, S and Hirayama, T and Mitsui, Y and Watanabe, M and Hirakawa, H and Sadahira, T}, title = {Gut, vaginal, and urinary microbiome alterations in women with genitourinary syndrome of menopause: A systematic review.}, journal = {Maturitas}, volume = {211}, number = {}, pages = {109031}, doi = {10.1016/j.maturitas.2026.109031}, pmid = {42341424}, issn = {1873-4111}, abstract = {BACKGROUND AND OBJECTIVE: Genitourinary syndrome of menopause (GSM) is a chronic condition caused by estrogen deficiency, encompassing vaginal dryness, dyspareunia, and urinary symptoms. Alterations in the vaginal, urinary, and gut microbiome may contribute to GSM pathophysiology. We synthesize the evidence on microbiome composition and diversity across these compartments in postmenopausal women with GSM.<br><br>METHODS: PubMed, Scopus, and Embase were searched from inception to April 2026 for studies assessing the microbiome in postmenopausal women with GSM using 16S rRNA gene sequencing, metagenomics, or culture-based methods.<br><br>RESULTS: Twenty-three studies (5027 participants) were included: 15 examined the vaginal microbiome, seven the urinary microbiome, and one the gut microbiome. Postmenopausal women consistently showed reduced Lactobacillus abundance and increased microbial diversity. Estrogen therapy partially restored Lactobacillus dominance but did not uniformly improve symptoms. In the SWAN cohort (n&#xa0;=&#xa0;1320), sexual pain was the only GSM symptom independently associated with a specific community state type (CST IV-C1; OR 2.26, 95% CI 1.20-4.23). Specific species showed associations with distinct symptom domains: Prevotella with urinary symptoms, Finegoldia magna with recurrent urinary tract infection, and Streptococcus with sexual pain. Parallel Lactobacillus depletion and pathobiont enrichment across all three compartments pointed toward a vaginal-bladder-gut axis, potentially linked through estrobolome disruption and bacterial translocation.<br><br>CONCLUSION: The postmenopausal genitourinary microbiome is characterized by Lactobacillus depletion and increased diversity, but microbiome restoration alone does not predict symptom resolution. The shared microbial alterations across compartments suggest a vaginal-bladder-gut axis that may collectively drive GSM, but this requires multi-compartment longitudinal validation. PROSPERO registration: CRD420261335478.}, }
@article {pmid42341530, year = {2026}, author = {Lu, B and Wang, P and Hu, J and Qian, J and Shen, J and Tang, S and Zong, Y}, title = {Aqueous PFOS exposure decouples gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {406}, number = {}, pages = {128638}, doi = {10.1016/j.envpol.2026.128638}, pmid = {42341530}, issn = {1873-6424}, abstract = {Wetland interfaces regulate greenhouse-gas exchange and carbon retention, yet contaminant exposure may disrupt the relationship between these two processes. Whether aqueous perfluorooctane sulfonate (PFOS), a persistent aquatic contaminant, alters this relationship remains unclear. Here, we used a controlled rhizobox mesocosm with paired planted and unplanted treatments across an aqueous PFOS gradient (0, 10, 100, and 1000 μg L[-1]) to resolve plant-mediated and background soil responses. We combined endpoint, time-weighted 24-h CO2 and CH4 flux partitioning with [13]CO2 tracing of root-derived carbon, rhizosphere priming estimates, soil organic carbon fractionation into particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and metagenomic profiling. PFOS induced clear exposure-dependent and non-linear responses. Low-to-medium PFOS stimulated root-associated CO2 fluxes and maintained positive rhizosphere priming, whereas high PFOS suppressed rhizosphere CO2 and root respiration, weakened net plant CO2 uptake, and shifted soil organic carbon priming to a net negative response. In contrast, at H-P, MAOC was significantly higher than the control in both bulk and rhizosphere compartments, indicating that mineral-associated carbon retention can persist even when biological carbon processing weakens. Metagenomic profiling further suggested compartment-specific microbial filtering, reduced genetic potential for polymer depolymerization, and reweighted methane-related functions under PFOS exposure. Together, these results show that aqueous PFOS exposure can decouple gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms. These findings indicate that lower gaseous carbon release under PFOS exposure should not be interpreted straightforwardly as stronger carbon-retention function or enhanced carbon sequestration, particularly without longer-term field validation.}, }
@article {pmid42341576, year = {2026}, author = {Gupta, G and Fortin, RM and Labrie, S and Filteau, M}, title = {Genomic insights and antifungal potential of Pseudomonas species isolated from maple sap, including the novel species Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126738}, doi = {10.1016/j.syapm.2026.126738}, pmid = {42341576}, issn = {1618-0984}, abstract = {Fungal contamination poses a significant challenge in maple sap collection systems and postproduction processes, which affects the quality and shelf life of maple syrup. As an alternative to chemical treatments, microorganisms offer promising biocontrol potential. This study investigates nine Pseudomonas strains isolated from maple sap for their antifungal activity and genomic features. Whole-genome sequencing followed by comparative genomic analysis identified five distinct Pseudomonas species, including two previously uncharacterized taxa for which we propose the names Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov., in accordance with the nomenclatural guidelines of the SeqCode. Strain distributions from metagenome recruitment suggest they originate from sapwood, and previous metataxonomic data show that the amplicon sequence variant matching P. edsoni predominated maple sap samples. Genome mining using antiSMASH and BAGEL4 identified gene clusters associated with the synthesis of antifungal compounds, such as hydrogen cyanide, siderophores, cyclic lipopeptides, and ribosomally synthesized peptides. Antifungal assays demonstrated inhibitory activity against food spoilage fungi, with P. edsoni strains being active against Kluyveromyces lactis. The absence of activity in the cell-free supernatant and the presence of Type VI secretion systems in the genomes point toward contact-dependent mechanisms. Collectively, these findings reveal previously unrecognized taxonomic diversity and ecological specialization in maple sap-associated Pseudomonas, providing a basis for the rational development of Pseudomonas-based antifungal strategies in maple syrup production and quality control.}, }
@article {pmid42341885, year = {2026}, author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L}, title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113373}, doi = {10.1016/j.diabres.2026.113373}, pmid = {42341885}, issn = {1872-8227}, abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).<br><br>METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n&#x202f;=&#x202f;103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.<br><br>RESULTS: Mean UPF intake was 15.5&#x202f;% of total food intake. Higher UPF intake was independently associated with higher triglycerides (&#x3b2; per 20&#x202f;g/1000&#x202f;kcal&#x202f;=&#x202f;3.62&#x202f;mg/dL; 95&#x202f;%CI 1.16-6.08) and lower HDL-cholesterol (&#x3b2;&#x202f;=&#x202f;&#x202f;-&#x202f;0.98&#x202f;mg/dL; 95&#x202f;%CI&#x202f;-&#x202f;1.72 to&#x202f;-&#x202f;0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).<br><br>CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.}, }
@article {pmid42341953, year = {2026}, author = {Cao, S and Han, YC and Wang, XC and Chen, R and Xing, BS}, title = {Unraveling the short- and long-term effects of lignocellulosic pretreatment derivatives on the anaerobic co-digestion of corn straw and food waste: Digester performance, microbial community, and metabolic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135234}, doi = {10.1016/j.biortech.2026.135234}, pmid = {42341953}, issn = {1873-2976}, abstract = {Lignocellulosic pretreatment hydrolysates often contain inhibitory derivatives, particularly furan inhibitors (furfural and 5-hydroxymethylfurfural) and phenolic compounds, which can suppress anaerobic digestion. In this study, a CS/FW mesophilic AcoD system was investigated through short-term single- and mixed-inhibitor batch tests and long-term operation in two continuous stirred tank reactors (CSTRs), with mixed-inhibitor concentrations increased stepwise at fixed ratios. The results revealed that the maximum concentrations of furfural, phenol, and 5-hydroxymethylfurfural tolerated by the AcoD system were 100, 50, and 50 mg/L, respectively, in short-term batch tests, whereas during long-term operation, twofold greater concentrations in the same ratio were tolerated, leading to a 4.2 % increase in methane yield compared with that of the control. At high concentrations of 1000:500:500 mg/L, the hydrolysis, acidification, and methanogenesis rates were strongly suppressed. Furfural showed the strongest inhibition on polysaccharide and protein degradation, indicating that hydrolysis was the main affected stage during AcoD. Metagenomic analysis revealed that the relative abundance of Methanobacterium increased from 39.03 % to 69.50 %, indicating a selective microbial adaptation. In contrast, the overall abundance of genes involved in both acetoclastic and hydrogenotrophic methanogenesis decreased, suggesting a reduction in community-level methanogenic functional potential, which was consistent with the observed 97.4 % decline in methane yield. Meanwhile, the relative abundances of oxidative stress defense genes, katE (EC:1.11.1.6) and GPX (EC:1.11.1.9), in the test group increased by 10.2 % and 19.9 %, respectively, indicating enhanced antioxidant capacity of the microbial community. These findings provide insights into the management of inhibitor-rich pretreatment hydrolysates during AcoD of CS and FW.}, }
@article {pmid42342666, year = {2026}, author = {Jia, X and Jiang, L and Gong, Y and Chu, X and Yu, W and Du, J and Zhang, J and Shang, X and Wang, P and Wang, J and Li, Y and Wang, Z and Zhou, R and Li, Z and Zhu, Y and Wu, B and Li, J and Yang, Q}, title = {Fusobacterium periodonticum promotes colorectal tumorigenesis via decanoic acid-driven neutrophil chemotaxis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74591-y}, pmid = {42342666}, issn = {2041-1723}, abstract = {Gut microbiota dysbiosis and immune dysregulation are closely associated with the development of colorectal cancer. Identifying the mechanistic links among specific microbial species, metabolites, and immune responses is crucial for uncovering novel insights into its pathogenesis. Here we show, through metagenomic and metabolomic analyses of clinical cohorts, that Fusobacterium periodonticum is significantly enriched in colorectal cancer patients and strongly correlated with elevated decanoic acid levels. Single-cell transcriptomic results further reveal tissue-specific neutrophil enrichment in colorectal cancer tissues, characterized by high CXCL8 expression and activation of neutrophil-related immune pathways. Cellular experiments demonstrate that decanoic acid induces late apoptosis/necrosis of neutrophils, enhances their chemotaxis through a pertussis toxin-sensitive G-protein-dependent mechanism, and upregulates genes involved in leukocyte migration and tumorigenesis. Mouse models further confirm that F. periodonticum colonization increases intestinal dysplasia and decanoic acid levels, and that decanoic acid intervention promotes tumor progression by facilitating neutrophil infiltration and modulating the local immune microenvironment. Our study reveals an important role of F. periodonticum in colorectal tumorigenesis via decanoic acid-medicated neutrophil chemotaxis, providing mechanistic insights into the pathogenesis of colorectal cancer.}, }
@article {pmid42342687, year = {2026}, author = {Rubbab, B and Adenwalla, A and Spottiswoode, N and Haston, JC and Firmani, S and Singh, S and Rajaram, V and Ramos, J and Ali, IKM and Whittemore, B and Hanners, NW}, title = {Neurosurgical Biopsy and Resection for Diagnosis and Treatment of Balamuthia mandrillaris Amebic Encephalitis, United States.}, journal = {Emerging infectious diseases}, volume = {32}, number = {7}, pages = {}, doi = {10.3201/eid3207.260725}, pmid = {42342687}, issn = {1080-6059}, abstract = {We report a systematic case review of antemortem neurosurgical resections and biopsies and outcomes including new lesions after procedure and survival in Balamuthia mandrillaris granulomatous amebic encephalitis. The investigation was prompted by a 5-year-old patient in the southwestern United States who was treated with nitroxoline, the 2021 Centers for Disease Control and Prevention regimen, and underwent 2 resections; initial resection site recurrence and a new lesion after resection prompted the question whether complete resection versus biopsy is associated with better outcomes. We conducted a literature review and found no substantial difference between neurosurgical resection versus biopsy-only groups. Limitations include case review, number of cases, and incomplete data available. Additional analyses comparing neurosurgical outcomes with outcomes of those diagnosed via blood or cerebrospinal fluid and metagenomic next-generation sequencing might provide more definitive answers. This case and systematic review provide evidence that treatment with nitroxoline and neurosurgical resection could contribute to survival in Balamuthia encephalitis case-patients.}, }
@article {pmid42342731, year = {2026}, author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H}, title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42342731}, issn = {2055-5008}, support = {100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 323134//Norges Forskningsr&#xe5;d/ ; 323134//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.}, }
@article {pmid42342987, year = {2026}, author = {Saw, JH and Shlafstein, MD and Pavloudi, C and Monsalve, N and Prescott, RD and Chain, PSG and Decho, AW and Donachie, SP}, title = {Amplicon and metagenomic data from fumarole-associated geothermal features of Hawai'i.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07734-x}, pmid = {42342987}, issn = {2052-4463}, support = {2442122//National Science Foundation/ ; 1711856//National Science Foundation/ ; LANLF59T//Office of the Chief Information Officer, U.S. Department of Energy/ ; 80NSSC18K1064/NASA/NASA/United States ; }, abstract = {The Hawaiian Islands are among the most geologically and volcanically active places on Earth. While the Hawaiian Archipelago is known for its animal and plant diversity, much less is known about microbial diversity in the area's diverse habitats. In this study, we focused on steam vent associated biofilms found on the most volcanically active island of Hawai'i, also known as the Big Island. From 46 samples from various biofilms and associated features around fumaroles emitting water steam, we generated amplicon and metagenomic sequences. This represents a total of 276 Gbp of raw sequencing data. From the shotgun metagenomic data, we constructed 363 non-redundant medium- to high-quality metagenome-assembled genomes (MAGs) that are at least 70% complete and with less than 5% contamination. Of these, ten MAGs belong in the domain Archaea, and 353 belong in the domain Bacteria. This dataset could provide valuable insights into microbial diversity and ecology around volcanic features in Hawai'i and elsewhere.}, }
@article {pmid42332682, year = {2026}, author = {Zhu, Q and Duan, Q and Wang, F and Shao, ZJ and Hu, W and Bi, YK and Wang, X and Li, JL and Zhu, D and Lv, ZH and Yang, ZF and Yin, YR}, title = {Characterization of an alkali- and glucose-tolerant β-glucosidase from Karamay saline-alkali soil and its structural basis for glucose tolerance.}, journal = {BMC biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12896-026-01191-5}, pmid = {42332682}, issn = {1472-6750}, support = {32560004 and 32570003//National Natural Science Foundation of China/ ; 202501AU070181 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; XZ202501ZY0019//the Science and Technology Projects of the Xizang Autonomous Region/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; 2025DNS01//the Dali Prefecture Science and Technology Bureau/ ; }, abstract = {BACKGROUND: Industrial applications of β-glucosidases are often constrained by high salinity, alkaline conditions, and glucose inhibition.<br><br>RESULTS: A glycoside hydrolase family 1 &#x3b2;-glucosidase, B0-BG40, was mined from the metagenome of saline-alkali soil in Karamay, Xinjiang, China. When heterologously expressed in Escherichia coli, B0-BG40 exhibited optimal activity at 45&#xa0;&#xb0;C and pH 8.6, retaining&#x2009;>&#x2009;60% of its maximal activity over 20-55&#xa0;&#xb0;C and pH 5.6-9.6. The enzyme was highly stable at 25&#xa0;&#xb0;C, 40&#xa0;&#xb0;C and 45&#xa0;&#xb0;C and under alkaline conditions, maintaining&#x2009;>&#x2009;85% residual activity after prolonged incubation and showing activity enhancement following incubation at pH 8.0-10.0. B0-BG40 also tolerated up to 2.0&#xa0;M NaCl and 4.0&#xa0;M glucose, and displayed weak glucose inhibition (Ki = 1033.5 mM). Combined with the results of protein homology modeling and molecular docking, a reasonable mechanistic hypothesis was proposed: the excellent glucose tolerance of the enzyme may be related to its narrow and deeply recessed catalytic channel, and this special channel structure could hinder glucose molecules from entering the active site.<br><br>CONCLUSIONS: B0-BG40 is a salt-, alkali-, and glucose-tolerant &#x3b2;-glucosidase with strong potential for applications in food and feed processing and cellulosic ethanol production.}, }
@article {pmid42332773, year = {2026}, author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q}, title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.}, journal = {BMC medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12916-026-05012-6}, pmid = {42332773}, issn = {1741-7015}, support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; }, abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.<br><br>METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.<br><br>RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles&#x2009;=&#x2009;1.82; 95%CI&#x2009;=&#x2009;1.17-2.81; p-trend&#x2009;=&#x2009;0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction&#x2009;=&#x2009;0.01). Similar interactions were seen for total fiber (p&#x2009;=&#x2009;0.09), soluble fiber (p&#x2009;=&#x2009;0.09), and insoluble fiber (p&#x2009;=&#x2009;0.11), without statistical significance.<br><br>CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.}, }
@article {pmid42333020, year = {2026}, author = {Habiba, MU and Rahman, MM and Augustin, MA and Varela, C and Morris, H and Bozkurt, H}, title = {Traditional Fermented Dairy Products as Reservoirs of Bifidobacterium With Probiotic Potential: From Microbial Diversity to Functional Characterization.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {4}, pages = {e70540}, doi = {10.1111/1541-4337.70540}, pmid = {42333020}, issn = {1541-4337}, support = {//Adelaide University/ ; //University of Adelaide Research Scholarship/ ; }, mesh = {*Probiotics ; *Bifidobacterium/physiology/isolation &amp; purification ; *Cultured Milk Products/microbiology ; Fermentation ; Animals ; Food Microbiology ; Humans ; *Dairy Products/microbiology ; }, abstract = {Traditional fermented dairy products (TFDPs) are complex microbial ecosystems that may serve as reservoirs of many microorganisms, including those with probiotic potential such as Bifidobacterium species and lactobacilli. Although bifidobacteria are widely used as probiotic microorganisms in defined formulations, their occurrence, persistence, and functional relevance within TFDPs remain incompletely understood. This review critically synthesizes current evidence on the diversity, ecological roles, and traits associated with probiotic potential of Bifidobacterium spp. detected in TFDPs, including raw-milk fermentations, artisanal dairy products, and selected controlled dairy systems. Species such as Bifidobacterium animalis, Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium breve have been reported across yogurt, kefir, airag (traditional Mongolian fermented dairy beverage from mare milk), and raw milk cheeses, often at low abundance or as transient microbial community members. Many isolates from fermented dairy products exhibit traits commonly associated with probiotic functionality, including acid/bile tolerance, adhesion capacity, exopolysaccharide production, and antimicrobial activity. However, most reports remain limited to presence/absence or in vitro assays, with limited in vivo or clinical validation. Advances in molecular and omics-based approaches have improved detection, characterization, and safety evaluation; however, translation into validated applications remains constrained by challenges in isolation, viability, and strain-level confirmation. Importantly, detection of bifidobacteria in TFDPs does not confer probiotic status, which requires strain-level identification, demonstrated safety, adequate viable counts at consumption, and clinical evidence of health benefit. Collectively, TFDPs, as culturally embedded microbial reservoirs, may support the discovery of novel bifidobacterial strains for future development of functional foods or probiotic products following rigorous validation.}, }
@article {pmid42333270, year = {2026}, author = {Ibitoye, OA and Anyanwu, CN and Agbaje, AB and Fasogbon, IV and Dangana, RS and Akinola, SA and Tibyangye, J and Adam, AA and Aja, PM}, title = {Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.}, journal = {Biology methods &amp; protocols}, volume = {11}, number = {1}, pages = {bpag029}, pmid = {42333270}, issn = {2396-8923}, abstract = {Antimicrobial resistance (AMR) is a global health and environmental challenge, driven by complex interactions among microbial communities, resistance genes, and selective pressures in various ecological niches. Traditional surveillance procedures often fall short in capturing the full diversity and dynamics of resistance reservoirs in the environment. This review examines the integration of artificial intelligence (AI) and machine learning (ML) with next-generation sequencing (NGS) technologies for comprehensive resistome profiling. We discuss advances in multi-omics approaches, particularly metagenomics, microbiome-based analytics, and metatranscriptomics. We also highlight computational workflows that enable high-resolution mapping of resistance genes, their mobile genetic elements, and host associations. The role of AI/ML in resistome prediction, classification, and source tracking, as well as the incorporation of environmental metadata for contextual interpretation is discussed based on the selected literature. Moreover, we assess current challenges and propose future directions for developing standardized, scalable, and interpretable bioinformatic pipelines in AMR surveillance. This review primarily elucidates the potential of integrated AI-omics platforms to revolutionize aquatic environmental AMR monitoring and inform risk assessment and mitigation strategies.}, }
@article {pmid42334513, year = {2026}, author = {Zhang, X and Du, L and Jin, X and Sun, J and An, G and Li, L and Yang, P and Li, F}, title = {Nocardia brasiliensis endophthalmitis initially misdiagnosed as uveitis: a case report.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00602-0}, pmid = {42334513}, issn = {1869-5760}, support = {YXKC2020026//Henan Provincial Health Commission/ ; 82301271//National Natural Science Foundation of China/ ; 82230032//National Natural Science Foundation of China/ ; 82101108//National Natural Science Foundation of China/ ; 2025Hx39//First Affiliated Hospital of Zhengzhou University/ ; SBGJ202101011//Health Commission of Henan Province/ ; }, abstract = {BACKGROUND: Endophthalmitis caused by Nocardia brasiliensis is extremely rare and typically affects immunocompromised individuals, frequently leading to severe vision loss due to diagnostic delays. We report a case of N. brasiliensis endophthalmitis in an older man without prior history of systemic immunosuppression but with newly identified diabetes mellitus, characterized by an indolent initial course followed by fulminant progression.<br><br>CASE PRESENTATION: A 67-year-old man without known systemic immunosuppression presented with a two-month history of recurrent right-eye pain and redness, followed by rapid vision loss and a hypopyon. Aqueous humor analysis and metagenomic sequencing identified N. brasiliensis. Despite intravitreal amikacin, systemic antimicrobial therapy, and subsequent pars plana vitrectomy with silicone oil tamponade, intraocular inflammation advanced, resulting in worsening corneal opacification, irreversible structural damage, and a final best-corrected visual acuity of light perception.<br><br>CONCLUSIONS: N. brasiliensis endophthalmitis may progress rapidly and result in severe, irreversible ocular damage, even in patients without overt systemic immunodeficiency. Early microbiologic identification and prompt, targeted antimicrobial therapy combined with timely surgical intervention are critical, although visual outcomes may remain poor in advanced cases.}, }
@article {pmid42334609, year = {2026}, author = {Zheng, Y and Chen, C and Guan, D and Huang, Y and Xiong, L and Liu, R}, title = {Viral community dynamics and functional succession in advanced drinking water treatment processes.}, journal = {Archives of microbiology}, volume = {208}, number = {9}, pages = {}, pmid = {42334609}, issn = {1432-072X}, mesh = {*Drinking Water/virology/microbiology ; *Water Purification/methods ; Bacteria/genetics/classification/isolation &amp; purification ; *Viruses/genetics/classification/isolation &amp; purification ; China ; Metagenomics ; Water Microbiology ; }, abstract = {Viruses play a significant role in microbial ecology, yet their impact on drinking water systems remains poorly understood. We collected water from different treatment process streams of an ozone-bioactivated carbon (O3-BAC) advanced drinking water treatment plant in eastern China. DNA viral metagenomic sequencing was then performed to analyze viral abundance, community structure, diversity, host prediction, virulence factors, potential viral pathogens, and functional genes, including carbohydrate-active enzymes (CAZymes), auxiliary metabolic genes (AMGs), and antibiotic resistance genes (ARGs). The results revealed that treatment reduced viral abundance and diversity, although certain taxa not detected in raw water or sedimentation water (e.g., Preplasmiviricota) were detected in sand-filtered water and finished water. Caudoviricetes were the most abundant viruses in the water treatment process. The virus host types were predominantly bacteria, mainly Lactobacillus, Mycoplasma, Staphylococcus, Bacillus, and Streptococcus. Functional analysis revealed viral involvement in carbohydrate degradation via CAZymes and modulation of host metabolism through AMGs and ARGs to support viral replication. Potential human pathogens were identified within Poxviridae and Herpesviridae. This study provides novel insights into DNA viral ecological dynamics in engineered water systems and supports enhanced pathogen control strategies.}, }
@article {pmid42334937, year = {2026}, author = {Ma, C and Liu, S and Won, S and Koslicki, D}, title = {MetagenomicKG: a knowledge graph for metagenomic applications.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag421}, pmid = {42334937}, issn = {1367-4811}, abstract = {MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored.<br><br>RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction.<br><br>CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.<br><br>SUPPLEMENTARY INFORMATION: available at Bioinformatics online.}, }
@article {pmid42334999, year = {2026}, author = {Masukawa, H and Kobayashi, R and Watanabe, J and Tanizaki, A and Morono, Y and Ito, M and Terada, T and Takaki, Y and Tsuda, M and Matsui, Y and Arai, T and Takai, K and Kameya, M and Arai, H and Yamamoto, M}, title = {Electrosynthetic bacterial growth under conditions simulating electric discharge in deep-sea hydrothermal fields.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag108}, pmid = {42334999}, issn = {1751-7370}, abstract = {Microbial electrosynthesis is a metabolic process in which extracellular electrons are utilized as the primary energy source for carbon fixation. While microbial electrosynthesis has been proposed as a novel concept for ecological primary production, our understanding of how such microorganisms are distributed in natural environments remains limited. In this study, we constructed a laboratory-scale electrochemical cultivation system that simulates electric discharge conditions in deep-sea hydrothermal fields. Microscopic counts revealed increased cell numbers in the electrochemical culture, and 16S rRNA gene analysis revealed a significant enrichment of a novel Thiomicrorhabdus species. Quantitative PCR confirmed proliferation and enrichment of a metagenome-assembled genome (MAG), named the SREC-4. Electrochemical cultivation with 13C-labeled CO2 as a substrate indicated significant 13C incorporation specifically in Thiomicrorhabdus cells including MAG SREC-4. The genome of MAG SREC-4 revealed the possession of the putative extracellular electron uptake pathway in addition to the autotrophic sulfur-oxidizing aerobic respiration pathways typically found in Thiomicrorhabdus members. The putative extracellular electron uptake pathway was found in a phylogenetic clade in Thiomicrorhabdus mainly formed by strains derived from hydrothermal fields. These results provide the direct experimental evidence from enrichment cultures derived from hydrothermal fields that an organism inhabiting deep-sea hydrothermal fields can grow electrosynthetically, and suggest that this ability is shared by other Thiomicrorhabdus species, specifically those found in similar environments. This finding suggests electrosynthetic growth may be widely distributed in Thiomicrorhabdus populations dwelling in deep-sea hydrothermal fields, the largest natural electrogenic environment on Earth.}, }
@article {pmid42335476, year = {2026}, author = {Valentino, V and De Filippis, F and Ercolini, D}, title = {Fermented foods: lessons learned from metagenomics.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103545}, doi = {10.1016/j.copbio.2026.103545}, pmid = {42335476}, issn = {1879-0429}, abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.}, }
@article {pmid42335503, year = {2026}, author = {Liu, LM and Fang, HB and Wang, YF and Zhang, YL and Yu, QQ and Zhang, WY and Liu, J and Miao, H and Zhao, YY}, title = {Niaoduqing particles ameliorated tubulointerstitial fibrosis by suppressing IκB/NF-κB signalling pathway via inhibiting host- and gut microbiota-mediated tryptophan co-metabolism.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128592}, doi = {10.1016/j.micres.2026.128592}, pmid = {42335503}, issn = {1618-0623}, abstract = {Tubulointerstitial fibrosis (TIF) is an inevitable outcome of progressive chronic kidney disease (CKD). Niaoduqing particles (NDQ) were developed for the treatment of CKD. However, the molecular mechanisms underlying the effect of NDQ on TIF remain unclear. Fecal gut microbiota (GM) and serum metabolites were analyzed using metagenomics and metabolomics in unilateral ureteral obstruction (UUO)-induced TIF rats. NDQ treatment attenuated UUO-induced TIF in rats in a dose- and time-dependent manner. The increased abundance of eight pathogenic bacteria, including Bacillus wiedmannii, Enterococcus mundtii and Fusobacterium varium, showed strong positive correlations with TID scores, whereas the reduced abundance of two probiotic bacteria, Ruminococcus flavefaciens and Clostridium celatum, showed strong negative correlations with tubulointerstitial damage (TID) scores. NDQ treatment reversed these aberrant microbial alterations, indicating its capacity to remodel GM dysbiosis. TID scores were strongly correlated with host- and GM-mediated tryptophan co-metabolites, including indoxyl sulfate, tryptamine and indole-3-acetic acid, in both TIF- and NDQ-treated TIF rats, and NDQ intervention normalized these metabolic disturbances. Notably, Fusobacterium varium and Enterococcus faecium exhibited strong linear correlations with indoxyl sulfate, indole-3-acetic acid, and indole-3-aldehyde in the TIF rat model. Furthermore, NDQ suppressed IκB/NF-κB signaling pathway in both TIF rats and TGF-β1-induced NRK-52E cells. These inhibitory effects were partially reversed by NF-κB p65 knockdown. This study is the first to demonstrate that NDQ alleviates TIF by reshaping microbial dysbiosis and modulating host- and GM-mediated tryptophan metabolism. These findings support that NDQ mitigates TIF by suppressing IκB/NF-κB signaling pathway through regulation of host-microbiota-derived tryptophan metabolism.}, }
@article {pmid42335537, year = {2026}, author = {Gong, H and Xian, ZN and Hu, J and Luo, J and Wang, Y and Liu, X and Zhu, N}, title = {Low-intensity electrical stimulation enhances phthalate ester biodegradation by activated sludge through real-time multi-scale regulation.}, journal = {Water research}, volume = {304}, number = {}, pages = {126306}, doi = {10.1016/j.watres.2026.126306}, pmid = {42335537}, issn = {1879-2448}, abstract = {Phthalate esters (PAEs) are ubiquitous contaminants that are poorly removed by conventional biological treatment processes. This study investigated the enhancement of PAE biodegradation in activated sludge under low-intensity electrical stimulation. A single-chamber electrostimulated aerobic microbial system (EAMS) was established and operated at 0.6-2.1 V to explore the physiological, genetic, and community-level responses of microorganisms. Moderate stimulation (0.9-1.5 V, electric field strength 180-300 V·m[-1], current 10.6-136.0 μA, current density 0.5-6.8 mA·m[-2]) increased the biodegradability of the three PAEs by 11%-20%. Electrical stimulation significantly enhanced the physiological activity and community synergy of the microbial community dominated by non-electroactive bacteria. Metagenomic and metatranscriptomic analyses revealed that the genomic abundance of PAE-degrading genes was unchanged, but their expression was strongly upregulated (20-40-fold). Electrical stimulation enhanced PAE biodegradation by activating the metabolic and transcriptional machinery of the resident microbial community, rather than by selecting for specific degraders. This activation led to elevated expression of key degradation genes and consequently improved biodegradation efficiency. These findings suggest that electrical stimulation acts as a functional activator of indigenous microbial communities, providing a rapid and broadly applicable strategy for improving biodegradation efficiency without requiring extensive community restructuring.}, }
@article {pmid42335557, year = {2026}, author = {Sun, X and Jia, C and Song, X and Zhao, X and Han, M and Yin, H and Zhang, P}, title = {Incorporating benthic microbial thresholds into ecological carrying capacity to sustain ecosystem services of coastal oyster farming.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130316}, doi = {10.1016/j.jenvman.2026.130316}, pmid = {42335557}, issn = {1095-8630}, abstract = {Oyster aquaculture provides crucial ecosystem services by mitigating coastal eutrophication. However, intensive farming frequently leads to benthic organic overloading, which threatens this bioremediation capacity. Current Ecological Carrying Capacity (ECC) assessments focus on the interaction between yield and pelagic metrics, leaving a critical management loophole regarding benthic sediment health. To address this gap, we conducted a large-scale benthic environmental and metagenomic investigation across five intensive oyster (Crassostrea gigas) farming areas in the Shandong Peninsula, China. Our results revealed that biodeposit-driven organic loading promoted total sulfur (TS) accumulation, triggering a non-linear functional regime shift in the benthic nitrogen cycle. Breakpoint analysis identified a critical threshold at a sedimentary TS concentration of 0.89 g kg[-1], beyond which the denitrification was redirected toward dissimilatory nitrate reduction to ammonium (DNRA), concurrently elevating the risk of greenhouse gas (N2O) emissions. Crucially, a profound spatial decoupling was observed between macroscopic farming yield and benthic micro-ecological status. Shallow-water areas with low yields suffered severe benthic degradation, whereas deep-water areas sustaining highly intensive yields maintained robust eutrophication mitigation functions. This paradox underscores the decisive role of the ecosystem's assimilative capacity over absolute farming load. These findings challenge the traditional yield-focused Ecological Carrying Capacity (ECC) assessments. We therefore advocate for incorporating thresholds of microbial-driven biogeochemical potentials into the ECC management framework to ensure the holistic sustainability of coastal aquaculture.}, }
@article {pmid42335767, year = {2026}, author = {Li, T and Guo, T and Cui, M and Cao, Y and Zhi, Z and Wang, P and Li, Q and Zhang, J}, title = {Rearing systems shape the successional dynamics of the gut microbiota, resistome, and mobilome in Lueyang Black-boned chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107322}, doi = {10.1016/j.psj.2026.107322}, pmid = {42335767}, issn = {1525-3171}, abstract = {Understanding the ecological factors shaping antimicrobial resistance (AMR) dissemination in agricultural environments is critical for global "One Health". Here, we performed metagenomic sequencing to investigate the impact of intensive cage-reared (CR) and free-range (FR) systems on the gut microbiota, resistome, and mobilome dynamics of Lueyang Black-boned chickens across different production stages. Our analyses revealed that distinct rearing systems drove resistome alterations by reshaping microbial community assembly and horizontal gene transfer (HGT) pathways. Specifically, the CR system imposed strong deterministic stress, thereby enriching opportunistic taxa (such as Desulfovibrio) and promoting a highly connected but topologically fragile microbial network. Conversely, the FR system exhibited a higher total abundance of commensal resistance genes, a process mainly driven by diverse transposon-mediated integrations including tnpA and ISBf10. In contrast, the CR system was associated with high-risk, clinically relevant resistance determinants. These included extended-spectrum beta-lactamases and multidrug resistance cassettes. Targeted network tracking unmasked highly divergent potential host-vector-ARG associations. Resistance expansion under confined CR conditions showed strong vector-dependency, being fundamentally linked to the broad-host-range plasmid IncQ1 alongside clinically relevant mobilization elements, including Class 1 integrons. Longitudinally, the FR resistome achieved ecological stabilization. In contrast, the CR microbiota exhibited continued genetic flux, continuously acquiring transient resistance elements during the observed production period. These findings demonstrate that welfare-friendly rearing management serves as a critical ecological intervention to limit the proliferation of mobile, high-risk resistance traits. Ultimately, future agricultural surveillance must transition beyond quantifying total resistance gene abundance to prioritize functional risk assessments and mobilization potential.}, }
@article {pmid42335821, year = {2026}, author = {Rehman, A and Wang, X and Yousaf, M and Wang, J and Li, Z}, title = {Biotransformation of Microcystin-LR in marine sediments: Mechanism and global potential.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142754}, doi = {10.1016/j.jhazmat.2026.142754}, pmid = {42335821}, issn = {1873-3336}, abstract = {Microcystin-LR (MC-LR), a potent hepatotoxin produced during cyanobacterial harmful algal blooms, can be transported from freshwater systems to coastal marine environments through riverine discharge and estuarine mixing, yet its environmental fate in coastal sediments remains poorly understood. Here, we investigated the biotransformation mechanism of MC-LR in coastal sediments using LC-MS/MS, metagenomics, metabolic modeling, molecular docking, and genome binning. The results showed that MC-LR was transformed primarily via co-metabolism, following pseudo-first-order kinetics. Notably, we identified a novel biotransformation pathway in the marine environment that differs from the conventionally recognized mlr-dependent pathway observed in terrestrial systems. Biotransformation in marine sediments involves peptide ring opening, formation of linear MC-LR, stepwise peptide shortening, and conversion of the Adda-containing fragment into smaller aromatic compounds. Metabolic modeling and ecological network analysis further revealed that the microbial community facilitates this co-metabolic biotransformation through a cross-feeding mechanism, in which different taxonomic groups share complementary functions for co-substrate transformation, peptide bond cleavage, and aromatic compound degradation. Metagenomic profiling and genome binning demonstrated that MC-LR transformation is coupled with glutathione metabolism, and key genes involved in MC-LR transformation (e.g., CAAX, pepA, pepN, paaA, paaG, paaZ) were mainly associated with members of the Pseudomonadota, Myxococcota, and Acidobacteriota. Global screening of publicly available MAGs revealed that CAAX genes linked to MC-LR transformation are widely distributed across aquatic environments, with 16,209 CAAX-containing MAGs identified from 498 sampling locations worldwide, including 6892 marine MAGs from 317 oceanic sites. Overall, this study clarifies the biotransformation mechanism of MC-LR in marine sediments and highlights the widespread genetic potential for its biotransformation across global aquatic environments.}, }
@article {pmid42335822, year = {2026}, author = {He, T and Liu, J and Li, Y and Ohgami, N and Wei, X and Peng, T and Zhang, X and Zhang, R and Du, J and Deng, Y and Jiang, H and Zhang, P and Zhang, Y}, title = {Long-term groundwater arsenic exposure is associated with altered arsenic methylation capacity and gut microbiota composition in a rural Chinese population.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142658}, doi = {10.1016/j.jhazmat.2026.142658}, pmid = {42335822}, issn = {1873-3336}, abstract = {This study investigated the relationship between long-term groundwater arsenic exposure, arsenic methylation capacity, and gut microbiota in adults from rural northern China. Arsenic detoxification relies in part on methylation processes, and growing evidence suggests that the gut microbiome may participate in arsenic biotransformation, yet population-based data integrating exposure, metabolism, and microbial profiles remain scarce. We recruited 258 participants from two neighboring villages supplied by centralized wells with contrasting arsenic levels (control, n = 138; exposure, n = 120). Total urinary arsenic was measured in all participants, and arsenic species were quantified in a subgroup (n = 60) to derive primary and secondary methylation indices (PMI and SMI). Fecal metagenomes were sequenced to characterize taxonomic composition and functional potential based on KEGG and GO annotations. Individuals in the exposure village showed higher levels of urinary inorganic arsenic and methylated metabolites. While PMI was comparable between groups, SMI was significantly reduced among exposed individuals, indicating impaired secondary methylation. Arsenic exposure was also associated with pronounced alterations in gut microbial diversity and community structure. Several anaerobic taxa, largely linked to fermentative metabolism, were positively associated with SMI after multivariable adjustment. Functional analyses further revealed differences in pathways related to transport, environmental sensing, and metabolism. These findings suggest that chronic arsenic exposure is associated with reduced methylation efficiency and shifts in gut microbial composition and function, and that the gut microbiome may contribute to interindividual variability in arsenic metabolism and toxicity.}, }
@article {pmid42335936, year = {2026}, author = {Ter Horst, PAG and Marshall, IPG and Egas, RA and Klomp, R and Schutgens, MAW and van Alen, T and Jetten, MSM and Slomp, CP and Welte, CU}, title = {Electrogenic CH4 oxidation on a bioanode: putative extracellular electron transport system in Methylobacter sp.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag067}, pmid = {42335936}, issn = {1574-6941}, abstract = {Aerobic methanotrophs are frequently detected in oxygen-limited, stratified coastal environments. Known adaptations, including high-affinity terminal oxidases and oxygen-binding bacteriohemerythrins, help explain methane oxidation at extremely low oxygen concentrations, yet their activity and ecological role under fully anoxic conditions remain uncertain. Here, we show that an anoxic, poised-anode bioelectrochemical system inoculated with a methane-oxidizing sediment enrichment produced methane-dependent current, with rapid current loss upon methane removal and recovery after re-addition. Metagenomic analysis revealed the selective enrichment of a Methylobacter population encoding a porin-cytochrome complex and numerous multiheme c-type cytochromes, suggesting extracellular electron transfer potential. A complementary phylogenomic survey across Methylococcales identified homologs of this gene cluster in multiple lineages, but with a scattered phylogenetic distribution indicative of modular acquisition. Comparative synteny further revealed conserved gene order across genomes, supporting horizontal transfer of the locus as a functional unit. Together, these results demonstrate that aerobic methanotrophs may employ extracellular electron transfer strategies to dissipate methane-derived electrons when oxygen-dependent respiration is constrained.}, }
@article {pmid42336533, year = {2026}, author = {Yu, L and Jiang, L and Liu, C and Wang, S and Zhu, G}, title = {High co-occurrence but low heterogeneity of virulence factors and resistance genes in farmland soil.}, journal = {Journal of environmental sciences (China)}, volume = {166}, number = {}, pages = {273-282}, doi = {10.1016/j.jes.2025.11.031}, pmid = {42336533}, issn = {1001-0742}, abstract = {Virulence factors (VFs), antibiotic resistance genes, and metal resistance genes in farmland soil pose significant threats to food security, soil health, and human well-being. Numerous studies have reported on the characteristics and hazards of resistance genes in the soil, but the co-occurrence of VFs and resistance genes has received little attention as a potential threat to the ecological environment. Here, we investigated the mechanism of interaction between VFs and resistance genes in farmland soil samples worldwide, especially in China, the most antibiotic-contaminated country. Metagenomics and metagenome binning analysis provided direct evidence that VFs and resistance genes could co-occur universally in the same microbial cell in farmland soil, dramatically enhancing the pathogenic ability of soil microorganisms and severely raising the threat to ecological security. We found that the spatial distribution of resistance genes and VFs in farmland topsoil exhibited low heterogeneity. These findings contribute to our understanding of VFs and resistance genes in farmland soil, which is beneficial for ensuring the healthy development of agriculture and food security.}, }
@article {pmid42336534, year = {2026}, author = {Zhai, F and Li, B and Zhao, X and Zhao, P and Yang, S and Li, X and Wang, T and Liu, G and Yan, P}, title = {Bioelectrochemical mitigation of soil antibiotic resistance: Disruption of bacteriophage transmission and resistant hosts.}, journal = {Journal of environmental sciences (China)}, volume = {166}, number = {}, pages = {283-294}, doi = {10.1016/j.jes.2025.11.008}, pmid = {42336534}, issn = {1001-0742}, abstract = {The proliferation of antibiotic resistance genes (ARGs) in environment poses a threat to global public health. Although microbial fuel cell (MFC) has been demonstrated to mitigate ARG amplification, the mechanism remains unclear. This study employed metagenomic sequencing combined with the DeepARG-LS model for profiling ARGs and further analyzed the effects of MFCs on them in tetracycline-contaminated soil. Consequently, tetracycline addition (AT treatment) elevated total ARG abundance by 31 %, whereas MFC application (MT treatment) reduced it by 12 %. The deep learning model revealed a 38 % reduction in the richness of ARG subtypes in the MT compared to the AT. Proteobacteria dominated as ARG hosts, accounting for 78 % of ARGs in the AT, but declined by 18 % in the MT. Notably, the archaeal Nitrososphaeraceae was identified as a host for tetA(48). Species-level analysis identified 12 ARG-carrying bacterial taxa, the abundance of most of which was suppressed (abundance) by MFCs. The richness of ARGs host bacteria was 38 % lower in the MT treatment than that in the AT treatment. Meanwhile, the abundance of the indole biosynthesis gene (tryptophanase, EC 4.1.99.1) exhibited a consistent trend with the richness of ARGs hosts. Mechanistically, the suppression of ARG-host bacteria may be attributed to enhanced indole biosynthesis (as indicated by increased tryptophanase abundance), coupled with reduced abundances of mobile genetic elements (84 %) and virulence factors (11 %), and a decline in phage-mediated ARG transmission (19 %). Overall, these findings provide insights into bioelectrochemical controlling ARG dissemination in soils.}, }
@article {pmid42336879, year = {2026}, author = {Feng, C and Lu, H and Bian, J and Wang, H and Jia, H and Li, X and Yang, M and Song, H and Tan, W and Wang, L}, title = {Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01054-z}, pmid = {42336879}, issn = {2055-5008}, support = {2025ZD01900200//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; }, abstract = {Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.}, }
@article {pmid42336888, year = {2026}, author = {Liu, Y and Xiong, G and Gao, L and Li, Y and Zhou, X and Yao, H and Wei, G and Yang, M and Yin, Y and Peng, J and Dong, L and Zhang, G}, title = {Foliar metal micronutrients reshape rhizosphere soil multifunctionality by filtering microbial life-history strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01071-y}, pmid = {42336888}, issn = {2055-5008}, support = {2022YFC3501802, 2022YFC3501803, and 2022YFC3501804//National Key Research and Development Program/ ; 2023-I2M-2-006//CAMS Innovation Fund for Medical Sciences(CIFMS) Grant/ ; CI2023E002, CI2024E003//Chinese Academy of Chinese Medical Sciences/ ; CI2026A03809//Chinese Academy of Chinese Medical Sciences/ ; 82304663//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ16-XRZ-072, ZZ17-YQ-025, ZXKT22052, and ZXKT22060//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; Z181100006218020//Beijing Nova Program/ ; }, abstract = {Foliar application of metal micronutrients is increasingly adopted in intensive cultivation systems, yet its potential ecological risks to rhizosphere functions remain poorly understood. Here, using the medicinal plant Panax notoginseng as a model, we conducted a gradient foliar amendment experiment with iron (Fe), zinc (Zn), and copper (Cu) to evaluate how aboveground metal inputs regulate rhizosphere soil multifunctionality (MF) through microbial life-history strategies. By integrating 16S rRNA amplicon sequencing, metagenomics, root transcriptomics, and a newly developed quantitative Yield-Acquisition-Stress tolerance (qYAS) framework, we disentangled the microbial mechanisms underlying divergent functional responses to metal amendments. Foliar Fe significantly enhanced multifunctionality, including nutrient provision and element cycling, while Cu and Zn reduced nutrient provision and element cycling, but enhanced plant pathogen abundances. These changes were closely associated with shifts in bacterial life-history strategies: Fe promoted Y-strategists characterized by efficient carbon use, streamlined genomes, and high network connectivity, whereas Cu and Zn enriched AS-strategists with larger genomes and negative associations with multifunctionality. Partial least squares path modeling (PLS-PM) further identified microbial strategies as key mediators linking foliar metal inputs, plant performance, soil properties, and multifunctionality. This study provides a trait-based microbial framework for evaluating foliar metal fertilization and guiding safer nutrient management.}, }
@article {pmid42336979, year = {2026}, author = {Solymosi, N and Pap, B and Nagy, S&#xc1; and Tóth, AG and Kevély, FJ and Maróti, G and Csabai, I and Kóthay, K and Magyar, D}, title = {Metagenomic peek into a corn mummy.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59149-8}, pmid = {42336979}, issn = {2045-2322}, abstract = {Numerous studies have shown that metagenomics has opened a dimension in reading the contents of archaeological remains as time capsules. Corn mummies are ritual objects from ancient Egypt, created by forming human-shaped figures from cereal grains grown in a mixture of water and earth. The aim of our study was to determine whether ancient DNA could be preserved in the mummy, and if so, which organisms it might have originated from. To find answers, we performed metagenomic analyses on samples taken from a corn mummy dating to the second half of the third century BC. Alongside a number of clearly modern contaminants, we identified organisms that cannot be excluded as being of historical origin. Besides considerable amounts of bacterial sequences belonging to the genus Bacillus, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus and Paenibacillus, we also found traces of plants, animals, and humans. Sequences assigned to the genus Triticum showed the highest similarity to ancient T. turgidum ssp. dicoccum specimens from Egypt and the southern Levant. The fragments identified as of Lepidopteran origin showed the greatest similarity to Sphingidae genomes. Analysis of the human-derived sequences revealed L3 (mtDNA), E, and J (Y chromosome) haplotypes, which are common lineages in Africa today.}, }
@article {pmid42135082, year = {2026}, author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P}, title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].}, journal = {Life sciences}, volume = {398}, number = {}, pages = {124457}, doi = {10.1016/j.lfs.2026.124457}, pmid = {42135082}, issn = {1879-0631}, }
@article {pmid42135536, year = {2026}, author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO}, title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {17}, pages = {8264-8275}, pmid = {42135536}, issn = {1614-7499}, mesh = {Seasons ; *Fungi ; Biodiversity ; Geologic Sediments ; Microbiota ; Phylogeny ; }, abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.}, }
@article {pmid42135633, year = {2026}, author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X}, title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05137-x}, pmid = {42135633}, issn = {1471-2180}, support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; }, abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.<br><br>RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p&#x2009;<&#x2009;0.05, |log2FC| &#x2265; 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+&#x2009;52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.<br><br>CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.}, }
@article {pmid42136553, year = {2026}, author = {Yang, L and Chen, X and Jia, A and Liu, Q and Chu, J}, title = {Atypical Streptococcus sinensis infective endocarditis complicated by bacterial meningitis: A case report and literature review.}, journal = {The Journal of international medical research}, volume = {54}, number = {5}, pages = {3000605261447124}, pmid = {42136553}, issn = {1473-2300}, mesh = {Humans ; Male ; *Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Streptococcus/isolation &amp; purification/genetics ; *Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis ; *Streptococcal Infections/microbiology/drug therapy/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Vancomycin/therapeutic use ; *Endocarditis/microbiology/complications/drug therapy ; Mitral Valve/microbiology ; Ceftriaxone/therapeutic use ; Echocardiography ; }, abstract = {Infective endocarditis caused by Streptococcus sinensis complicated by bacterial meningitis is exceedingly rare. We report a case of a middle-aged man who initially presented with ischemic symptoms in both lower limbs. Echocardiography revealed mitral valvular vegetations, and blood cultures confirmed S. sinensis. During antibiotic therapy, the patient developed somnolence, dysarthria, and left-sided weakness. Metagenomic next-generation sequencing of cerebrospinal fluid detected S. sinensis, thereby confirming infective endocarditis complicated by bacterial meningitis. Given the high surgical risk, combination antimicrobial therapy with vancomycin and ceftriaxone was administered. The patient's consciousness recovered, and inflammatory and cerebrospinal fluid parameters gradually normalized. This case demonstrates that S. sinensis-associated infective endocarditis can occur in patients with immunocompetent status and often involves the mitral valve, with potential intracranial complications. Early identification by blood culture, metagenomic next-generation sequencing, and 16S rRNA sequencing enables precise pathogen diagnosis. Standardized antibiotic therapy and individualized surgical assessment are crucial to optimize outcomes. For patients with neurological complications, multidisciplinary management is essential to improve survival and long-term prognosis.}, }
@article {pmid42136736, year = {2026}, author = {Takahashi, Y and Sada, RM and Matsuo, H and Yamamoto, S and Matsuzaki, S and Okada, A and Sunada, A and Takao, M and Yamamoto, G and Chuang, CK and Liu, CH and Kutsuna, S}, title = {Diagnostic challenges in postoperative pelvic infections associated with Metamycoplasma hominis: a two-case analysis using metagenomic sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823299}, pmid = {42136736}, issn = {2235-2988}, mesh = {Humans ; Female ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoplasma hominis/genetics/isolation &amp; purification ; Middle Aged ; *Pelvic Infection/diagnosis/microbiology ; *Postoperative Complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Adult ; *Mycoplasma Infections/diagnosis/microbiology ; }, abstract = {Postoperative gynecological infections may present diagnostic challenges, particularly in the presence of fastidious genital mollicutes and inherently mixed microbial DNA, both of which limit the diagnostic performance of microbiological methods, including Gram staining, conventional culture, 16S rRNA gene PCR followed by Sanger sequencing. This study aimed to illustrate the limitations of conventional microbiological methods in the diagnosis of gynecologic pelvic infections and highlight key considerations for the clinical use of metagenomic next-generation sequencing (mNGS), based on two contrasting cases of postoperative pelvic infections associated with Metamycoplasma hominis (M. hominis). In both cases, neither conventional culture nor 16S rRNA gene PCR/Sanger sequencing identified the causative organism, and shotgun mNGS was subsequently performed. Although the mNGS findings differed markedly between the two cases, M. hominis was considered the most plausible pathogen. These two cases show that the clinical relevance of organisms detected by mNGS should not be judged by read counts alone, particularly in non-sterile specimens or after antibiotic exposure. Even low-abundance reads may represent clinically meaningful pathogens when interpreted within the clinical context. They also highlighted the value of mNGS as a complementary diagnostic tool for gynecological pelvic infections when conventional diagnostic methods are intrinsically limited.}, }
@article {pmid42136790, year = {2026}, author = {Ariyasiri, A and Altaf, A and Mirza, H and Rehman, M}, title = {Genomics for precision surgical source control in anti-microbial resistant infections: A global review with focus on resource-limited settings.}, journal = {Pakistan journal of medical sciences}, volume = {42}, number = {411AASC}, pages = {S151-S156}, pmid = {42136790}, issn = {1682-024X}, abstract = {BACKGROUND &amp; OBJECTIVE: Antimicrobial resistance (AMR) critically threatens surgical safety, impairing perioperative prophylaxis and complicating infection management. Timely surgical source control is essential but relies on accurate microbiological diagnosis. Conventional culture-based methods are slow and insensitive, often leading to empirical broad-spectrum therapy. This review evaluates the role of advanced genomic diagnostics in enhancing surgical source control for AMR infections, with a focus on challenges and opportunities in low- and middle-income countries (LMICs) like Pakistan.<br><br>METHODOLOGY: A narrative review was conducted via a structured search of PubMed, Google Scholar, and ScienceDirect (January 2015-October 2025). Studies involving genomic tools in the management of AMR-related surgical infections were included. Evidence was synthesized thematically, covering genomic platforms, clinical applications, implementation barriers, and LMIC specific perspectives.<br><br>RESULTS: Genomic tools, particularly metagenomic next-generation sequencing (mNGS) and rapid multiplex PCR, demonstrate superior sensitivity (80.6-95.45%) and faster turnaround times (e.g., roughly 27 hours for mNGS) compared to culture. They improve pathogen detection in complex infections (e.g., prosthetic joints, necrotizing soft tissue), guide targeted antibiotic therapy, and can reduce broad-spectrum use. However, major implementation barriers exist, including high costs, need for specialized infrastructure and expertise, bioinformatic challenges, and ethical data concerns, which are especially pronounced in LMICs.<br><br>CONCLUSION: Genomic diagnostics offer a powerful approach to accelerate and refine surgical source control in the era of AMR. Strategic investments in local capacity, affordable platforms, and integration with antimicrobial stewardship are needed to realize their potential for improving surgical outcomes, particularly in resource-limited settings.}, }
@article {pmid42136862, year = {2026}, author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M}, title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1805596}, pmid = {42136862}, issn = {2296-858X}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.<br><br>OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.<br><br>METHODS: Skin samples were collected from 12&#x202f;AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).<br><br>RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p&#x202f;=&#x202f;0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p&#x202f;=&#x202f;0.042) and between moderate and severe groups (p&#x202f;=&#x202f;0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.<br><br>CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.}, }
@article {pmid42136870, year = {2026}, author = {Zhou, Y and Chen, L and Wang, L and Zhao, Z and Tu, J and Chen, H and Wang, S}, title = {Cavitary nodule caused by Emergomyces orientalis in a diabetic patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829356}, pmid = {42136870}, issn = {2296-858X}, abstract = {Emergomyces orientalis is a rare thermally dimorphic fungus belonging to the family Ajellomycetaceae. It exists in the environment as a mold producing conidia, which are inhaled and transform into yeast-like cells at body temperature to cause disseminated infections. While primarily associated with immunocompromised individuals, especially those with HIV. Diagnosis remains challenging due to its morphological similarity to Blastomyces dermatitidis and the frequent failure of routine cultures. Thus, molecular methods such as metagenomic next-generation sequencing (mNGS) have become crucial for early identification. This case report describes a 51-year-old man with type 2 diabetes mellitus presented (T2DM) with a 10-day history of back pain, pharyngeal discomfort, and scant sputum. Chest CT showed multiple bilateral pulmonary nodules, one of which had cavitated. mNGS of a percutaneous lung biopsy confirmed Emergomyces orientalis. Histopathology also supported the diagnosis. The patient was discharged on oral itraconazole after partial symptomatic improvement, with outpatient follow-up arranged. Two months of antifungal therapy resulted in mild reduction of cavitary lesions on follow-up CT.}, }
@article {pmid42137133, year = {2025}, author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K}, title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {85-96}, pmid = {42137133}, issn = {2008-2258}, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).<br><br>METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.<br><br>RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.<br><br>CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.}, }
@article {pmid42137225, year = {2026}, author = {Meknas, A and Bessonov, K and Eagle, SHC and Peterson, CL and Robertson, J and Ricker, N and Signorelli, T and Nash, J and Reimer, A}, title = {Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42137225}, issn = {2516-8290}, abstract = {This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.}, }
@article {pmid42137573, year = {2026}, author = {Sun, J and Gao, W and Tan, H}, title = {The role of targeted next-generation sequencing and ultrasound in diagnosing fetal cytomegalovirus infection: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1734139}, pmid = {42137573}, issn = {2296-2360}, abstract = {BACKGROUND: Cytomegalovirus (CMV) infection is a leading cause of congenital infection and neonatal morbidity. Conventional diagnostic methods, such as polymerase chain reaction (PCR) and amniocentesis, remain important in the diagnosis of congenital CMV infection, although each method has its own limitations in clinical practice.<br><br>CASE PRESENTATION: A 31-year-old woman, gravida 3 para 1, presented for routine prenatal evaluation. At 18 weeks of gestation, ultrasound revealed echogenic bowel and fetal ascites. Amniocentesis at 19 weeks showed normal chromosomal results, but targeted next-generation sequencing (tNGS) detected CMV DNA with a high viral load, confirming intrauterine infection.<br><br>RESULTS: Despite counseling regarding poor fetal prognosis, the patient chose to continue the pregnancy under close ultrasound surveillance. Progressive hydrops fetalis was observed at 23 weeks, and the pregnancy was terminated at 24 weeks.<br><br>CONCLUSION: This case suggests that combining tNGS with ultrasound may provide complementary diagnostic information in selected cases of suspected fetal infection. In this patient, tNGS supported the identification of CMV in amniotic fluid when conventional genetic testing was unremarkable. However, as this is a single-case report, the broader diagnostic performance and clinical utility of tNGS require further validation in larger studies.}, }
@article {pmid42137610, year = {2026}, author = {Oguzie, JU and Cummings, DB and Groves, JT and Hagan, AG and Rodriguez, J and Hernandez-Vidal, G and Moreno-Degollado, G and Shittu, I and Marushchak, LV and Nguyen-Tien, T and Trujillo-Vargas, CM and Silva, DB and Li, F and Richeson, JT and Schneider, NE and Gray, GC}, title = {Detection and Genomic Characterization of Novel Respiratory Viruses in US and Mexican Cattle Farms.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {}, pages = {3247802}, pmid = {42137610}, issn = {1865-1682}, mesh = {Animals ; Cattle ; United States/epidemiology ; *Cattle Diseases/virology/epidemiology ; Mexico/epidemiology ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Farms ; Humans ; Genome, Viral ; *Viruses/isolation &amp; purification/genetics/classification ; *Virus Diseases/veterinary/epidemiology/virology ; }, abstract = {Respiratory virus infections in cattle cause an estimated more than $1 billion in production losses and can threaten human health. During February 2024 to May 2025, we employed a One Health approach to surveil for respiratory viruses among cattle, farm workers, and environmental samples from 11 US and Mexican beef or dairy cattle farms. We studied nasal and ocular swabs from cattle, nasal swabs from cattle workers, bioaerosol samples, and other environmental farm samples using molecular and virological techniques. Among 26 distinct viruses identified in cattle, we detected bovine nidovirus 1, influenza D virus (D/OK-like and D/660-like), bovine coronavirus, bovine rhinitis A and B viruses, bovine respirovirus 3 and bovine respiratory syncytial virus (BRSV); 11 of the 26 detected viruses were non-bovine-associated. Two bovine rhinitis A virus was markedly divergent (provisionally designated BRAV-4). Environmental metagenomics additionally identified influenza D virus, bovine coronavirus, and bovine rhinitis B virus. One human nasal swab tested positive for SARS-CoV-2 (cladeLF.7.3). Our findings reveal the presence of emerging, co-circulating, and environmentally linked pathogens at the human-animal-environment interface, underscoring the constant need for One Health surveillance to safeguard livestock and mitigate zoonotic risk.}, }
@article {pmid42137790, year = {2026}, author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D}, title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1788826}, pmid = {42137790}, issn = {1664-302X}, abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.}, }
@article {pmid42137793, year = {2026}, author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM}, title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1641069}, pmid = {42137793}, issn = {1664-302X}, abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.}, }
@article {pmid42137803, year = {2026}, author = {Liu, Y and Chen, C and Gao, J}, title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818141}, pmid = {42137803}, issn = {1664-302X}, abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.}, }
@article {pmid42137806, year = {2026}, author = {Doughan, GE and Walthart, BK and Schau, CE and Skoland, KJ and Mou, KTY and Brown, JT and Bonnema, JL and Plummer, PJ and Zhang, D and Li, G and Karriker, LA}, title = {Presence of antimicrobial resistance genes in biofilms from swine drinking water pipes before and after treatment with peracetic acid.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1770950}, pmid = {42137806}, issn = {1664-302X}, abstract = {Biofilms can be problematic to swine drinking water systems as they can harbor pathogens, decrease water quality, and may contribute to antimicrobial treatment failure. Water-administered antimicrobials are used for disease treatment in swine populations, yet, little is known about water line ecology and the impact it can have on antimicrobial resistance and stewardship. Water line cleaning and disinfection may aid in removal of water line biofilms, improve swine health, and antimicrobial stewardship. Water line samples were collected pre-treatment (0), 24 h post-treatment with 0.78% CID 2000 Pro (peracetic acid) (1), and 3, 5, 7, 14, 21, 42, 56, and 77-days post-treatment from six wean-to-finish swine farms in Iowa, USA. Biofilm was aseptically extracted from the interior of the water line pipe (n = 119) and submitted for metagenomic analysis to detect antimicrobial resistance genes (ARGs). This study demonstrates high prevalence of ARGs in swine water line biofilms that could confer resistance to both medically important antimicrobials to humans and animals such as aminoglycosides, beta-lactams, fluoroquinolones, colistin, and fosfomycin. From 115 samples, a frequency of 3,904 ARGs were reported, with 184 unique ARGs defined. Four samples contained no ARGs. One hundred and fifty-one integron genes representing three classes were found in 115 of 119 samples, indicating mechanisms of potential spread of multiple drug resistance. ARGs and integron genes combined were significantly lower on average by 10 unique ARGs/ integron genes 24-h post-treatment (1) when compared to pre-treatment (0) counts (p-value = 0.01). The number of unique ARG and integron genes quickly rebounded and were not statistically significant compared to pre-treatment counts on post-treatment dates 3, 5, and 7 (adjusted p-value ≥ 0.05), and by post-treatment date 14, unique ARG and integron genes were significantly higher than pre-treatment (adjusted p-value = 0.012). This study demonstrates that swine water line biofilms can harbor antimicrobial resistance genes which could have potential clinical impacts on pig health and treatment response.}, }
@article {pmid42137815, year = {2026}, author = {Geng, S and Shi, X and Zhang, Q and Yang, J and Yang, C and Yang, L}, title = {Organic fertilizer enhances microbial functional genes related to nitrogen and phosphorus cycling in rubber tree (Hevea brasiliensis) rhizosphere.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833968}, pmid = {42137815}, issn = {1664-302X}, abstract = {INTRODUCTION: Nitrogen (N) and phosphorus (P) are the essential nutrient for rubber growth. However, the effect of organic fertilizer application on soil microbial communities and functional genes related to N and P cycling in rubber plantation are unclear.<br><br>METHODS: A field trial was established in a rubber plantation with two treatments: organic fertilizer (OF) and an unfertilized control (CK). In this study, we used metagenomics analysis to examine the structural and functional alterations in the microbial community within the rhizospheric soil of rubber when organic fertilizers were applied.<br><br>RESULTS: Results showed that compared with the CK treatments, the OF treatment significantly increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP) contents. Taxonomic analysis revealed that OF treatment significantly enriched the phyla Pseudomonadota and Myxococcota, and the genera Pseudolabrys and Gaiella. At the functional level, organic fertilization significantly up-regulated key genes associated with N cycling, including organic N metabolism (gltB), N transport (nrtA, nrtB, nrtC), denitrification (norB, nosZ), nitrification (nxrB), and dissimilatory nitrate reduction (napA, napC). Regarding the P cycle, organic fertilization leads to the downregulation of the high-affinity phosphate transporter gene pstS and the concurrent upregulation of genes governing organic P mineralization (phnA, phoN), regulation (phoB), polyphosphate synthesis (ppk1), and polyphosphate degradation (spoT, relA). The variation partitioning analysis (VPA) results indicated that pH, SOM, and nitrogen nutrients (comprising TN and AN) explained 71.52% of the variation in the abundance of nitrogen-cycling functional genes, while pH, SOM, and phosphorus nutrients (comprising TP and AP) explained 64.95% of the variation in the abundance of phosphorus-cycling functional genes.<br><br>CONCLUSION: In summary, the application of organic fertilizer reshapes soil microbial communities and enhances the functional potential for nitrogen (N) and phosphorus (P) cycling. Our study provides a mechanistic basis for developing sustainable nutrient management strategies to optimize N and P bioavailability in tropical rubber agroecosystems.}, }
@article {pmid42137872, year = {2026}, author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC}, title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1783141}, pmid = {42137872}, issn = {2296-861X}, abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.<br><br>METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120&#x202f;days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.<br><br>RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p&#x202f;=&#x202f;0.001) and d56 (p&#x202f;=&#x202f;0.03) but did not result in significant change in WAZ (p&#x202f;=&#x202f;0.69) or weight gain (p&#x202f;=&#x202f;0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.<br><br>DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.<br><br>CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.}, }
@article {pmid42137970, year = {2026}, author = {Feser, M and Arend, D and Beier, S and Bolger, M and Lübke, NC and Meister, M and Steilen, L and Usadel, B and Scholz, U}, title = {Evolving bioinformatics services - the journey of KPI metrics with Scorpion.}, journal = {Journal of integrative bioinformatics}, volume = {}, number = {}, pages = {}, pmid = {42137970}, issn = {1613-4516}, abstract = {Key Performance Indicators (KPIs) are essential for evaluating project success and establishing control mechanisms to monitor development, performance, and user acceptance of services in joint projects. However, the absence of standardized frameworks and effective monitoring tools, combined with service providers' reluctance due to fears of comparability, has limited their adoption in scientific contexts. To address this gap, we developed Scorpion, a flexible tool for KPI monitoring in project management. Scorpion enables service providers to retain control over their metrics while supporting centralized reporting. It offers both web-based and programmatic access, with features for KPI submission, visualization, and user and service management. Initially created for bioinformatics and biodiversity projects, Scorpion is applicable across diverse domains. It is particularly valuable for initiatives like the German National Research Data Infrastructure (NFDI), where funding agencies require KPI reporting for evaluation. We present the Scorpion framework, highlighting its design principles, features, and potential to improve project management practices. Use cases illustrate how Scorpion enhances KPI monitoring efficiency and accuracy, contributing to better impact evaluation, quality assurance, and informed decision-making in project and service management.}, }
@article {pmid42138445, year = {2026}, author = {Ndhlovu, K and Salawu-Rotimi, A and Bopape, FL and Mtsweni, PN and Babalola, OO and Hassen, AI}, title = {Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70360}, pmid = {42138445}, issn = {1758-2229}, support = {135456//National Research Foundation (NRF), South Africa/ ; }, mesh = {South Africa ; *Glycine max/growth &amp; development/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Bradyrhizobium/genetics/isolation &amp; purification/classification ; Metagenomics ; Nitrogen Fixation ; Phylogeny ; *Biodiversity ; Farms ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prior to the introduction of the exotic inoculant strain of Bradyrhizobium, South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.}, }
@article {pmid42138618, year = {2026}, author = {Ran, L and Mao, Y and He, B and Pan, H and Ma, H}, title = {Wildfire-Altered Soil Water-Extractable Organic Matter Drives Divergent Greenhouse Gas Emissions in Anaerobic Subsurface Soils.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {21}, pages = {15078-15088}, doi = {10.1021/acs.est.6c04642}, pmid = {42138618}, issn = {1520-5851}, mesh = {*Greenhouse Gases ; *Soil/chemistry ; *Wildfires ; Water ; Methane ; Carbon Cycle ; Soil Microbiology ; }, abstract = {Intensifying global climate change has increased wildfire frequency. Wildfire-altered soil water-extractable organic matter (burned-WEOM) is hydrologically transported to unburned areas, profoundly affecting cross-ecosystem carbon-nitrogen cycling and greenhouse gas (GHG) emissions. Taking soils from unburned subtropical forests as the research object, this study combined anaerobic incubation with high-resolution mass spectrometry and metagenomic sequencing to elucidate the regulatory mechanisms of burned-WEOM on soil GHG emissions under anaerobic conditions. The results showed that burned-WEOM increased CO2 emissions by 17.0%, induced a 164.6% surge in N2O emissions, and simultaneously inhibited CH4 emissions by 52.9%. With unique properties of high unsaturation and strong electron exchange capacity, burned-WEOM not only reshapes soil organic matter composition but also drives differential GHG emissions by enhancing complete carbon fixation pathways and recalcitrant carbon decomposition, increasing the abundance of anaerobic methane oxidation (AMO) genes and methanotrophs, enriching denitrifying microorganisms (especially fungi), and boosting N2O-generating gene activity without altering the reduction pathway. Moreover, WEOM molecular characteristics drive differences in GHG emissions: CH4 is mainly fueled by reduced, unsaturated lipid-like compounds, N2O is associated with nitrogen-rich, complex aromatic compounds, and CO2 has a broader range of source substrates. This study provides insights that may improve mechanistic understanding of postfire GHG dynamics and inform process representations in climate models.}, }
@article {pmid42138754, year = {2026}, author = {Guimarães, LO and Couto, RDS and Reginato, SL and Mucci, LF and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, E}, title = {Wyeomyia confusa Lispivirus (WcLispV-SP): a novel neotropical mosquito virus in the Lispiviridae family.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42138754}, issn = {1432-8798}, mesh = {Animals ; Phylogeny ; Genome, Viral ; *Culicidae/virology ; Open Reading Frames ; Brazil ; Viral Proteins/genetics ; RNA, Viral/genetics ; *Mononegavirales/genetics/classification/isolation &amp; purification ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {Metatranscriptomic analysis of Wyeomyia confusa mosquitoes collected in the Atlantic Forest (Pindamonhangaba, São Paulo, Brazil) led to the identification of a previously uncharacterized virus, designated Wyeomyia confusa Lispivirus (WcLispV-SP), classified within the family Lispiviridae, genus Canmovirus. The viral genome consists of a negative-sense single-stranded RNA (ssRNA-) of 12,698 nucleotides, encoding six open reading frames (ORFs): nucleoprotein (N), two hypothetical proteins (HP/1 and HP/2), glycoprotein (G), ORFan protein, and RNA-dependent RNA polymerase (RdRp-L). Phylogenetic analysis supports the classification of WcLispV-SP as a distinct species within the genus Canmovirus. Structural analysis of the RdRp revealed conserved domains and catalytic motifs characteristic of members of the order Mononegavirales, supporting its functional integrity. These findings expand the known diversity of the Lispiviridae family and highlight the utility of metagenomic approaches for the discovery and characterization of RNA viruses associated with Neotropical sylvatic mosquitoes.}, }
@article {pmid42138983, year = {2026}, author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A}, title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42138983}, issn = {1465-2080}, mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.}, }
@article {pmid42139081, year = {2026}, author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Dietary niches drive microbial community assembly, network reorganization, and symbiont evolution in freshwater fish gut microbiomes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42139081}, issn = {1751-7370}, support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; }, mesh = {Animals ; *Symbiosis ; Fresh Water ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; China ; *Diet ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.}, }
@article {pmid42139090, year = {2026}, author = {Parienti, JJ and Yang, SS and Grinspoon, S}, title = {Selected Industry Highlights From IDWeek 2025.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S85-S86}, doi = {10.1093/cid/ciag206}, pmid = {42139090}, issn = {1537-6591}, mesh = {Humans ; *HIV Infections/complications/drug therapy ; High-Throughput Nucleotide Sequencing ; }, abstract = {This supplement presents scientific reports from industry-sponsored IDWeek 2025 symposia, highlighting selected advances in infectious diseases and HIV care through clinical case scenarios. One article explores therapeutic approaches to metabolic complications in people with HIV, emphasizing treatment strategies and the clinical reasoning that supports individualized management of excess adiposity. The second examines the clinical integration of metagenomic next-generation sequencing for diagnosing central nervous system infections, outlining both its opportunities and limitations within current diagnostic pathways.}, }
@article {pmid42139092, year = {2026}, author = {Waldrop, G and Reddy, SP}, title = {Metagenomic Next-generation Sequencing in Central Nervous System Infections: Clinical Strategies, Evidence, and Best Practices.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S92-S99}, doi = {10.1093/cid/ciag120}, pmid = {42139092}, issn = {1537-6591}, support = {//Delve Bio/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Immunocompromised Host ; Female ; Middle Aged ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections are diagnostically challenging due to their nonspecific clinical presentations and wide array of potential pathogens. The rising population of immunocompromised patients further complicates this landscape, increasing the prevalence of atypical and opportunistic infections that are often missed by conventional testing.<br><br>OBJECTIVE: This article provides guidance on the use and clinical interpretation of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in suspected CNS infections.<br><br>DISCUSSION: We highlight the paradigm shift from targeted molecular testing to agnostic mNGS, emphasizing key factors that impact diagnostic utility, including specimen handling, neuroanatomical factors, host inflammatory response, and pathogen kinetics. Using illustrative cases, we demonstrate how these biological and technical variables influence test sensitivity and result adjudication. We further discuss the impact of mNGS on clinical decision-making and current limitations regarding cost and turnaround time.<br><br>CONCLUSIONS: Cerebrospinal fluid mNGS is a transformative diagnostic tool, particularly for unusual presentations and in immunocompromised hosts. However, it does not replace clinical judgment and requires careful multidisciplinary interpretation. When integrated thoughtfully with clinical and laboratory data, mNGS can meaningfully reduce the diagnostic gap in CNS infections.}, }
@article {pmid42139793, year = {2026}, author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG}, title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.}, journal = {Veterinary microbiology}, volume = {319}, number = {}, pages = {111070}, doi = {10.1016/j.vetmic.2026.111070}, pmid = {42139793}, issn = {1873-2542}, mesh = {Animals ; *Diarrhea/veterinary/microbiology/epidemiology ; *Feces/microbiology ; Cattle ; *Cattle Diseases/microbiology/parasitology/epidemiology ; *Escherichia coli/genetics/isolation &amp; purification ; Denmark/epidemiology ; Metagenome ; Age Factors ; Metagenomics ; *Escherichia coli Infections/veterinary/microbiology ; Severity of Illness Index ; }, abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.<br><br>METHODS: Stool samples from Danish diary calves (n&#x202f;=&#x202f;32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon &#x3b1;-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3&#x202f;+). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.<br><br>RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.<br><br>CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.}, }
@article {pmid42139982, year = {2026}, author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R}, title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128553}, doi = {10.1016/j.micres.2026.128553}, pmid = {42139982}, issn = {1618-0623}, mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; *Water Microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; Eutrophication ; China ; Biodiversity ; }, abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.}, }
@article {pmid42140024, year = {2026}, author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L}, title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.}, journal = {International journal of food microbiology}, volume = {457}, number = {}, pages = {111847}, doi = {10.1016/j.ijfoodmicro.2026.111847}, pmid = {42140024}, issn = {1879-3460}, mesh = {*Microbiota ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/classification/isolation &amp; purification/genetics/metabolism ; Hot Temperature ; China ; *Volatile Organic Compounds/analysis ; Taste ; Humans ; *Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; *Wine/microbiology/analysis ; }, abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.}, }
@article {pmid42140051, year = {2026}, author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M}, title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.}, journal = {Marine pollution bulletin}, volume = {230}, number = {}, pages = {119879}, doi = {10.1016/j.marpolbul.2026.119879}, pmid = {42140051}, issn = {1879-3363}, abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.}, }
@article {pmid42140215, year = {2026}, author = {Hughes, N and Sathiananthamoorthy, S and Sergaki, C}, title = {Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101400}, doi = {10.1016/j.lanmic.2026.101400}, pmid = {42140215}, issn = {2666-5247}, abstract = {Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.}, }
@article {pmid42140378, year = {2026}, author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA}, title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {590}, number = {}, pages = {121086}, doi = {10.1016/j.cca.2026.121086}, pmid = {42140378}, issn = {1873-3492}, abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.}, }
@article {pmid42140478, year = {2026}, author = {Sheidae Mehne, Z and Honarjou, E and Khamoushi Kahdouee, M}, title = {Chronic infections of the spine: A systematic review of microbial etiologies, diagnostic approaches, and treatment outcomes.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {169}, number = {}, pages = {108769}, doi = {10.1016/j.ijid.2026.108769}, pmid = {42140478}, issn = {1878-3511}, mesh = {Humans ; Treatment Outcome ; Chronic Disease ; *Spinal Diseases/microbiology/diagnosis/therapy ; Mycobacterium tuberculosis/isolation &amp; purification ; Spine/microbiology ; Tuberculosis, Spinal/diagnosis/microbiology/therapy ; }, abstract = {OBJECTIVES: Chronic spinal infections are uncommon but potentially devastating conditions, frequently associated with delayed diagnosis, heterogeneous microbiology, and complex management. Existing evidence remains fragmented, and a comprehensive synthesis of microbial etiologies, diagnostic approaches, and treatment outcomes is needed.<br><br>METHODS: A systematic review was conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between October 2015 and September 2025 involving adult patients with chronic spinal infections. Data were extracted on causative pathogens, diagnostic modalities, medical and surgical interventions, and clinical outcomes. Risk of bias was assessed using standardized methodological criteria.<br><br>RESULTS: Fifty-five studies comprising 3036 patients were included. Mycobacterium tuberculosis was the most frequently identified pathogen, followed by Brucella species and pyogenic bacteria. Metagenomic next-generation sequencing (mNGS) demonstrated the highest diagnostic yield, with reported sensitivities ranging from 82% to 92%, and showed particular utility in detecting mixed or atypical infections. Biomarker-based and RNA-derived assays demonstrated promising performance in differentiating tuberculous spondylitis from other spinal conditions. Surgical interventions, including minimally invasive and combined approaches, were associated with high fusion and neurological recovery rates.<br><br>CONCLUSION: Chronic spinal infections show marked microbiological heterogeneity. Integrating molecular diagnostics with tailored surgical and antimicrobial strategies may improve diagnostic accuracy and clinical outcomes.}, }
@article {pmid42140665, year = {2026}, author = {Vollmers, J and Correa Cassal, M and Kaster, AK}, title = {Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280099.124}, pmid = {42140665}, issn = {1549-5469}, abstract = {Because the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single-cell genome sequencing have individual drawbacks, which can limit the quality and completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole-genome amplification techniques, which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions with sufficient DNA amounts, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, coassemblies become highly optimized for coabundance variation-based binning approaches. "Midi-metagenomics" enables accurate metagenome-assembled genome (MAG) reconstruction from individual sorted samples with higher quality than coassembly and binning of multiple distinct samples and therefore improves analyses of uncultivated microorganisms.}, }
@article {pmid42140743, year = {2026}, author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC}, title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {5}, pages = {}, pmid = {42140743}, issn = {2051-1426}, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.<br><br>METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1&#xd7;10[11]&#x2009;or 4&#xd7;10[11]&#x2009;colony forming unit (CFU)/day) plus pembrolizumab (200&#x2009;mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.<br><br>RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-na&#xef;ve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-na&#xef;ve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95%&#x2009;CI 5.6 to not reached) and 1.8 months (95%&#x2009;CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.<br><br>CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-na&#xef;ve metastatic NSCLC with PD-L1 >50%.<br><br>TRIAL REGISTRATION NUMBER: NCT05877430.}, }
@article {pmid42140896, year = {2026}, author = {Blázquez-Sánchez, P and Gunkel, J and Useini, A and Zlobin, A and Zakary, JD and Schöler, A and Graefe, N and Engelberger, F and Cantanhede, F and Frank, R and Zhao, Z and Zarei, A and Butenschön, E and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C and Künze, G}, title = {Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140896}, issn = {2041-1723}, support = {887913//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ScaDS.AI//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {*Polyethylene Terephthalates/metabolism/chemistry ; Biocatalysis ; *Protein Engineering/methods ; *Hydrolases/metabolism/genetics/chemistry ; Recycling ; Enzyme Stability ; Biodegradation, Environmental ; Molecular Dynamics Simulation ; Metagenome ; *Bacterial Proteins/metabolism/genetics/chemistry ; }, abstract = {Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.}, }
@article {pmid42140961, year = {2026}, author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM}, title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140961}, issn = {2041-1723}, support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, mesh = {*Introduced Species ; *Asteraceae/microbiology ; Species Specificity ; Microbiota ; Ecosystem ; Bacteria/genetics ; }, abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.}, }
@article {pmid42141123, year = {2026}, author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X}, title = {Decoding the human gut bacterial plasmids in colorectal cancer.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10278-w}, pmid = {42141123}, issn = {2399-3642}, abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.}, }
@article {pmid42141277, year = {2026}, author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G}, title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.}, journal = {Nature food}, volume = {7}, number = {5}, pages = {428-440}, pmid = {42141277}, issn = {2662-1355}, mesh = {*Soil Microbiology ; *Microbiota ; *Ecosystem ; Agriculture ; Soil/chemistry ; Climate Change ; Global Warming ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.}, }
@article {pmid42141292, year = {2026}, author = {Ghori, R and Ramadoss, D and Ramsland, PA and Blanch, EW and Ammanabrolu, BS}, title = {Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {42141292}, issn = {1433-4909}, mesh = {*Microbiota ; India ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Salinity ; *Metagenome ; }, abstract = {Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.}, }
@article {pmid42141512, year = {2026}, author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L}, title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {23}, pages = {16540-16551}, doi = {10.1021/acs.est.6c04146}, pmid = {42141512}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Lactuca ; Tetracycline ; }, abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.}, }
@article {pmid42141881, year = {2026}, author = {Nagy, A and Erdélyi, K and Molnár, Z and Lőrincz, RB and Nagy, O and Koroknai, A and Csonka, N and Kerényi, K and Forgách, P and Horváth, E and Soltész, Z and Nagy, G and Takács, M and Barcsay, E and Szomor, K and Tóth, GE and Cadar, D}, title = {Hungary as a source of West Nile virus diversity and spread in Europe: insights from the 2024 transmission season.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {31}, number = {16}, pages = {}, pmid = {42141881}, issn = {1560-7917}, mesh = {Humans ; Hungary/epidemiology ; *West Nile virus/genetics/isolation &amp; purification/classification ; *West Nile Fever/epidemiology/transmission/virology ; Animals ; Phylogeny ; Phylogeography ; *Culex/virology ; Seasons ; Birds/virology ; Europe/epidemiology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Bayes Theorem ; Incidence ; Male ; Mosquito Vectors/virology ; Middle Aged ; }, abstract = {BACKGROUNDWest Nile virus (WNV) has become established across Europe, with Hungary serving as a key transmission hub since 2004. Following reduced activity during 2020-22, the 2024 season marked a resurgence with the largest geographical distribution ever recorded in Europe.AIMTo analyse the 2024 WNV transmission season in Hungary using a One Health approach and characterise circulating strains within the European phylogeographic context using comprehensive genomic surveillance.METHODSComplete and near-complete genome sequencing was performed on 55 specimens from 38 humans, 15 birds and two Culex pipiens mosquito pools using amplicon-based next-generation sequencing. Phylogeographic analysis incorporated 637 European WNV genome sequences (2004-24) with time-scaled Bayesian phylogenetic reconstruction and continuous spatial diffusion modelling.RESULTSHungary reported 113 human WNV cases in 2024 (n = 111 autochthonous, 2 imported), a 3.7-fold increase from 2023 (incidence: 1.16 vs 0.31 per 100,000 population). Neuroinvasive disease predominated (92%, n = 104) with a 7.9% case fatality rate. All 55 sequenced strains belonged to WNV lineage 2. Phylogeographic analysis revealed Hungary's central role in European WNV dissemination since 2004, with multiple introductions and local diversification across distinct clades. Continuous spatial modelling identified Hungary as a persistent transmission hub with bidirectional viral flow to neighbouring countries, contributing to northward expansion.CONCLUSIONHungary remains a critical WNV transmission hub in Central Europe with established endemicity of multiple lineage 2 clades. The analysis highlights Hungary's role as both a recipient and major source of European WNV diversity, emphasising the need for coordinated surveillance and climate-adapted preparedness strategies.}, }
@article {pmid42142571, year = {2026}, author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Seasonal shifts in the Belgrade airborne resistome and virulome: A metagenomic perspective.}, journal = {Environmental research}, volume = {303}, number = {Pt 2}, pages = {124700}, doi = {10.1016/j.envres.2026.124700}, pmid = {42142571}, issn = {1096-0953}, mesh = {*Seasons ; *Air Microbiology ; Serbia ; *Microbiota ; *Metagenome ; Metagenomics ; *Bacteria/genetics ; Environmental Monitoring ; }, abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.}, }
@article {pmid42142769, year = {2026}, author = {Zhang, Z and Hu, Y and Zu, G and Dang, Q and Sun, X and Wu, Y}, title = {Molecular mechanisms of dissolved organic matter transformation and microbial interactions in composting.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134880}, doi = {10.1016/j.biortech.2026.134880}, pmid = {42142769}, issn = {1873-2976}, mesh = {Animals ; *Bacteria/metabolism ; Carbon ; Chickens ; *Composting/methods ; *Dissolved Organic Matter/metabolism/chemistry ; *Food Loss and Waste ; Manure ; Mass Spectrometry ; *Soil Microbiology ; Thermodynamics ; }, abstract = {Industrial composting of food waste digestate (FW) and chicken manure (CM) involves distinct dissolved organic matter (DOM) transformation pathways and different microbial interaction mechanisms. This study used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and shotgun metagenomics (for microbial community profiling) to compare interactions between DOM and microbial communities in the two composting processes. Results show that FW is dominated by labile organic matter (OM). This dominance increases the degree of DOM oxidation and the relative abundance of CHO. This labile carbon environment selected for a simplified microbial community dominated by key genera, yet facilitated active potential molecular transformations (PMTs) of DOM. These PMTs were characterized by an increase in thermodynamically limited processes (TLPs), indicating a carbon source-oriented pathway. In contrast, PMTs of DOM in CM favor thermodynamically favorable processes (TFPs), exhibiting higher aromaticity and CHOS abundance. The microbial community remains highly diverse, strongly connected, and functionally complementary, forming a synergistic network that supports coupled nitrogen-sulfur transformations. Environmental factors differentially regulate the two systems. This study indicates that the initial chemical properties of the composting feedstock fundamentally shape the PMTs of DOM pathways and the microbial communities they drive, providing an important theoretical basis for optimizing organic solid waste resource recovery processes.}, }
@article {pmid42142806, year = {2026}, author = {Samuelsen, &#xd8; and López-Causapé, C and Aarestrup, FM and Bortolaia, V and Brouwer, MSM and Cantón, R and Egli, A and Grad, YH and Hamprecht, A and Haussler, S and Holt, KE and Hopkins, KL and Howden, BP and Jeannot, K and Kahlmeter, G and Köser, CU and Mathers, AJ and Naas, T and Pournaras, S and Ruppé, E and Schön, T and Stoesser, N and Turnidge, J and Werner, G and Wright, GD and Giske, CG and Oliver, A}, title = {The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.05.012}, pmid = {42142806}, issn = {1469-0691}, abstract = {SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of whole genome sequencing (WGS) in antimicrobial susceptibility testing (AST) concluded that WGS antimicrobial susceptibility prediction (WGS-ASP) was not a sufficiently robust alternative to AST to guide clinical decision making at that stage and that more evidence was required [1]. Since then, the use of WGS, bioinformatic tools, machine learning (ML)/artificial intelligence (AI), databases, and prediction approaches has greatly expanded, along with an increased knowledge of resistance mechanisms and their contribution to antimicrobial susceptibility. In response, a new EUCAST ad hoc subcommittee was established in 2024 to review the literature, with the aim of assessing the current potential and limitations of WGS-ASP.<br><br>METHODS: As in the previous report, the subcommittee reviewed the literature on a 'by organism' basis but expanded the list to also include enterococci, Haemophilus influenzae, and Bacteroides fragilis in addition to those already included in the first version: Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, and Mycobacterium tuberculosis. Additional sections were included to cover advances in metagenomics, other omics technologies and ML/AI. The full report was compiled and reviewed by all subcommittee members before public consultation in November 2025.<br><br>Significant progress has been achieved in WGS-ASP, with growing evidence supporting its ability to distinguish wild-type from non-wild-type isolates and, consequently, susceptible from resistant strains, particularly for M. tuberculosis and when clinical breakpoints align with the epidemiological cut-off (ECOFF). Despite these advances, important challenges remain before WGS-ASP can be adopted as a clinical decision-making tool. Addressing these gaps will require integrated phenotypic and genotypic surveillance to strengthen the evidence base for complex resistance mechanisms and newer antimicrobial agents, alongside comparative assessments that consider both ECOFF and clinical breakpoints. The analyses will require reference method phenotypic AST and high-quality genomic data. It is critical to ensure that datasets reflect the target populations and encompass the full spectrum of antimicrobial susceptibility, while developing unified interpretation frameworks and harmonized bioinformatics tools to standardize outputs. Robust external quality assessment schemes will be essential for clinical validation, and emerging technologies such as AI and ML offer promising avenues to enhance predictive accuracy. Finally, improvements in cost and turnaround time, coupled with evaluations of setting-specific cost-effectiveness, will be key to enabling practical implementation of WGS-ASP.}, }
@article {pmid42143007, year = {2026}, author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW}, title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pan.2026.05.002}, pmid = {42143007}, issn = {1424-3911}, abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.<br><br>METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.<br><br>RESULTS: Significant differences in both &#x3b1;-diversity and &#x3b2;-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.<br><br>CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.}, }
@article {pmid42143215, year = {2026}, author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ}, title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05149-7}, pmid = {42143215}, issn = {1471-2180}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.<br><br>RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.<br><br>CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.}, }
@article {pmid42143222, year = {2026}, author = {Yao, Y and Li, Z and Luo, L and Lu, X and Wang, H}, title = {Central nervous system infection associated with Human herpesvirus 7 presenting with predominant persecutory delusions as initial psychiatric manifestations after allogeneic stem cell transplantation: a rare case report with diagnostic and therapeutic implications.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13040-z}, pmid = {42143222}, issn = {1471-2334}, support = {82300248//National Natural Science Foundation of China/ ; 82100143//National Key Research and Development Program of China grant 2022YFC2304600/ ; }, abstract = {BACKGROUND: Human Herpesvirus 7 (HHV-7)-associated central nervous system (CNS) infection is an extremely rare complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT), with no prior reports of initial presentation dominated by psychiatric symptoms.<br><br>CASE PRESENTATION: We report a unique case of a 14-year-old female with high-risk acute lymphoblastic leukemia (ALL) who developed acute persecutory delusions and auditory hallucinations as the sole initial manifestations 54 days post-allo-HSCT. Brain magnetic resonance imaging (MRI) revealed multifocal lesions in the right frontal lobe and bilateral parieto-occipital regions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) confirmed the presence of HHV-7, establishing the diagnosis of HHV-7-associated CNS infection. The patient achieved complete clinical and radiological remission following a comprehensive treatment regimen combining antiviral therapy, glucocorticoids, intravenous immunoglobulin (IVIG), and antipsychotic medication.<br><br>CONCLUSIONS: This is the first documented case of HHV-7-associated CNS infection post-allo-HSCT presenting with persecutory delusions as the initial symptom, expanding the clinical spectrum of HHV-7-related CNS complications in immunocompromised hosts. Our findings emphasize the importance of considering atypical viral encephalitis in the differential diagnosis of acute psychiatric symptoms post-allo-HSCT and highlight the value of early neuroimaging and CSF mNGS for timely diagnosis and targeted intervention.}, }
@article {pmid42143235, year = {2026}, author = {Zhong, M and Zhang, H and Yan, H and Li, Y and Zhu, D and Hu, S and Tan, L and Peng, L and Xie, X and Lan, G}, title = {Clinical characteristics, diagnosis and prognosis of Talaromyces marneffei pneumonia in kidney transplant recipients: a retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13557-3}, pmid = {42143235}, issn = {1471-2334}, support = {2025JJ70074//Natural Science Foundation of Hunan Province/ ; 2024JJ2088//Natural Science Foundation of Hunan Province/ ; 2023JJ30755//Natural Science Foundation of Hunan Province/ ; 82370760//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic dimorphic fungus that increasingly affects immunocompromised individuals, including kidney transplant recipients. However, data on the clinical features, diagnosis, treatment, and prognosis of Talaromyces marneffei pneumonia (TMP) in this population remain limited.<br><br>METHODS: This retrospective study included 8 HIV-negative kidney transplant recipients diagnosed with TMP at the Second Xiangya Hospital of Central South University between January 2015 and January 2025. Clinical data, including demographic characteristics, clinical manifestations, imaging findings, microbiological results, treatment regimens and outcomes, were collected and analyzed.<br><br>RESULTS: The cohort consisted of 7 males and 1 female with a mean age of 45.12&#x2009;&#xb1;&#x2009;9.03 years. The median time from transplantation to TMP onset was 356.5 days (IQR, 302.75-771.75). All patients presented with fever, and chest CT showed diverse pulmonary lesions, including nodules and patchy opacities. Metagenomic next-generation sequencing (mNGS) was the primary diagnostic tool, identifying TM in 7 cases (87.5%), with a mean diagnostic time of 5&#x2009;&#xb1;&#x2009;2.56 days, while conventional culture was positive in only 3 cases. All patients received antifungal therapy, mainly amphotericin B for induction followed by oral azoles for maintenance. Immunosuppressive regimens were adjusted during treatment. All patients achieved clinical cure without severe adverse events, and graft function remained stable.<br><br>CONCLUSIONS: TMP is a rare but serious infection in kidney transplant recipients receiving long-term immunosuppression. Early diagnosis using mNGS combined with conventional culture can improve detection efficiency. Timely antifungal therapy with amphotericin B followed by azole maintenance, along with careful adjustment of immunosuppressants, is associated with favorable prognosis.}, }
@article {pmid42143297, year = {2026}, author = {Feng, J and Wang, Y and Han, J and Li, J and Xu, W and Hu, X}, title = {Gestational psittacosis: a systematic review of clinical manifestations and outcomes.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13575-1}, pmid = {42143297}, issn = {1471-2334}, support = {2025359//Scientific Research Project of Chengdu Municipal Health Commission/ ; 2025GZX002//Primary Health Care Research Project of Ganzi County People's Hospital/ ; 2024-YF09-00021-SN//Key Research and Development Support Program of Chengdu Science and Technology Bureau/ ; SCKFKY20250217//2025 Scientific Research Project of Sichuan Rehabilitation Medical Association/ ; }, abstract = {BACKGROUND: Gestational psittacosis is a rare but severe zoonotic infection caused by Chlamydia psittaci. This systematic review aims to evaluate the clinical characteristics, diagnostic challenges, therapeutic interventions, and maternal-fetal outcomes of this condition.<br><br>METHODS: A systematic search was conducted in PubMed, Embase, Web of Science, CNKI, and Wanfang Data from inception to October 31, 2025. Two investigators independently performed study selection and data extraction encompassing maternal demographics, clinical manifestations, laboratory findings, diagnostic modalities, antimicrobial regimens, and maternal-fetal outcomes.<br><br>RESULTS: A total of 32 cases from 30 publications were included. The median maternal age was 29 years (IQR: 26-32), and the median gestational age at diagnosis was 26.5 weeks (IQR: 21-30). All patients presented with fever (32/32, 100%), and common symptoms included headache (17/32, 53%), cough (15/32, 47%), and dyspnea (15/32, 47%). Severe disease was frequent: 66% (21/32) required intensive care unit (ICU) admission, 34% (11/32) required endotracheal intubation, and maternal mortality was 13% (4/32). Thrombocytopenia (26/32, 81%), hepatic dysfunction (27/32, 84%), renal impairment (18/32, 56%), and disseminated intravascular coagulation (DIC) (15/32, 47%) were the most prominent laboratory abnormalities. Diagnostic approaches evolved from serology to molecular methods. Recent studies have demonstrated the potential value of metagenomic next-generation sequencing (mNGS) in diagnosis, but further research is needed to confirm its clinical utility. The overall fetal and neonatal mortality was 68% (21/31 with available data), primarily due to stillbirth, spontaneous abortion, or therapeutic induction. These estimates reflect outcomes among reported cases and may overestimate true population-level risk.<br><br>CONCLUSION: Gestational psittacosis is a rare but life-threatening infection associated with substantial maternal morbidity and a high risk of fetal loss, although these outcomes may be influenced by publication bias. mNGS has facilitated earlier diagnosis in recent case reports; however, comparative performance data for gestational psittacosis remain limited.<br><br>TRIAL REGISTRATION: PROSPERO, CRD420251275911 (Registered 30 December 2025).<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42143373, year = {2026}, author = {Huntington, CA and Bonavita, CM and Wells, HL and Tiemann, JD and Navarrete-Macias, I and Johnson, RF and Hensley, LE and Anthony, SJ}, title = {Optimization of environmental air sampling for viral metagenomics in a cave-roosting bat assemblage.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-026-00218-3}, pmid = {42143373}, issn = {2524-4655}, support = {#2412522//NSF/ ; }, abstract = {BACKGROUND: Environmental air sampling holds significant potential as a tool for viral surveillance. Its use in agricultural and indoor settings has demonstrated its feasibility and effectiveness but despite this, it has rarely been used in wildlife settings.<br><br>METHODS: To enable future applications, we optimized key parameters in air sampling methodology using a cave-roosting bat assemblage as a model system. We systematically investigated the impact of sampling conditions (flow rate, sampling duration, and sampling location/deployment time) and post-sampling treatments (DNA/RNA Shield ratios and secondary filtration) on three viral metrics - total mammalian virus abundance, mammalian RNA virus abundance, and Shannon diversity index - generated from next-generation sequencing data.<br><br>RESULTS: We first showed that air sampling can recover broad viral diversity, including alphacoronaviruses and betacoronaviruses. The sampling conditions for maximizing viral metrics were larger air sample volumes (&#x2265;24,000 liters) and sampling inside the cave while the bats were roosting, as opposed to at the cave entrance during emergence. Post-sampling treatments had limited impact on viral metrics, but their application may vary depending on the objectives of the study.<br><br>CONCLUSION: This work provides a proof-of-concept for applying air sampling for wildlife viral surveillance in a cave-roosting bat assemblage and identifies key sampling parameters.}, }
@article {pmid42143423, year = {2026}, author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Cupples, AM}, title = {Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities.}, journal = {Journal of environmental management}, volume = {408}, number = {}, pages = {129957}, doi = {10.1016/j.jenvman.2026.129957}, pmid = {42143423}, issn = {1095-8630}, mesh = {*Trichloroethylene/metabolism ; Biodegradation, Environmental ; *Dichloroethylenes/metabolism ; Rhodococcus/metabolism ; Propane/metabolism ; }, abstract = {Aerobic cometabolism offers a viable strategy for the remediation of chlorinated solvent plumes at oxic sites where anaerobic approaches are limited. Here, propane-enriched mixed cultures (derived from agricultural soils and an impacted site sediment) which previously degraded 1,4-dioxane, were evaluated for their capacity to also degrade trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), and 1,1-dichloroethene (1,1-DCE) over successive transfers. Sustained biodegradation of TCE and cDCE was observed across multiple enrichments and cultures enriched on one compound generally degraded the other. In contrast, 1,1-DCE biodegradation was restricted to a subset of cultures and removal times increased over transfers. Further, 1,1-DCE removal was absent at elevated concentrations, both trends consistent with inhibitory or toxic effects. Whole genome sequencing analyses revealed pronounced substrate-dependent selection of microbial communities, with cDCE-degrading cultures being dominated by Mycobacterium and Mycolicibacterium, whereas TCE-degrading cultures were dominated by Rhodococcus. Rhodococcus metagenome-assembled genomes (MAGs) in the TCE degrading cultures classified as R. opacus or R. wratislaviensis. 1,1-DCE degrading cultures were dominated by Pseudonocardia, although the associated MAGs contained a truncated propane monooxygenase alpha subunit, suggesting other enzymes were responsible for 1,1-DCE transformation. Functional gene analysis identified both group 5 (prmABCD) and putative group 6 propane monooxygenases (although their expression was not examined). Together, these results demonstrate that substrate-specific pressures govern propanotrophic community structure and function, and highlight distinct roles of key actinobacterial genera in chlorinated ethene cometabolism. These findings support the development of propane-based bioaugmentation strategies for the treatment of mixed chlorinated solvent contamination under aerobic conditions.}, }
@article {pmid42143455, year = {2026}, author = {Jia, W and Li, J and Wang, K and Cheng, L and Jin, N and Yang, Q and Zhang, D and Xia, X and Xu, N and Wang, M and Meng, J and Zhu, Y and Ding, A}, title = {Convergent shifts in microbial communities: Petroleum hydrocarbon contamination suppresses matrix heterogeneity.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142349}, doi = {10.1016/j.jhazmat.2026.142349}, pmid = {42143455}, issn = {1873-3336}, mesh = {*Groundwater/microbiology/chemistry ; *Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; *Petroleum/analysis ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota/drug effects ; Bacteria/genetics/metabolism ; Petroleum Pollution ; }, abstract = {Accurate characterization of microbial communities in aquifers is essential for understanding groundwater ecosystem responses to petroleum hydrocarbon contamination. However, existing studies have focused primarily on groundwater, largely overlooking the coupled interactions between groundwater and aquifer sediments, which may bias aquifer-scale evaluations of microbial functional potential. In this study, contaminated groundwater and corresponding aquifer sediment samples were collected from a petroleum hydrocarbon impacted site, together with uncontaminated groundwater and sediment samples outside the contaminant plume as controls. Petroleum hydrocarbon concentrations and principal component analysis (PCA) revealed comparable contamination levels in groundwater and aquifer sediments. Integrating 16S rRNA gene sequencing analysis and metagenomic sequencing analysis, we found that microbial communities in contaminated groundwater exhibited broader niche breadth, higher niche overlap, and increased representation of low-molecular-weight carbon (LMW-C) metabolism, particularly pathways associated with ribose and amino sugar utilization. In contrast, aquifer sediment communities showed higher abundances of multidrug efflux pump genes and functional pathways involved in naphthalene and benzene degradation (PAH-C and MAH-C). Further correlation and community assembly analyses indicated that petroleum hydrocarbon contamination was the primary driver shaping microbial communities in both matrices, overriding intrinsic physicochemical differences. Meanwhile, sediment-specific properties, such as stronger sorption capacity for organic matter and differences in microbial lifestyles contributed to the observed divergence between groundwater and sediment communities. Overall, this study demonstrates that contamination induced selection dominates microbial community assembly in aquifers, and provides a mechanistic basis for improving the evaluation of natural attenuation potential and informing remediation strategies in contaminated aquifer systems.}, }
@article {pmid42143457, year = {2026}, author = {Zhang, Z and Lv, M and Wang, R and Wang, B and Du, R and Lou, Y and Wang, C and Jiang, X and Hou, H and Li, Z and Chen, F}, title = {Micro-nano biochar interfaces promote adsorption-reduction coupling to accelerate bioelectrodechlorination in groundwater.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142393}, doi = {10.1016/j.jhazmat.2026.142393}, pmid = {42143457}, issn = {1873-3336}, mesh = {*Charcoal/chemistry ; *Groundwater/chemistry ; *Trichloroethylene/chemistry ; *Water Pollutants, Chemical/chemistry ; Adsorption ; Electrodes ; Water Purification/methods ; Halogenation ; Biofilms ; Oxidation-Reduction ; }, abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as trichloroethylene (TCE), are frequently detected high-toxicity contaminants in groundwater. Bioelectrodechlorination provides a sustainable alternative for CAHs remediation, but its practical application is hindered by limited interfacial reactivity due to low CAHs bioavailability and inefficient electron supply. Herein, we propose the construction of biochar-based functional electrodes featuring micro-nano interfacial architectures with hierarchical porosity, excellent biocompatibility, and enhanced interfacial extracellular electron transfer (EET) relative to carbon felt, which strengthened the coupling among local contaminant enrichment, cathode-associated biofilm development, and interfacial electron transfer, thereby accelerating TCE reductive dechlorination. The biochar-modified electrode increased the TCE dechlorination rate by 3.67-fold and reduced the interfacial charge-transfer resistance by 1.79-fold. Cathodic polarization at -0.5 V (vs. SCE) achieved the optimal balance between performance and energy efficiency, delivering 98.7% removal within 48 h at a low energy consumption of 4.1 Wh kg[-1] TCE, whereas less negative or more negative potentials decreased dechlorination efficiency by 4.3-11.0%. Under optimized conditions, TCE was efficiently removed and predominantly converted to cis-1,2-DCE. Biochar functionalization promoted biofilm development and selectively enriched electroactive and dechlorinating populations. Metagenomic analysis revealed marked upregulation of reductive dehalogenase genes (tceA, rdhA) and EET-related genes (cytc-c, e-pilin, and riboflavin). Environmental-economic benchmarking further demonstrated that biochar-based bioelectrodechlorination outperforms organic carbon-driven bioreduction and conventional electroreduction in removal efficiency, electron utilization, process controllability, and material sustainability.}, }
@article {pmid42143575, year = {2026}, author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J}, title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42143575}, issn = {1751-7370}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Plasmids/genetics ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Escherichia coli/genetics/drug effects ; Feces/microbiology/chemistry ; Metabolomics ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.}, }
@article {pmid42143599, year = {2026}, author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S}, title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70140}, pmid = {42143599}, issn = {1943-3670}, support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral &amp; Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jus&#xe9;lius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.<br><br>METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.<br><br>RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).<br><br>CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.<br><br>PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.}, }
@article {pmid42143831, year = {2026}, author = {Deng, Y and Yuan, X and Xu, Y and Jiang, H and Xue, J and Jiang, Y and Wang, Y}, title = {Acetoclastic methanogenesis associated with arsenic methylation in a reducing aquifer: Pathway-specific patterns and mechanistic insights.}, journal = {Water research}, volume = {301}, number = {}, pages = {126114}, doi = {10.1016/j.watres.2026.126114}, pmid = {42143831}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Arsenic/metabolism/chemistry ; Methylation ; *Methane/metabolism ; Water Pollutants, Chemical ; }, abstract = {The distribution of methylated arsenic (MeAs) in reducing groundwater systems remains incompletely understood, in part due to uncertainties regarding how specific methanogenic pathways may influence arsenic biomethylation, a critical issue in arsenic biogeochemistry and risk assessment. To explore this question, we integrated hydrogeochemical characterization, carbon isotopic tracing, metagenomic analysis, and pathway-specific enrichment experiments, focusing on MeAs-rich alluvial-lacustrine aquifers in the central Yangtze River Basin. A strong positive correlation between arsM and mcrA abundances (r = 0.84, p < 0.001) points to a co-occurrence of genetic potential for arsenic methylation and methanogenesis in the studied aquifer. Metagenome-assembled genome (MAG) analysis showed a pathway-specific distribution of arsM gene, a higher proportion of acetoclastic methanogen MAGs harbored complete arsM genes (14.29 %), compared to methylotrophic (9.09 %) and hydrogenotrophic (0.00 %) methanogens. In pathway-specific enrichment assays under controlled laboratory conditions, acetoclastic cultures exhibited the highest capacity for stepwise arsenic methylation (MMA and DMA production), with methylation efficiency reaching approximately 10.2 %, whereas methylotrophic cultures produced only transient MMA and hydrogenotrophic cultures showed minimal methylation. These observations provide insights into pathway-dependent differences in methanogen-associated arsenic methylation, highlighting a possible biogeochemical link between methanogenesis and arsenic cycling in the studied aquifer. These findings contribute to understanding potential controls on MeAs occurrence in reducing groundwater and provide a basis for further investigations in comparable hydrogeological settings.}, }
@article {pmid42144568, year = {2026}, author = {Rui, Z and Wang, X and Yu, C}, title = {Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70924}, pmid = {42144568}, issn = {1526-4998}, support = {QKEZDZX[2024]010//the Guizhou Provincial Major Scientific and Technological Program/ ; theNationalNaturalScienceFoundationofChina//32160375/ ; }, abstract = {BACKGROUND: Fusarium oxysporum causes damping-off disease in Pinus massoniana seedlings. While Trichoderma koningiopsis can enhance seedling resistance by regulating rhizosphere plant growth-promoting rhizobacteria (PGPR), the specific bacterial compositions and their role in disease resistance remained undefined. To elucidate this mechanism, we used amplicon and metagenomic sequencing to identify T. koningiopsis-assembled PGPR. Synthetic PGPR communities were constructed from isolated strains to validate their effects on disease suppression and growth promotion.<br><br>RESULTS: Microbial community analysis indicated that T. koningiopsis reshaped the bacterial community: Actinospica, Dyella, and Streptomyces decreased in presence, and Bacillus and Arthrobacter increased. A total of 153 PGPR strains were isolated from the T. koningiopsis-inoculated treatment. Of these, eight strains demonstrated significant inhibitory effects against F. oxysporum, ranging from 33.81% to 59.52%. Four synthetic communities (SynComs) (C1, C2, HT, and 2K) were further constructed, exhibiting superior inhibitory effects against F. oxysporum compared to individual strains. Compared to the control, the C2 and HT SynComs increased seedling height by 10.18% and 9.44%, and reduced disease incidence by 50% and 36.67%, respectively. These treatments also enhanced protective enzyme activity and alleviated membrane damage. At the molecular level, the C2 and HT SynComs boost plant resistance by modulating the plant hormone and mitogen-activated protein kinase (MAPK) signaling pathways, thereby activating the expression of crucial resistance genes such as PR1, FLS2, and CAT1.<br><br>CONCLUSION: Trichoderma koningiopsis alters the composition of rhizosphere PGPR community. The synthetic PGPR community assembled under the influence of T. koningiopsis effectively enhances damping-off resistance and promotes the growth of Masson pine seedlings. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42145141, year = {2026}, author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R}, title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {15353141261449964}, doi = {10.1177/15353141261449964}, pmid = {42145141}, issn = {1556-7125}, abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.}, }
@article {pmid42145647, year = {2026}, author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H}, title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.06.26352545}, pmid = {42145647}, abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.}, }
@article {pmid42146067, year = {2026}, author = {Cooper, G and Ayotte, SH and Du, ML and Wood, JD and Opp, B and Bothner, B and Peyton, BM}, title = {Arsenic detoxification within thermo-alkaline biofilms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783099}, pmid = {42146067}, issn = {1664-302X}, abstract = {INTRODUCTION: The fundamental principles driving community composition and dynamics of microbial mats in thermoalkaline springs are largely uncharacterized. High in not only temperature but also arsenic (As), the microbial populations of Yellowstone National Parks (YNP), USA thermal springs require unique detoxification mechanisms to survive and carry out basic biological functions.<br><br>METHODS: While many studies have focused on which microorganisms are present, few studies have integrated the use of metagenome sequencing, imaging techniques, and mass spectrometry to gain insight into how structure and function of the mat dwelling organisms might be impacted by the high arsenical species in the ecosystem.<br><br>RESULTS: Here, we demonstrate via metagenome sequencing that community composition, including microbial genera Roseiflexus, Thermus, and Synechococcus, and as detoxification abilities change with mat depth and distance from the springs. Arsenical speciation confirmed the generation of bioarsenicals by mat-dwelling microorganisms. Microscopy revealed stratification of microorganisms in the mat, potentially reflecting their arsenic redox capabilities.<br><br>DISCUSSION: These data demonstrate how microbial mats are modular, stratified systems that shape and are shaped by environmental and geochemical gradients. Together, these findings characterize novel complexity and associations between geochemical cycles of metals and metabolic adaptations necessary for microorganisms to inhabit thermal springs. In conclusion, these findings demonstrate physiochemical heterogeneity of microbial mats in YNP.}, }
@article {pmid42146533, year = {2026}, author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV}, title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42146533}, issn = {2692-8205}, abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R[2]=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.}, }
@article {pmid42146661, year = {2026}, author = {Miller, CJ and Pope, CE and Lavitt, MH and Caverly, LJ and LiPuma, JJ and Penewit, K and Lewis, JD and Salipante, SJ and Hoffman, LR}, title = {The Unified Human Virome Database: A toolkit for expanded human virome analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42146661}, issn = {2692-8205}, abstract = {Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes from human gastrointestinal, airway, skin, and urogenital sample metagenomes. We developed an associated toolkit that uses UHVDB to characterize viruses and their potential activity from metagenomes, then applied this toolkit to 1,983 airway sample metagenomes from people with cystic fibrosis. Over half of detected viruses lacked evidence of potential activity and were detected transiently. UHVDB is nearly three times larger than prior viral databases and its ability to identify likely active viruses enables rigorous analysis of viruses from diverse human sample types, expanding the capacity to define virus contributions to health and disease.}, }
@article {pmid42146906, year = {2026}, author = {Orletskaia, VA and Olekhnovich, EI}, title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0065}, pmid = {42146906}, issn = {2001-0370}, abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.}, }
@article {pmid42147179, year = {2026}, author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S}, title = {The Gut Microbiome Profile of Lions in Etosha National Park, Namibia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {42147179}, issn = {2693-5015}, abstract = {BACKGROUND: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking.<br><br>RESULTS: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea.<br><br>CONCLUSIONS: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3,4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.}, }
@article {pmid42148043, year = {2026}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.}, journal = {Environmental health perspectives}, volume = {134}, number = {1}, pages = {75-90}, pmid = {42148043}, issn = {1552-9924}, mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics &amp; numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; }, abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.}, }
@article {pmid42148573, year = {2026}, author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC}, title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0411725}, doi = {10.1128/spectrum.04117-25}, pmid = {42148573}, issn = {2165-0497}, abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.}, }
@article {pmid42148581, year = {2026}, author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S}, title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0377525}, doi = {10.1128/spectrum.03775-25}, pmid = {42148581}, issn = {2165-0497}, abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.}, }
@article {pmid42148582, year = {2026}, author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L}, title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0346925}, doi = {10.1128/spectrum.03469-25}, pmid = {42148582}, issn = {2165-0497}, abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.}, }
@article {pmid42148731, year = {2026}, author = {Qiu, H and Zhang, Z and Qian, H}, title = {Evolutionary plasticity of cyanobacteria under persistent anoxia: mechanistic insights from marine blue holes and global ecological implications.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {6}, pages = {e0025126}, pmid = {42148731}, issn = {1098-5336}, mesh = {*Oxygen/metabolism ; *Cyanobacteria/genetics/physiology ; *Synechococcus/genetics/physiology/metabolism ; *Seawater/microbiology ; Anaerobiosis ; *Biological Evolution ; Adaptation, Physiological ; }, abstract = {Cyanobacteria are generally viewed as obligate oxic photoautotrophs. However, this paradigm was challenged by Z. Li, H. Zhang, T. Wei, L. He, and Y. Wang in Applied and Environmental Microbiology(92:e02576-25, 2026, https://doi.org/10.1128/aem.02576-25); this group identified transcriptionally active Synechococcus in the dark, permanently anoxic Yongle Blue Hole using integrated metagenomic and transcriptomic analyses. This finding suggests adaptive streamlining under long-term oxygen limitation, expands the recognized ecological range of phototrophic microorganisms, and highlights the potential relevance of microbial adaptation to future ocean deoxygenation.}, }
@article {pmid42148775, year = {2026}, author = {Shi, W and Liu, L and Wu, L and Wang, X and Peng, Y and Liu, X and Li, C and Xu, J and Wu, Z and Dong, X and Zheng, Q}, title = {Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035426}, doi = {10.1128/msystems.00354-26}, pmid = {42148775}, issn = {2379-5077}, abstract = {UNLABELLED: Salinity gradients drive microbial diversity and evolution in estuarine-coastal ecosystems, yet viral adaptation remains less well understood. We used metagenomics to study viral adaptation and functions in three representative estuarine-coastal regions in China. Our results reveal salinity-associated adaptations in DNA viruses, with viruses enriched in medium- to high-salinity environments exhibiting higher frequencies of acidic isoelectric points and charged amino acids compared to those enriched in low-salinity environments. Viral genomes encode diverse genes related to ion transporters and organic osmolyte metabolism, suggesting potential roles in osmotic stress responses. Viral microdiversity also varied systematically along the salinity gradient, indicating reduced genetic variation and stronger purifying selection under more saline conditions. Furthermore, we identified diverse AMGs linked to nutrient cycles, with salinity-driven enrichment revealing viral roles in host metabolism. Overall, our findings highlight salinity as a key driver of viral evolution and functional potential in estuarine-coastal ecosystems, providing new insights into how viruses adapt to environmental gradients.<br><br>IMPORTANCE: Salinity is a defining environmental gradient in estuarine-coastal systems, yet its role in shaping viral molecular evolution remains poorly understood. By integrating metagenomes, viromes, and metatranscriptomes across three estuaries, this study demonstrates that salinity exerts a strong and consistent imprint on DNA viruses. Increasing salinity selects for viral genomes encoding ion-transport and osmolyte-related proteins and drives systematic shifts in viral proteome composition toward osmoadaptive physicochemical properties. At the population level, higher salinity is associated with reduced viral microdiversity and stronger purifying selection, indicating constrained evolutionary space under osmotic stress. Viral auxiliary metabolic gene repertoires are structured along salinity gradients, with functional differentiation in carbon, nutrient, and nucleotide metabolism. Together, these findings identify salinity as a key evolutionary filter linking viral physiological adaptation, evolutionary dynamics, and functional potential in estuarine and coastal ecosystems.}, }
@article {pmid42148776, year = {2026}, author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y}, title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029226}, doi = {10.1128/msystems.00292-26}, pmid = {42148776}, issn = {2379-5077}, abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.<br><br>IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.}, }
@article {pmid42149293, year = {2026}, author = {Fulke, AB and Ratanpal, S}, title = {Integrated pragmatic approach of bioinformatics and cheminformatics for tracking the fecal pollution in an urban marine environment.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42149293}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Feces/microbiology/chemistry ; *Computational Biology ; *Water Pollution/statistics &amp; numerical data/analysis ; *Cheminformatics ; Cities ; *Water Pollutants, Chemical/analysis ; Humans ; }, abstract = {Fecal contamination in urban marine environments poses an alarming global threat to public health, ecosystems, and economies. Traditional fecal indicator bacteria (FIB) methods, while accessible, suffer from delayed results and inability to differentiate pollution sources. To overcome this, microbial source tracking (MST) employs molecular techniques like qPCR to rapidly identify specific origins (human, animal) using genetic markers. Complementary chemical source tracking utilizes distinct chemical signatures (e.g., sterols and pharmaceuticals) for detection, offering low limits and temporal stability. The burgeoning fields of bioinformatics and cheminformatics are crucial for processing the complex, high-volume data generated by these advanced methods. Bioinformatics tools analyze metagenomic data for microbial community profiling and source attribution, while cheminformatics automates the acquisition of chemical-specific data for environmental exposure modeling, enhancing efficiency and transparency. An integrated pragmatic approach leverages these capabilities with Geographic Information Systems (GIS) and remote sensing. GIS serves as a unifying platform, integrating diverse spatial, temporal, sensor, and analytical data to enable comprehensive spatial analysis, real-time monitoring, and predictive modeling of fecal plumes. Hence, this review is aimed toward this holistic framework, which is essential for effective, targeted management strategies to safeguard water quality.}, }
@article {pmid42149451, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {233-242}, pmid = {42149451}, issn = {1940-6029}, mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; }, abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.}, }
@article {pmid42149452, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {243-259}, pmid = {42149452}, issn = {1940-6029}, mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs &amp; derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.}, }
@article {pmid42149940, year = {2026}, author = {Sandi, JD and Brock-Fisher, TM and Kallon, TMPS and Paye, MF and Fofanah, IU and Nosamiefan, D and Kamara, MS and Teh, AJ and Turay, A and Wilkason, C and Baudi, I and Tomkins-Tinch, C and I'Anson, C and Stachler, E and Pekar, JE and Ozonoff, A and Park, D and Happi, C and Sabeti, PC and Grant, DS}, title = {Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {5}, pages = {e0014354}, pmid = {42149940}, issn = {1935-2735}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Sierra Leone ; *Yellow fever virus/genetics/isolation &amp; purification/classification ; *Genome, Viral ; Humans ; Phylogeny ; *Yellow Fever/virology/epidemiology ; Male ; Public Health ; Sequence Analysis, DNA ; Whole Genome Sequencing ; Genotype ; }, abstract = {Yellow fever virus (YFV), a mosquito-borne orthoflavivirus that causes severe hemorrhagic disease, is endemic in parts of South America and Africa, yet genomic data from Sierra Leone is lacking despite ongoing case-based surveillance. Using hybrid-capture metagenomic sequencing, we generated a complete 10,611 nt YFV genome (98% coverage) from an adult male patient who reported to the Kailahun Government Hospital with fever and muscle pain. Phylogenetic analysis assigned the genome to the West African II genotype via the YFV Nextstrain build. The Sierra Leone genome showed 57 substitutions, three of which were non-synonymous (NS2B: N79S, NS3: V515I, and NS5 (RdRp domain): A643V), relative to its most recent common ancestor with other genomes from Senegal and the Netherlands. Bayesian phylogenetics estimated the time to the most recent common ancestor with these genomes as January 14, 2001 (95% HPD: December 17, 1987 - April 28, 2009), potentially indicative of long-standing transmission within West Africa that has not been genomically characterized, rather than specific localization to Sierra Leone. Together, these findings underscore the need for expanded genomic surveillance to monitor YFV spread and evolution.}, }
@article {pmid42150467, year = {2026}, author = {Wang, X and Zhang, Y and Yu, J and Yang, S and Zhang, T and Song, J and Sun, Z}, title = {Metagenomic insights into nitrate- and sulfate-enhanced anoxic biodegradation of PAHs in subsurface soil.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120281}, doi = {10.1016/j.ecoenv.2026.120281}, pmid = {42150467}, issn = {1090-2414}, mesh = {*Nitrates/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism/analysis ; *Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Sulfates/metabolism ; Metagenomics ; *Bacteria/metabolism/genetics ; Soil/chemistry ; }, abstract = {Anoxic biodegradation is pivotal for remediating PAH-contaminated subsurface soils, yet its mechanisms remain poorly understood. In this study, nitrate and sulfate were used as electron acceptors to stimulate the anoxic biodegradation of PAHs in soil by indigenous bacteria. A 180-day anoxic incubation experiment was conducted, coupled with high-throughput sequencing for bacterial community composition, quantitative PCR for microbial abundance, metagenomic sequencing for functional gene profiling, and gas chromatography-mass spectrometry for PAH quantification, to characterize microbial community properties, key functional genes, and their contributions to PAH degradation. After 180 days of incubation, the addition of electron acceptors significantly increased the abundances of total and potential PAH-degrading bacteria (which increased by 0.11-0.24 and 0.09-0.46 orders of magnitude per gram of soil, respectively) and promoted the removal of 3- and 4-ring PAHs (59-64% and 26-33%, respectively). Notably, the degradation efficiency followed the order of NO3[-] > mixed electron acceptors > SO4[2-], revealing a clear preference for nitrate. Nitrate amendment selectively enriched key PAH-degrading taxa like Bacillus. Metagenomic analysis revealed the underlying microbial mechanisms: the functional pathway ko00624 (PAH degradation) was enriched, and the abundances of 15 key genes (e.g., pcaH, ligB, and pht5) involved in upstream and downstream metabolic steps were positively correlated with degradation efficiency. Comparative analysis showed that differences across treatments stemmed primarily from ‌elevated expression of shared core genes (e.g., pht4, phdG, nidB), with nitrate (SN) treatment showing the greatest enrichment. These findings elucidate electron acceptor-driven anoxic PAH transformation, highlighting nitrate's dual role as a nutrient and favorable electron acceptor, and provide a basis for targeted subsurface bioremediation.}, }
@article {pmid42150504, year = {2026}, author = {Pan, Z and Wang, W and Torabi, E and Zhang, M and Su, Z and Xu, X and Yin, Y and Xu, W and Duan, Y and Chen, J and Maróti, G and Huang, Q}, title = {Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142406}, doi = {10.1016/j.jhazmat.2026.142406}, pmid = {42150504}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; Metagenomics ; *Metals, Heavy/toxicity/analysis ; Oryza ; China ; Adaptation, Physiological ; Metagenome ; *Microbiota/drug effects ; Bacteria/genetics ; }, abstract = {The spatial heterogeneity of multi-metal contamination and its ecological consequences for soil microbial communities remain poorly characterized on a national scale, particularly within paddy ecosystems. This study investigated microbial ecological and genomic responses to heavy metal stress across 48 paddy soils from major rice-growing regions in China, categorized into low (LMS), moderate (MMS), and high (HMS) contamination levels. Our results indicate that multi-metal contamination triggered a significant restructuring of microbial communities, which was accompanied by increased alpha diversity and the enrichment of metal-tolerant taxa (e.g., Planctomycetes and Cyanobacteria). Conversely, microbial co-occurrence networks exhibited systematic simplification as contamination levels increased, characterized by reduced connectivity and a significant loss of keystone taxa. This suggests a transition from functionally redundant communities to modularized, survival-oriented network configurations. Metagenomic analysis revealed positive correlations between metal contamination and the abundance of nitrogen, phosphorus, and sulfur-cycling genes, while carbon-cycling genes remained relatively stable. Furthermore, genome-resolved metagenomics demonstrated widespread co-localization of metal resistance genes (MRGs) and nutrient cycling genes within metagenome-assembled genomes, particularly among key taxa (e.g., Burkholderiaceae, MBNT15). Collectively, these findings elucidate the mechanistic basis of microbial adaptation to multi-metal stress in paddy soils, providing critical insights for optimizing soil health management, developing targeted bioremediation strategies, and enhancing environmental risk assessment frameworks for contaminated agricultural ecosystems.}, }
@article {pmid42150526, year = {2026}, author = {Thompson, LR}, title = {Microbial ecology: Rise of the planet of the microbes.}, journal = {Current biology : CB}, volume = {36}, number = {10}, pages = {R432-R434}, doi = {10.1016/j.cub.2026.03.072}, pmid = {42150526}, issn = {1879-0445}, mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; }, abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.}, }
@article {pmid42150690, year = {2026}, author = {Kruger, F and den Haan, R}, title = {Adaptive laboratory evolution and rational engineering enabled xylose utilisation and xylan conversion in natural isolates of Saccharomyces cerevisiae.}, journal = {Journal of biotechnology}, volume = {417}, number = {}, pages = {17-30}, doi = {10.1016/j.jbiotec.2026.05.007}, pmid = {42150690}, issn = {1873-4863}, abstract = {Second-generation biofuels produced from renewable lignocellulosic biomass (LCB) are attractive alternatives to environmentally damaging, non-renewable fossil fuels. A key challenge in converting LCB to bioethanol is the incomplete utilisation of all available sugars. To address this, the hemicellulose fraction, consisting mainly of xylan, should be converted to the desired product alongside cellulose. This study aimed to develop natural isolate strains of Saccharomyces cerevisiae capable of xylose utilisation and xylan degradation. Strains YI13, YI59 and FIN1 were selected for potential industrial applications due to their high fermentation performance levels under environmental stress and enhanced ethanol production compared to laboratory strains. Xylose utilisation was achieved in these strains by introducing heterologous xylose isomerase (XI) and xylulokinase (XKS) gene cassettes and a xylose transporter (XTR), followed by adaptive laboratory evolution (ALE) in minimal xylose media. The evolved strains were further engineered for cell-associated xylosidase and secreted xylanase activities, yielding variants with strong enzyme activities, optimized xylose metabolism, and high ethanol production from both xylose and xylan. The final engineered version of YI13 showed the best xylose and xylan conversion, with maximum ethanol titres of ∼7.1 g/L from 20 g/L xylose and ∼4.7 g/L from 40 g/L xylan, among the highest ethanol titres from polymeric xylan by direct microbial conversion reported to date. The development of these S. cerevisiae strains provides a useful platform for future development of robust xylan-converting S. cerevisiae strains for large-scale ethanol production, although validation on real-world lignocellulosic feedstocks is still required.}, }
@article {pmid42151282, year = {2026}, author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G}, title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49725-3}, pmid = {42151282}, issn = {2045-2322}, support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Universit&#xe0; e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; }, abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.}, }
@article {pmid42151303, year = {2026}, author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E}, title = {The soil microbiome of the Caatinga drylands in Brazil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50433-1}, pmid = {42151303}, issn = {2045-2322}, support = {20-122//Conrad Prebys Foundation/ ; }, abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.}, }
@article {pmid42151510, year = {2026}, author = {de Souza Pereira, LF and Tavares, TCS and Martins, DT and Dias Dantas, CW and de Souza, FOR and Prazeres, MCC and Faturi, C and Rogez, HLG and Ramos, RTJ and Cardenas Alegria, OV and Ribeiro Carneiro Nunes, A}, title = {Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42151510}, issn = {1618-1905}, abstract = {The Amazon rainforest represents nearly 40% of the world's tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils-particularly those under fertilization-showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.}, }
@article {pmid42151682, year = {2026}, author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS}, title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3000}, number = {}, pages = {251-275}, pmid = {42151682}, issn = {1940-6029}, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; }, abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.}, }
@article {pmid42152463, year = {2026}, author = {Forshee, MD and Nachman, EJ and Shenoy, ER and Danhof, HA and Ermann Lundberg, L and Roos, S and Britton, RA}, title = {Limosilactobacillus reuteri promotes melatonin release from human intestinal organoids via 5'ectonucleotidase activity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2670854}, pmid = {42152463}, issn = {1949-0984}, mesh = {*Melatonin/metabolism ; *Limosilactobacillus reuteri/metabolism/growth &amp; development/enzymology ; Humans ; *Organoids/metabolism/microbiology ; *Intestines/microbiology ; Probiotics ; Adenosine/metabolism ; }, abstract = {Strains of Limosilactobacillus reuteri have been used to prevent or treat various conditions; however, the mechanisms by which they exert beneficial effects are not completely understood. Infant colic is one example in which L. reuteri DSM 17938 reduces clinical symptoms. While the etiology of colic is unknown, abnormal melatonin levels in infants have been suggested as a possible contributor. L. reuteri DSM 17938 has been shown to produce adenosine from AMP via production of the extracellular enzyme 5'ectonucleotidase (5'NT). Adenosine is a potent signaling molecule that impacts several important aspects of host physiology, including the release of melatonin from the pineal gland in the brain. A second major source of melatonin production is enteroendocrine cells in the intestine. We hypothesized that the adenosine generated via the 5'NT activity of L. reuteri DSM 17938, would stimulate melatonin release from human intestinal organoids. Here, we characterized the growth conditions that impact L. reuteri DSM 17938 5'NT activity, including carbon source utilization and required metal cofactors. We found zinc to be an essential cofactor for 5'NT activity by L. reuteri and observed carbon utilization altered 5'NT activity levels. Stachyose and raffinose increased levels of 5'NT activity while sucrose decreased 5'NT activity. We demonstrated that L. reuteri DSM 17938 stimulates melatonin release from pediatric human intestinal organoids in a 5'NT-dependent manner. Surprisingly, adenosine was necessary, but not sufficient, for the induction of epithelial melatonin release, thereby suggesting that an additional secreted factor was also required. Furthermore, L. reuteri BG-R46[®], an evolved strain of DSM 17938 that is known to express higher 5'NT activity, was shown to induce higher levels of melatonin secretion. Taken together, this work identifies zinc and carbon sources as key factors altering L. reuteri 5'NT activity levels and demonstrates that the L. reuteri strains stimulate intestinal melatonin release via 5'NT.}, }
@article {pmid42152762, year = {2026}, author = {Yang, W and Guo, J}, title = {Unveiling the Hidden Resistome: A Comprehensive Risk Assessment of Latent Antibiotic Resistance Genes in China's Wastewater.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70330}, doi = {10.1111/1462-2920.70330}, pmid = {42152762}, issn = {1462-2920}, support = {2021YFD1600400//National Key Research and Development Program of China/ ; }, mesh = {*Wastewater/microbiology ; China ; Risk Assessment ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Metagenome ; Genes, Bacterial ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater systems are important reservoirs of antibiotic resistance genes (ARGs), but the ecological and health risks of numerous latent ARGs (LARGs) remain unclear. In this study, we analysed 636 wastewater metagenomic samples from China and constructed a database containing 1587 LARGs. Across all environments, LARGs encoding serine-β-lactamases were the most abundant and prevalent. A comprehensive risk assessment, integrating host pathogenicity, gene mobility and environmental prevalence, was performed on 561 LARGs identified in metagenome-assembled genomes. Most LARGs exhibited low levels across all three dimensions, suggesting limited transmission risk. Nevertheless, 37 high-risk LARGs were identified, indicating non-negligible threats. Functional validation showed that the top three extremely high-risk LARGs significantly enhanced host resistance to ampicillin and ciprofloxacin when expressed in Escherichia coli, while AlphaFold3 revealed typical resistance protein folding, further supporting their functional activity. Horizontal gene transfer analysis indicated that these high-risk genes have disseminated from wastewater to natural water bodies such as rivers via plasmid-mediated mechanisms. Collectively, wastewater acts not only as an 'accumulation pool' for LARGs but also as a potential source releasing 'super-risky' resistance gene into the environment. Therefore, urgent efforts are needed to monitor and control these high-risk LARGs and their mobile genetic elements to block their environmental spread.}, }
@article {pmid42152807, year = {2026}, author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A}, title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1471-0528.70266}, pmid = {42152807}, issn = {1471-0528}, support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.<br><br>DESIGN: Prospective cohort study integrated with mechanistic experiments.<br><br>SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).<br><br>POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.<br><br>METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.<br><br>MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.<br><br>RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.<br><br>CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.}, }
@article {pmid42152996, year = {2026}, author = {Chauhan, G and Bisht, N and Gautam, P and Arya, M and Kumari, A and Verma, D and Sharma, M}, title = {Cloning and Heterologous Expression of a Novel Thermo-Alkalistable GH-10 Xylanase (rXyn-GM) Retrieved from Tapovan Hot-Spring Soil Metagenome and its Characterization for Kinetic Parameters.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {417-430}, pmid = {42152996}, issn = {0046-8991}, abstract = {UNLABELLED: A cellulase-free xylanase gene of 927 bp size (Xyn-GM) was isolated from the metagenomic library of the Tapovan Hot Spring in Uttarakhand, India. This gene encodes a 308-amino acid xylanase enzyme classified under the glycoside hydrolase family 10 (GH-10). The Xyn-GM gene was introduced into the pET28a (+) vector and expressed in host cells of Escherichia coli BL21 (DE3). The recombinant xylanase (rXyn-GM), with a molecular weight ~ 32.5 kDa, was isolated through a one-step purification process using Ni[2][+]-NTA affinity chromatography. The purified enzyme exhibited broad thermostability (50-100 °C) and pH stability (4.0-11.0), with optimal activity at 70 °C and pH 9.0. Its activity increased by 67% in the presence of 1 mM Mn[2][+]. rXyn-GM retained ~ 65% activity after 2 h at 50 °C and 60 °C and ~ 75% activity at pH 9.0 after 3 h. It showed a preference for beechwood xylan, with kinetic parameters Km 20.9 mg/mL and Vmax 156.25 µmol/mg/min. Furthermore, rXyn-GM catalysed the production of xylo-oligosaccharides from beechwood xylan, suggesting its potential utility as prebiotics in the food and pharmaceutical industries.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01480-1.}, }
@article {pmid42153006, year = {2026}, author = {Yadav, S and Shipra, }, title = {Impact of Climate Change on Zoonotic Diseases and Antimicrobial Resistance.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {280-291}, pmid = {42153006}, issn = {0046-8991}, abstract = {UNLABELLED: Climate change along with infectious disease and antimicrobial resistance are imposing threat to public health globally. Climate change mediates frequent rise in antimicrobial resistance leading to the emergence of zoonotic vectors. Both climate change and AMR contribute significantly to global morbidity and mortality and impose burden on the healthcare sector. Overexploitation of antimicrobials in various sectors causes broader dissemination of AMR. Therefore, the application of a holistic "One Health Approach" is required to combat both climate change and antimicrobial resistance. Increasing public awareness about the negative consequences of climate change and antimicrobial resistance is essential. Also, the discovery of new antimicrobials has become the need of the present world. The application of metagenomics has the potential to shed light on microbial community dynamics (taxonomic abundance and predominant biochemical pathways) in response to climate change. The application of modern tools like functional metagenomics has the potential to yield new antimicrobial compounds for combating AMR.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01430-3.}, }
@article {pmid42153318, year = {2026}, author = {Chasapi, MN and Kontis, N and Lehmann, R and Tasneem, R and Patel, NS and Khan, SA and Martínez de Morentin, X and Chasapi, IN and Aplakidou, E and Galaras, A and Aldakheel, L and Su, M and Baltoumas, FA and Venkateswaran, K and Lagani, V and Gómez-Cabrero, D and Tegnér, J and Pavlopoulos, GA and Soares Rosado, A}, title = {Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42153318}, issn = {1477-4054}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; //KAUST Visiting Student Research Program (VSRP)/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; 23592-EMISSION//Research Projects to Support Faculty Members and Researchers/ ; }, mesh = {*Computational Biology/methods ; Culture Techniques ; Environmental Microbiology ; *Extremophiles/genetics/isolation &amp; purification/metabolism ; Machine Learning ; }, abstract = {Life thrives in Earth's most inhospitable environments, from boiling hydrothermal vents to hypersaline lakes and frozen polar deserts, thanks to the remarkable adaptations of extremophilic microorganisms. The study of these organisms has rapidly evolved from early cultivation-based discoveries to a data-rich discipline powered by advanced omics technologies. This review comprehensively outlines the current landscape and future directions in extremophile research, emphasizing the pivotal role of bioinformatics, machine learning (ML), and data-driven approaches. We begin by charting the evolution of methodologies, from innovative in situ cultivation techniques and robust biomolecule extraction protocols to modern multi-omics workflows (metagenomics, transcriptomics, proteomics, and metabolomics) that decode the genetic and functional basis of extremophiles. We then catalogue essential bioinformatics resources and specialized databases critical for annotating extremophile genomes and uncovering their unique adaptive strategies, including protein stabilization and syntrophic metabolic relationships. Finally, we explore the transformative potential of artificial intelligence (AI) and ML in overcoming fundamental challenges in the field. These include predicting the functions of uncharacterized "hypothetical" proteins, identifying novel extremozymes, modeling complex genotype-phenotype relationships, and guiding the targeted engineering of industrially relevant strains. By synthesizing insights across these domains, this review highlights how integrating computational biology and AI is poised to unlock the full biotechnological potential of extremophiles and redefine the boundaries of life itself.}, }
@article {pmid42153323, year = {2026}, author = {Wang, J and Liu, Y and Liu, F and Hou, T and Chen, S and Liu, S and Liu, Y}, title = {DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42153323}, issn = {1477-4054}, support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Science and Technology Development Plan Project of Jilin Province, China/ ; //Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Algorithms ; *Software ; Computational Biology/methods ; Autoencoder ; }, abstract = {DNA contigs binning is necessary to reconstruct metagenome-assembled genomes. Current metagenomic DNA contigs binning methods often leverage coverage profiles across multiple related metagenomes and have demonstrated strong performance on co-assembled contigs. However, in single-sample scenarios where coverage information is rare, their performance drops significantly, limiting the in-depth development of metagenomics at the individual sample level. To address this issue, we propose DCVBin, a novel single-sample metagenomic contigs binning method that incorporates semantic features extracted from a DNA language model. Specifically, our approach continues pretraining on a DNA language model to capture more domain-specific semantic representations, which are then integrated with 4-mer frequencies using a variational autoencoder. Clustering is subsequently performed using the k-means algorithm, in which the number of clusters is determined by single copy genes. Experimental results on six publicly available datasets demonstrate that DCVBin achieves high-accuracy single-sample metagenomic binning and outperforms other state-of-the-art methods. Furthermore, DCVBin is included into a disease diagnostic framework that is evaluated on a cohort of gut metagenomes from people with colorectal cancer and healthy people. The framework is shown to be accurate in predicting colorectal cancer using gut metagenomes and has identified a list of potential microbial biomarkers.}, }
@article {pmid42153643, year = {2026}, author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E}, title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048526}, doi = {10.1128/msystems.00485-26}, pmid = {42153643}, issn = {2379-5077}, abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.}, }
@article {pmid42153646, year = {2026}, author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV}, title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0013926}, doi = {10.1128/msphere.00139-26}, pmid = {42153646}, issn = {2379-5042}, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.}, }
@article {pmid42153961, year = {2026}, author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17087}, doi = {10.1002/advs.202517087}, pmid = {42153961}, issn = {2198-3844}, support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; }, abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.}, }
@article {pmid42154322, year = {2026}, author = {Greaves, JC and Rodriguez, RA}, title = {Revealing the hidden burden: wastewater-based epidemiology for underreported and emerging infectious diseases in communities.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42154322}, issn = {1573-2959}, mesh = {Humans ; *Wastewater/virology/microbiology ; *Communicable Diseases, Emerging/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater-based epidemiology (WBE) has become a transformative tool for infectious disease surveillance, providing population-level insights that complement and extend traditional case-based reporting. This review examines the expanding role of WBE in identifying and characterizing underreported, novel, and emerging human pathogens. Evidence reveals that wastewater analysis consistently detects enteric, respiratory, and neglected pathogens that are often missed by clinical systems, thereby revealing the hidden burden of infection within communities. Sequencing-based studies have identified numerous novel and divergent human viruses, highlighting the extensive diversity of the human virome. The frequent co-detection of multiple viral taxa also suggests that interactions and co-infections may influence viral evolution, disease manifestation, and transmission. Despite methodological challenges in quantification and biological validation, WBE has proven capable of detecting both known and novel pathogens before they are clinically recognized. Future developments in long-read sequencing, bioinformatics, and global data integration will enhance the precision and scope of wastewater genomics, positioning it as a central element of early-warning and One Health surveillance frameworks. By illuminating the unseen spectrum of infectious agents, WBE bridges environmental and clinical domains, offering a scalable and equitable strategy for global pathogen discovery and public health preparedness.}, }
@article {pmid42154337, year = {2026}, author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP}, title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {42154337}, issn = {1559-1182}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.}, }
@article {pmid42154370, year = {2026}, author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG}, title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.}, journal = {Advances in therapy}, volume = {}, number = {}, pages = {}, pmid = {42154370}, issn = {1865-8652}, abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.}, }
@article {pmid42154390, year = {2026}, author = {Khan, I and Irfan, M and Bacha, AS and Khan, I and Ali, Y and Li, Z}, title = {Host-Microbiota Metabolic Interactions in Atherosclerosis: Oral, gut, and Blood Perspectives.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42154390}, issn = {1867-1314}, abstract = {Atherosclerosis is a chronic inflammatory disease influenced by host-microbiota interactions beyond traditional risk factors. Microbial communities in the oral cavity, gut, and blood contribute to vascular dysfunction through metabolic and immune mechanisms, yet an integrated perspective across these compartments remains lacking. This narrative review synthesizes current evidence on the distinct and interconnected roles of oral, gut, and blood microbiotas in atherosclerosis pathogenesis. We critically evaluate key microbial metabolites, trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids, and their mechanisms of host metabolic and immune modulation. We also examine cross-compartment interactions, emerging multi-omics approaches, and the translational potential of microbiota-targeted interventions. Oral pathogens promote systemic inflammation and endothelial activation. Gut-derived metabolites such as TMAO exacerbate foam cell formation and impair reverse cholesterol transport, whereas SCFAs exert protective effects via immune modulation and gut barrier maintenance. Emerging evidence suggests that blood microbial components contribute to vascular inflammation, though methodological challenges remain. Multi-omics integration (metagenomics, metabolomics, host genomics) reveals interconnected metabolic networks linking microbial activity to atherosclerosis. Microbiota-targeted strategies, including dietary modulation, TMA lyase inhibitors, and probiotics, show promise for risk stratification and therapeutic intervention. The human microbiota regulates atherosclerosis through immunometabolic metabolites, offering promising biomarkers and therapeutic targets. However, clinical translation requires addressing interindividual variability, establishing causality, and standardizing methodologies. This review provides an integrated framework for leveraging microbiota-host interactions in precision cardiovascular medicine.}, }
@article {pmid42154500, year = {2026}, author = {Pouder, E and Alain, K and Mieszkin, S}, title = {Phylogenomic and metabolic insights into iron reduction metabolism in the genus Deferribacter belonging to the order Deferribacterales.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42154500}, issn = {2057-5858}, mesh = {*Phylogeny ; *Iron/metabolism ; Oxidation-Reduction ; Hydrothermal Vents/microbiology ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; }, abstract = {Iron is one of the most important elements of the Earth, yet its bioavailability is limited in oceanic environments. In this context, deep-sea hydrothermal ecosystems represent one of the major sources of iron. While some microorganisms involved in its biogeochemical cycle, particularly in Fe(III)-reduction, have been isolated from these ecosystems, the molecular mechanisms underpinning metabolic pathways remain hypothetical and incomplete. Therefore, this study aims to investigate the global metabolism of bacteria within the Deferribacter genus, isolated from hydrothermal systems and a petroleum reservoir, with a specific focus on the Fe(III)-reduction metabolism to identify genes potentially involved in this pathway. This study revealed a conserved carbon metabolism across the four species, while their energetic metabolism exhibited notable differences. These species appear to be able to use different elements as electron sources, showing their ability to adapt to different ecological (micro)niches, particularly in deep-sea hydrothermal vents. The marker genes known for Fe(III)-reduction were identified, with a contrast between the strains isolated from hydrothermal systems and the one isolated from a petroleum reservoir. To further explore this pattern, the study was extended, including 14 genomes of representative strains and 36 metagenome-assembled genomes affiliated to the Deferribacterales order. Phylogenomic analysis revealed a distribution pattern within this order that correlates with environmental origin. Canonical marker genes of Fe(III)-reduction were also identified, with their distribution primarily aligned with specific ecological niches.}, }
@article {pmid42154842, year = {2026}, author = {Wang, D and Wang, N and Liu, J and Zhao, C and Xing, X}, title = {The diagnostic value of fine-needle aspiration cytology in the early diagnosis of pulmonary cryptococcosis.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {68}, number = {}, pages = {e33}, pmid = {42154842}, issn = {1678-9946}, mesh = {Humans ; *Cryptococcosis/pathology/diagnosis ; Biopsy, Fine-Needle/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Lung Diseases, Fungal/pathology/diagnosis ; Early Diagnosis ; Adult ; Aged ; Lung/pathology/microbiology ; }, abstract = {Pulmonary cryptococcosis, an invasive fungal infection caused by Cryptococcus spp., is often misdiagnosed as tuberculosis or lung cancer due to overlapping clinical and radiological features, leading to treatment delays. In this descriptive study, we aim to characterize the diagnostic findings and clinical utility of fine-needle aspiration cytology (FNAC) in a series of patients with pulmonary cryptococcosis, within the context of other available diagnostic modalities. We retrospectively analyzed 10 patients with pulmonary cryptococcosis who underwent imaging-guided percutaneous lung aspiration. Wright-Giemsa-stained cytology smears were examined under oil immersion, enabling clear visualization of the characteristic morphological features of Cryptococcus. In this case series, FNAC provided a rapid cytological diagnosis within two hours in all 10 cases, consistent with the results obtained by metagenomic next-generation sequencing (mNGS) and serological testing. In contrast, conventional smear microscopy showed lower detection rates, and histopathology required longer processing times. The use of FNAC facilitated early diagnosis, enabling timely initiation of antifungal therapy and helping to avoid unnecessary surgical interventions. Our findings suggest that cytomorphological evaluation by FNAC is a rapid and valuable diagnostic tool in the early clinical management of pulmonary cryptococcosis, effectively complementing existing diagnostic methods.}, }
@article {pmid42154957, year = {2026}, author = {Lorca, R and Bretagne, MC and Boizeau, L and Cappy, P and Allenbach, Y and Rodriguez, C and Salem, JE}, title = {Immune checkpoint inhibitor myocarditis: a metagenomic investigation of infectious pathogens.}, journal = {European heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurheartj/ehag371}, pmid = {42154957}, issn = {1522-9645}, }
@article {pmid42155010, year = {2026}, author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN}, title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag249}, pmid = {42155010}, issn = {1535-4970}, abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of IPF. However, the role of gut microbiota in IPF pathogenesis is unknown.<br><br>OBJECTIVES: Determine associations between gut microbiota, disease severity and lung transplant-free survival in IPF.<br><br>METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n&#x2009;=&#x2009;411). CleanUP-IPF investigated the clinical efficacy of long-term anti-microbials in IPF. 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models and Cox regression models.<br><br>MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted (pp) DLCO). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (HR 0.34 95% CI 0.14-0.87, P&#x2009;=&#x2009;.02) in patients not assigned to anti-microbial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long term co-trimoxazole had worse survival (HR 6.09 95% CI 1.36-27.27, P&#x2009;=&#x2009;.02). Survival in pirfenidone treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.<br><br>CONCLUSIONS: In exploratory post-hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.}, }
@article {pmid42155550, year = {2026}, author = {Pandit, S and Hazra, S and Dinda, SK and Bhattacharjee, B and Basu, A and Pradhan, B and Kumar, K and Manna, D}, title = {Advances in the detection of deadly free-living amoebae (FLA).}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {2}, pages = {117465}, doi = {10.1016/j.diagmicrobio.2026.117465}, pmid = {42155550}, issn = {1879-0070}, mesh = {Humans ; *Amebiasis/diagnosis/parasitology ; *Molecular Diagnostic Techniques/methods ; *Amoeba/isolation &amp; purification/genetics/classification ; Balamuthia mandrillaris/isolation &amp; purification ; Naegleria fowleri/isolation &amp; purification ; Specimen Handling ; }, abstract = {Free-living amoebae (FLA), including Naegleria fowleri, Acanthamoeba castellanii, Balamuthia mandrillaris, and Sappinia pedata, are ubiquitous protozoa capable of causing severe infections such as primary amoebic meningoencephalitis (PAM), granulomatous amoebic encephalitis (GAE), and Acanthamoeba keratitis (AK). Early diagnosis remains challenging due to disease rarity, nonspecific clinical presentation, and limited access to specialized laboratory methods. Rapid and accurate detection is critical for patient management and public health response, particularly amid changing environmental exposures. This review summarizes current diagnostic approaches in clinical and environmental contexts, including specimen handling, microscopy, culture, immunohistochemistry, antigen detection, and molecular methods such as conventional PCR, real-time PCR, multiplex qPCR, LAMP, and metagenomic next-generation sequencing. Environmental surveillance, biomarker discovery, quality assurance, and standardized protocols are also discussed. By evaluating strengths and limitations of available tools, this review highlights diagnostic gaps and future priorities to enhance sensitivity, turnaround time, and global accessibility.}, }
@article {pmid42155712, year = {2026}, author = {Geng, R and Huang, B and Duan, Z and Zhao, F and Lü, X and Jiang, Z and Yi, Y}, title = {Antimicrobial Efficacy and Food Application Potential of Bacteriocins LL3 and LL4 from Traditional Dairy-Derived Lactococcus lactis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28309}, pmid = {42155712}, issn = {1525-3198}, abstract = {To combat foodborne pathogens like Salmonella, this study employed an activity-based screening followed by metagenomic mining of the active isolates to discover and characterize bacteriocins from Inner Mongolian dairy products. From the 15 active isolates, Lactococcus lactis D63 and D64 were identified as harboring a putative biosynthetic gene cluster (BGC) encoding 2 bacteriocins, LL3 and LL4. Both peptides form amphipathic α-helical structures that disrupt bacterial membranes, leading to intracellular leakage and cell death. They exhibited effective antimicrobial activity, particularly against Salmonella Typhimurium. Crucially, when applied in a simulated milk model under standard refrigeration (4°C), synthesized LL4 demonstrated robust preservative efficacy by effectively controlling S. Typhimurium, showing comparable performance to the commercial preservative Nisin. Genetic analysis revealed that this BGC exhibits low basal transcription under standard laboratory growth conditions and shares high homology with plasmid elements, suggesting it is a mobile genetic element acquired via horizontal gene transfer. This study presents LL3 and LL4 as promising natural preservatives and validates metagenomic mining as an efficient strategy for uncovering antimicrobial genes.}, }
@article {pmid42155775, year = {2026}, author = {Yao, X and Zhu, Y and Gao, P and Liu, T and Zhang, X and Liu, W and Li, J and Li, D and Zhang, Y and Zhang, Z}, title = {Limitations of endogenous denitrification in low carbon-to-nitrogen wastewater treatment: Insights into carbon allocation imbalance and metabolic adaptation.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134915}, doi = {10.1016/j.biortech.2026.134915}, pmid = {42155775}, issn = {1873-2976}, mesh = {*Carbon/metabolism ; *Denitrification ; *Nitrogen/metabolism ; *Wastewater/chemistry/microbiology ; *Water Purification/methods ; Bioreactors/microbiology ; *Adaptation, Physiological ; Polyhydroxyalkanoates/metabolism ; Bacteria/metabolism ; Glycogen/metabolism ; Sewage/microbiology ; }, abstract = {Endogenous denitrification (EnD) has been identified as a promising strategy for enhancing nitrogen removal from wastewater with a low carbon-to-nitrogen (C/N) ratio. However, the mechanisms limiting its effectiveness under carbon-starved conditions remain insufficiently understood. This 160-day study compared denitrification performance, carbon allocation, and metabolic responses in two sets of anaerobic/aerobic/anoxic-sequential batch reactors (A/O/A-SBR) under low (3-5) and high (10-15) C/N ratios. Under low C/N, total nitrogen (TN) removal decreased to 69.90 ± 13.31%, with effluent NO3[-]-N accounting for 87.43 ± 14.40% of TN. Concurrently, microbial activity was inhibited. Compared with high C/N ratio, microorganisms under low C/N preferentially allocated limited carbon to extracellular protein (PN) rather than to intracellular polyhydroxyalkanoates or glycogen. PN constitutes 47.39 ± 2.38% of the total internal carbon sources in unit sludge and functions primarily to maintain cellular structural stability. This carbon allocation pattern imposes limitations on the supply of carbon sources available for the EnD process. In addition, despite the enrichment of EnD functional bacteria (15.22 ± 2.03%), functional genes were primarily directed toward survival-related pathways (xenobiotics biodegradation and metabolism and amino acid synthesis). Constraints on energy metabolism further limited carbon utilization and denitrification. Concurrently, while the dispersion of denitrification-related genes under low C/N maintained system stability across multiple bacterial genera, it concomitantly reduced denitrification efficiency. This metabolic shift further limited EnD. This study provides novel insights into constraints on EnD from the perspectives of carbon source allocation and microbial metabolic adaptation, thereby establishing a theoretical foundation for the treatment of low C/N wastewater.}, }
@article {pmid42155781, year = {2026}, author = {Wang, J and Liu, S and Wang, Z and Guo, Y and Liu, J and Shi, L}, title = {Coupling heterotrophic and hydrogenotrophic partial denitrification via gel-based bio-carriers: microbial mechanisms and metabolic modeling.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {134914}, doi = {10.1016/j.biortech.2026.134914}, pmid = {42155781}, issn = {1873-2976}, mesh = {*Denitrification/physiology ; *Hydrogen/metabolism ; *Heterotrophic Processes ; *Models, Biological ; Bioreactors/microbiology ; *Bacteria/metabolism/genetics ; Gels ; Nitrates/metabolism ; Nitrites/metabolism ; }, abstract = {Partial denitrification (PD) has emerged as a pivotal technology for addressing the limited nitrite (NO2[-]) supply that hinders the widespread application of anammox, as it efficiently provides NO2[-]. However, its reliance on organic carbon sources restricts its broad implementation. In this study, a system of heterotrophic coupled with hydrogen-autotrophic PD was established using polyvinyl alcohol gel bio-carriers. Operated under a low COD/NO3[-]-N ratio of 2.00 for 90 days, the system achieved remarkable performances, with a NO2[-] transformation ratio (NTR) of 85.50 ± 3.10% and a nitrate (NO3[-]) removal rate (NRR) of 84.70 ± 5.00%. Metagenomic analysis revealed the effective enrichment ofHydrogenophaga(23.90%) as a key hydrogen-autotrophic denitrifier, which formed a functionally complementary consortium with heterotrophic denitrifiers (e.g.,Dokdonella). The abundance ratio of NO2[-] reduction genes in autotrophic to heterotrophic bacteria was 1.3:1. Furthermore, a putative metabolic model was constructed, which posits a potential cross-feeding interaction characterized by "hydrogen production by heterotrophs and consumption by autotrophs." The hydrogenase (EC:1.12.99.6) was proposed as a potential key gene facilitating this synergy between heterotrophic and autotrophic bacteria. The increased abundance ratio of nitrate reductase to nitrite reductase genes to 2.07 was identified as the key factor promoting the high accumulation of NO2[-]. Material characterization confirmed that the gel carriers possessed a hierarchical porous structure, with a mesopore-dominated pore size distribution conducive to hydrogen diffusion and the aggregation of functional microbial communities, thereby providing a stable micro-environment. This study offers a novel technological pathway for stable NO2[-] supply in the treatment of low-carbon wastewater.}, }
@article {pmid42155841, year = {2026}, author = {Zhang, M and Sun, H and Ren, Y and Chen, K and Yan, G and Li, B and Huang, Y and Tan, Z and Sun, W}, title = {Thiosulfate drives vanadium natural attenuation in oligotrophic mine tailings: Insights from DNA-SIP and metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {403}, number = {}, pages = {128368}, doi = {10.1016/j.envpol.2026.128368}, pmid = {42155841}, issn = {1873-6424}, mesh = {*Thiosulfates/metabolism/chemistry ; *Mining ; *Vanadium/metabolism/analysis ; Metagenomics ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; }, abstract = {Vanadium (V) accumulation in mine tailing ponds represents a persistent contamination source, posing severe risks to the surrounding ecosystems. Microbial V(V) reduction represents a key pathway of V detoxification, immobilization and attenuation. While thiosulfate (S2O3[2-]), a prevalent byproduct in tailing ponds, is thermodynamically capable of driving V(V) reduction, the occurrence of the S2O3[2-]-driven V(V) reduction and its underpinning microbial mechanisms remain elusive. Here, we investigated the potential of S2O3[2-] to fuel V(V) natural attenuation in the tailing sediment. Microcosm experiments demonstrated that S2O3[2-] amendment significantly accelerated V(V) reduction rates by 1.8-fold compared to thiosulfate-free controls, confirming a stoichiometric coupling between V(V) reduction and S2O3[2-] oxidation. Pseudomonas, Symbiobacterium and Actinotalea were proposed as the active autotrophic taxa responsible for this coupling process using DNA-stable isotope probing (SIP) combined with metagenomics. Metabolic reconstruction revealed a resilient microbial network based on functional redundancy. These key taxa harbored denitrification-related reductases (NarGHI, NapAB, and NirS/K) and respiratory electron-transfer components (cytochrome c oxidases), together with distinct thiosulfate oxidation genes including thiosulfate dehydrogenase (TsdA/DoxD) and sulfurtransferases (TST/GlpE), indicating potential pathways for the S2O3[2-]-driven V(V) reduction process. These findings expand our understanding of the coupled S-V biogeochemical cycle and highlight the intrinsic natural attenuation capacity of tailing environments. This work provides a mechanistic basis for assessing the environmental fate and mobility of vanadium in oligotrophic habitats.}, }
@article {pmid42156214, year = {2026}, author = {Wang, H and Chen, N and Feng, C and Mei, D and Gao, H and Liu, T}, title = {Carbon availability dictates the stability of nitrate-vanadium co-remediation in stratified biofilters.}, journal = {Water research}, volume = {302}, number = {}, pages = {126137}, doi = {10.1016/j.watres.2026.126137}, pmid = {42156214}, issn = {1879-2448}, mesh = {*Nitrates/metabolism ; *Carbon/metabolism ; Biodegradation, Environmental ; *Vanadium/metabolism/chemistry ; *Filtration/methods ; Denitrification ; *Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; }, abstract = {Thermodynamic hierarchies constrain the bioremediation of groundwater co-contaminated with nitrate (NO3[-]) and pentavalent vanadium (V(V)), denitrification preferentially consumes electron donors that would otherwise support metal reduction. Here, we show that spatial stratification of lignocellulosic residues (wheat straw → corn straw → corncob) can transiently alleviate competition between these competing processes, although system performance remains ultimately governed by carbon availability and kinetics. Over 330 days of operation, the stratified biofilter exhibited a biphasic response: (i) a carbon-sufficient phase (0 - 88 d) that enabled synergistic co-removal, increasing NO3[-] and V(V) loading capacities by up to 6.3-fold and 4.0-fold, respectively, relative to single-substrate controls; and (ii) a carbon-limited phase (88 - 330 d) in which denitrification persisted (>50% removal) while V(V) reduction collapsed (≈0%). Spatially resolved metagenomics (n = 15) revealed the mechanism as a thermodynamic "metabolic triage": under carbon limitation, microbial communities maintained denitrification pathways but selectively down-regulated V-reduction modules (sulfite reductase and multiheme cytochromes) by 59% - 69%. While distinct functional niches emerged-characterized by rapid efflux (top), deep reduction (middle), and sequestration (bottom), spatial organization alone could not override thermodynamic limits. Our findings establish that sustained metal co-remediation requires dynamic carbon management strategies to actuate latent genetic potential, providing a design framework for overcoming competitive inhibition in engineered aquifers.}, }
@article {pmid42156216, year = {2026}, author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B}, title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.}, journal = {Water research}, volume = {302}, number = {}, pages = {126133}, doi = {10.1016/j.watres.2026.126133}, pmid = {42156216}, issn = {1879-2448}, mesh = {*Aquaculture ; *Fresh Water ; Animals ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Metagenome ; }, abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.}, }
@article {pmid42156414, year = {2026}, author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and ,  and Guarner, F and Ehrlich, SD}, title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44895-6}, pmid = {42156414}, issn = {2045-2322}, support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; }, abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.}, }
@article {pmid42156610, year = {2026}, author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z}, title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {42156610}, issn = {1437-7772}, support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; }, abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.}, }
@article {pmid42156647, year = {2026}, author = {Ravikrishnan, A}, title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {1-23}, pmid = {42156647}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; }, abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.}, }
@article {pmid42156648, year = {2026}, author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A}, title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {25-32}, pmid = {42156648}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.}, }
@article {pmid42156649, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D}, title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {33-46}, pmid = {42156649}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; }, abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.}, }
@article {pmid42156650, year = {2026}, author = {Miliotis, G and Tumeo, A}, title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {47-73}, pmid = {42156650}, issn = {1940-6029}, mesh = {*Wetlands ; *Metagenomics/methods ; *Wastewater/microbiology ; *Water Purification/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; Water Microbiology ; }, abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.}, }
@article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, }
@article {pmid42156658, year = {2026}, author = {Roma Pi, J and Heinken, A}, title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {233-260}, pmid = {42156658}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; }, abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.}, }
@article {pmid42156769, year = {2026}, author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M}, title = {Functional restructuring of the global soil microbiome under multiple stressors.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73231-9}, pmid = {42156769}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.}, }
@article {pmid42156772, year = {2026}, author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and ,  and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E}, title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73193-y}, pmid = {42156772}, issn = {2041-1723}, support = {U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.}, }
@article {pmid42157110, year = {2026}, author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F}, title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08962-4}, pmid = {42157110}, issn = {1471-2229}, support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; }, abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.<br><br>RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.<br><br>CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype &#xd7; microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.}, }
@article {pmid42157119, year = {2026}, author = {Li, QX and Luo, LZ}, title = {Cutaneous MAC infection in an immunocompetent patient: a case report confirmed by mNGS.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13549-3}, pmid = {42157119}, issn = {1471-2334}, abstract = {BACKGROUND: Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are rare. Atypical clinical manifestations and the need for precise microbiological identification often result in misdiagnosis and underdiagnosis.<br><br>CASE PRESENTATION: A 65-year-old immunocompetent female initially presented with papular urticaria. Her symptoms improved transiently after anti-inflammatory treatment, but the lesions rapidly progressed to generalized erythematous nodules and ulcers accompanied by fever and lymphadenopathy. Routine microbiological culture and histopathological examination yielded negative results, while metagenomic next-generation sequencing (mNGS) identified Mycobacterium avium complex (MAC) as the causative pathogen.Triple antimicrobial therapy (clarithromycin, doxycycline, and levofloxacin) a favorable clinical response. This case indicates that cutaneous non-tuberculous mycobacterial (NTM) infection has atypical clinical manifestations and is frequently misdiagnosed as common cutaneous eruptions. mNGS can serve as a key diagnostic tool for suspected cutaneous NTM infection, effectively reducing misdiagnosis and missed diagnosis and providing a reliable basis for clinical diagnosis and treatment.<br><br>CONCLUSION: Cutaneous MAC infection, though rare, may occur in immunocompetent individuals. Clinicians should suspect NTM infection in treatment-refractory skin lesions. mNGS is valuable for etiological diagnosis when conventional tests are negative.}, }
@article {pmid42157131, year = {2026}, author = {Ji, T and Cheng, R and Lu, M}, title = {mNGS and IL-5: potential early diagnostic clues for clonorchiasis before eosinophil rise - a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13612-z}, pmid = {42157131}, issn = {1471-2334}, support = {2022YFC2303203-01//National Key R&amp;D Program of China/ ; Z-2017-24-2202//Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; }, abstract = {Clonorchiasis, caused by Clonorchis sinensis, often evades early diagnosis in non-endemic regions due to its nonspecific presentation and the delayed appearance of eosinophilia. We report an informative case of a 56-year-old male with acute fever, abdominal pain, and hepatitis, where conventional diagnostics and initial antimicrobial therapy failed. In this case, metagenomic next-generation sequencing (mNGS) of blood identified C. sinensis-specific reads, and cytokine profiling revealed a marked elevation in interleukin-5 (IL-5) before the onset of peripheral eosinophilia. Targeted treatment with praziquantel led to rapid clinical resolution. This case suggests the potential of integrating mNGS and IL-5 monitoring as early diagnostic tools for clonorchiasis, which can allow for intervention prior to classical biomarker emergence.}, }
@article {pmid42157143, year = {2026}, author = {Sheng, G and Zhao, C and Jiang, L and Zhang, X and Gao, F}, title = {Talaromyces marneffei infection of central nervous system in an immunocompetent child in a nonendemic area: a case report and literature review.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-06996-z}, pmid = {42157143}, issn = {1471-2431}, abstract = {BACKGROUND TALAROMYCES MARNEFFEI: (T. marneffei, formerly Penicillium marneffei) is a rare fatal fungus endemic in Southeast Asia and southern China. T. marneffei infections mainly occur in HIV-infected adults, and commonly involves the skin, lung, and reticuloendothelial system. T. marneffei infections of isolated central nervous system (CNS) in immunocompetent pediatric patients in nonendemic areas have rarely been reported. CASE PRESENTATION: We report a rare case of T. marneffei-induced disseminated encephalomyelitis in an immunocompetent girl from a nonendemic area of Eastern China. The main clinical manifestations were abdominal pain with distension and abnormal gait. Contrast-enhanced magnetic resonance imaging (MRI) revealed both brain and spinal cord lesions. The infection status of T. marneffei was quickly determined via the metagenomic next-generation sequencing (mNGS) of spinal cord biopsy tissue. T. marneffei induced disseminated encephalomyelitis was diagnosed. Following successful antifungal treatment with amphotericin B liposomes and voriconazole, the child recovered gradually. To date, only 3 cases of T. marneffei infection of the central nervous system in non-HIV-infected pediatric patients have been reported in the literature. Among them, one child had inborn errors of immunity, and the other two children were from endemic areas. Moreover, the clinical manifestations of those 3 reported cases were disseminated with common infection sites in the lungs. our patient represents a unique case of an immunocompetent child from a nonendemic area with isolated CNS infection. CONCLUSIONS: We report this rare case and aim to promote pediatric clinicians' recognition of T. marneffei isolated CNS infection in immunocompetent pediatric patients from nonendemic regions. Furthermore, the early use of mNGS is recommended when non-HIV-infected pediatric patients present with unexplained clinical manifestations and poor response to conventional treatments. Timely diagnosis and appropriate antifungal therapy can improve patient prognosis.}, }
@article {pmid42157342, year = {2026}, author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H}, title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42157342}, issn = {1674-9782}, support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; }, abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.<br><br>RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.<br><br>CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.}, }
@article {pmid42157352, year = {2026}, author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H}, title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42157352}, issn = {1297-9716}, support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; }, mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; }, abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.}, }
@article {pmid42157462, year = {2026}, author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR}, title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70320}, doi = {10.1111/1462-2920.70320}, pmid = {42157462}, issn = {1462-2920}, support = {R01GM085770/NH/NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; }, abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.}, }
@article {pmid42158361, year = {2026}, author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S}, title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2673265}, pmid = {42158361}, issn = {2993-3935}, abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.}, }
@article {pmid42158572, year = {2026}, author = {Wong, E and England, J and Jagadeesan, V}, title = {Scedosporium apiospermum Infective Endocarditis With Brain Abscesses in a Lung Transplant Recipient: Review of the Literature and Evaluating the Use of Next-Generation Sequencing.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {8041837}, pmid = {42158572}, issn = {2090-6625}, abstract = {Scedosporium apiospermum is an emerging cause of invasive mold infection in immunocompromised hosts, often with central nervous system involvement and limited susceptibility to amphotericin B. We describe a 36-year-old lung transplant recipient who presented with fever, meningismus, and multiple enhancing brain lesions nine months post-transplant. Cerebrospinal fluid studies, including metagenomic next-generation sequencing (mNGS), were negative. Cardiac imaging revealed a pedunculated right ventricular septal mass, and plasma cell-free DNA (cfDNA) testing (Karius) identified S. apiospermum. Subsequent brain biopsy and thrombectomy confirmed the diagnosis by histopathology and culture. Following surgical removal of the cardiac mass and treatment with voriconazole, the patient improved with near resolution of brain lesions. This case highlights disseminated S. apiospermum endocarditis diagnosed by plasma cfDNA despite negative CSF mNGS, underscoring that site-specific mNGS may be falsely negative in compartmentalized infections. Plasma cfDNA testing can complement conventional and tissue-based diagnostics for early detection of disseminated mold infections in transplant recipients.}, }
@article {pmid42158968, year = {2026}, author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W}, title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71946}, pmid = {42158968}, issn = {2045-7634}, support = {82200151//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; }, abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.<br><br>METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.<br><br>CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.}, }
@article {pmid42159114, year = {2026}, author = {Li, Y and Liu, J and Hu, W and Li, C and Zhang, L and Qiu, S and Zhu, S}, title = {The Value of Second-Generation Metagenomic Sequencing in the Diagnosis of Respiratory Infections.}, journal = {Clinical laboratory}, volume = {72}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2025.250525}, pmid = {42159114}, issn = {1433-6510}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Bacteria/genetics/isolation &amp; purification ; Young Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: This study aimed to compare the results of metagenomic next-generation sequencing (mNGS) and conventional culture detection of pathogenic bacteria in bronchoalveolar lavage fluid (BALF) of patients with respiratory tract infections and analyze the influencing factors and clinical significance of mNGS positive detection.<br><br>METHODS: We retrospectively analyzed BALF samples from 90 respiratory infection patients at the First People's Hospital of Yongkang City from June 1, 2024, through January 28, 2025, using mNGS and conventional culture testing to compare the positivity rate, pathogen distribution, and consistency of the two methods. The relationship between mNGS detection positivity and clinical indicators of patients and patient prognosis was analyzed.<br><br>RESULTS: The positive rate of mNGS detection was 77.78%, while the positive rate of conventional culture detection was 44.44%, and the difference was statistically significant (p < 0.05). mNGS can detect a wider variety of pathogens, mainly gram-negative bacilli, fungi, and atypical pathogens. mNGS has moderate consistency with conventional culture detection results in bacteria, fungi, and atypical pathogens, but low consistency in viruses and para-sites. The positive detection of mNGS is related to factors such as patient age, underlying diseases, peripheral blood white blood cells, and C-reactive protein, which are risk factors affecting the positive detection of mNGS.<br><br>CONCLUSIONS: The pathogenic diagnosis of mNGS in BALF of patients with lower respiratory tract infections is su-perior to conventional culture detection; it can detect more and a wider range of pathogens, helping to promote rational drug use and improve patient prognosis in clinical practice.}, }
@article {pmid42159601, year = {2026}, author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y}, title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42159601}, issn = {2057-5858}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.}, }
@article {pmid42159642, year = {2026}, author = {Ortigoza, PYA and Luiz, FN and Ghellere, GJ and Meyer, RF and Rosa, LH and Passarini, MRZ}, title = {Biogas production using the microbial community present in the soil from Deception Island, maritime Antarctica.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {17}, pages = {8426-8435}, pmid = {42159642}, issn = {1614-7499}, support = {118/2024//Institutional Program to Support Research Groups/ ; 440218/2023-3//CNPq PROANTAR/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Methane/biosynthesis ; *Biofuels ; Archaea/genetics/metabolism/classification ; Islands ; }, abstract = {The current energy crisis is increasing the production of sustainable energy, such as biogas, a fuel generated by the anaerobic digestion of organic waste. The use of oat, an agricultural waste, makes the anaerobic digestion more sustainable. Antarctic microbial communities can utilize a wide range of substrates and adapt to different temperatures. Thus, this study evaluated methane production through an innovative approach, using microbial enrichment, and assessed archaeal diversity through metagenomic techniques in Antarctic soils, Deception Island, Maritime Antarctica. Metagenomic analyses showed low archaeal diversity and abundance. The Euryarchaeota (95.2%) and Methanobrevibacter were the most abundant and frequent phylum and genus, respectively. The average biogas production values were 595 LN kg VS[-][1] and 561 LN kg VS[-][1] in tests with individual oat (IO) and oat with enriched mixed culture (O + MC), respectively. However, O + MC showed a higher methane production, 4% (319 LN kg VS[-][1]) more than the results from the IO test with inoculum. Soils from Deception Island may represent a promising source of methanogenic communities capable of producing methane using agricultural waste as an alternative for energy production. Future studies are needed to understand the methane production using soil samples from cold environments.}, }
@article {pmid42159838, year = {2026}, author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA}, title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42159838}, issn = {1678-4405}, mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.}, }
@article {pmid42159959, year = {2026}, author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T}, title = {Animal gut microbes and microbiomes in the 21st century and beyond.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42159959}, issn = {1869-1889}, abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.}, }
@article {pmid42160933, year = {2026}, author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M}, title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142454}, doi = {10.1016/j.jhazmat.2026.142454}, pmid = {42160933}, issn = {1873-3336}, mesh = {*Polybrominated Biphenyls/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Anaerobiosis ; Aerobiosis ; Bacteria/metabolism/genetics ; }, abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.}, }
@article {pmid42161086, year = {2026}, author = {Ziliani, A and Bovio-Winkler, P and Pabst, M and Cabezas, A and Etchebehere, C and Garcia, HA and López-Vázquez, CM and Brdjanovic, D and van Loosdrecht, MCM and Rubio-Rincón, FJ}, title = {Glycine-mediated microbial interactions in biological phosphorus removal systems.}, journal = {Water research}, volume = {302}, number = {}, pages = {126057}, doi = {10.1016/j.watres.2026.126057}, pmid = {42161086}, issn = {1879-2448}, mesh = {*Phosphorus/metabolism/isolation &amp; purification ; *Glycine/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Carbon/metabolism ; *Microbial Interactions ; Wastewater ; }, abstract = {Amino acids are less studied substrates in enhanced biological phosphorus removal (EBPR) systems. Glycine, a prevalent amino acid in wastewater, was used in this study to evaluate its role in EBPR processes. We operated a sequencing batch reactor (SBR) for over three months with glycine as the sole carbon source to investigate phosphorus removal performance and microbial dynamics using chemical and molecular analyses. The reactor supported EBPR activity, with glycine enabling anaerobic phosphorus release followed by aerobic uptake. The dissolved organic carbon to phosphorus (DOC:P) removal ratio of 100:9.9 closely matched values reported for systems dominated by polyphosphate-accumulating organisms (PAOs), and net phosphorus removal (20 mg PO4-P L[-1]) fell within the range reported for laboratory-scale EBPR systems fed with mixed carbon sources. Community analyses showed enrichment of Saccharimonadales alongside putative PAOs, including Ca. Phosphoribacter and Ca. Propionivibrio. Genome-resolved analyses indicate distinct but complementary metabolic potentials, including glycine transformation and lactate-related pathways, suggesting distributed carbon processing within the community. Together, these findings expand the understanding of amino acid utilization in EBPR systems and identify potential metabolic linkages that influence phosphorus removal under glycine-fed conditions.}, }
@article {pmid42161088, year = {2026}, author = {Liu, Q and Zhang, Y and Gong, H and Zhou, S and Yang, J and Zhu, D and Huang, Z and Zhu, Y and Niu, H and Dai, X}, title = {Microbial-driven molecular transformation of dissolved organic matter in water-jet loom wastewater reclamation: An integrated FT-ICR MS and metagenomic investigation.}, journal = {Water research}, volume = {302}, number = {}, pages = {126124}, doi = {10.1016/j.watres.2026.126124}, pmid = {42161088}, issn = {1879-2448}, mesh = {*Wastewater/chemistry ; Bioreactors ; Metagenomics ; *Dissolved Organic Matter ; Waste Disposal, Fluid ; Mass Spectrometry ; }, abstract = {Water-jet loom wastewater, a major textile effluent in China, contains recalcitrant dissolved organic matter (DOM) derived from synthetic sizing agents and lubricants, whose incomplete removal constrains high-quality water reuse. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics provide high-resolution molecular and genetic insights, optimizing treatment efficacy remains hindered by a fragmented understanding of the intricate links between molecular transformations and their microbial drivers. This study established a reactomic-genomic paradigm coupling potential mass difference (PMD)-based molecular network analysis with metagenomic enzyme annotation in a full-scale membrane bioreactor (MBR) system (10000 m[3]·d[-1]). Over 8,000 molecular formulae were resolved across the treatment train. The results revealed that the dissolved air flotation unit prior to MBR selectively removed hydrophobic lipids and aliphatic/peptide-like compounds, leading to the relative enrichment of lignins/CRAM-like recalcitrant matter. The bioreactor served as the major zone of molecular turnover, with oxidation and depolymerization identified as the dominant transformation classes. These transformations were consistent with the enrichment of a Sphingomonadaceae-associated functional guild and abundant oxygenase-related genes, highlighting the role of microbial oxidation in aromatic transformation. Furthermore, a source-oriented framework revealed MBR effluent DOM as a spatially assembled mixture of three components. The recalcitrant influent-derived fraction dominated total effluent intensity (74.3%), while the bioreactor-emergent fraction constituted a consistent biogenic baseline (12.0%). In contrast, the membrane-associated emergent fraction contributed to molecular diversity (45.4% of unique formulae) but weakly to total intensity (9.7%). These findings indicate that the key challenge for high-quality reuse lies in controlling persistent and compositionally complex DOM. This framework provides a molecular basis for targeted process optimization and supports the transition of textile wastewater treatment from discharge compliance toward chemistry-informed reuse.}, }
@article {pmid42161089, year = {2026}, author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S}, title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.}, journal = {Placenta}, volume = {181}, number = {}, pages = {168-174}, doi = {10.1016/j.placenta.2026.05.010}, pmid = {42161089}, issn = {1532-3102}, mesh = {Female ; Humans ; Pregnancy ; *Placenta/virology ; *DNA, Viral/analysis ; *RNA, Viral/analysis ; Pre-Eclampsia/virology ; Adult ; *Virome ; Cesarean Section ; }, abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.<br><br>METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n&#x202f;=&#x202f;6), (2) delivered by emergency caesarean section (n&#x202f;=&#x202f;6), and (3) complicated by preeclampsia (n&#x202f;=&#x202f;5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.<br><br>RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.<br><br>CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.}, }
@article {pmid42161263, year = {2026}, author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {6}, pages = {1033-1049.e8}, pmid = {42161263}, issn = {1934-6069}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological/genetics ; DNA Methylation ; Fecal Microbiota Transplantation ; Infant ; *Bacteria/genetics/drug effects ; Metagenomics ; Probiotics ; Feces/microbiology ; Akkermansia ; }, abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.}, }
@article {pmid42161874, year = {2026}, author = {,  and , }, title = {[Expert consensus on laboratory diagnosis of inflammatory bowel disease (2026)].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {}, pages = {1-17}, doi = {10.3760/cma.j.cn112150-20260413-00324}, pmid = {42161874}, issn = {0253-9624}, support = {82472361//Natural Science Foundation of China/ ; }, abstract = {In recent years, the incidence of inflammatory bowel disease (IBD) in China has shown a significant upward trend. The invasive nature of colonoscopy limits its widespread application in population screening and long-term follow-up, while conventional laboratory parameters still suffer from insufficient sensitivity and specificity. A single test is inadequate for comprehensively assessing the complex pathophysiological processes of IBD. To enhance diagnostic efficacy, it is necessary to establish a multi-index combined evaluation system, integrating comprehensive assessments across dimensions such as inflammatory activity, nutritional metabolism, coagulation function, and infection risk. This consensus integrates relevant hematological and fecal laboratory markers, establishes a stratified application pathway covering initial screening, differential diagnosis, activity monitoring, and efficacy evaluation, and standardizes the clinical application scenarios of indicators such as fecal calprotectin (FC), the anti-Saccharomyces cerevisiae antibody (ASCA)/perinuclear anti-neutrophil cytoplasmic antibody (pANCA) panel, CRP (C-reactive protein)/ESR (erythrocyte sedimentation rate), and NLR (neutrophil-to-lymphocyte ratio). Furthermore, this consensus systematically reviews the clinical potential of cutting-edge technologies, including 16S amplicon sequencing, metagenomic sequencing, and microRNA detection, highlighting their significant prospects in analyzing microbial community structure, identifying occult pathogens, and assessing host regulation. This consensus aims to optimize non-invasive testing strategies for IBD, reduce misdiagnosis and improper treatment, and provide a standardized framework for tiered diagnosis and treatment as well as precision prevention and management.}, }
@article {pmid42162115, year = {2026}, author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, &#xc5;V and Walter, S and Simon, R}, title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42162115}, issn = {2045-2322}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; }, abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.}, }
@article {pmid42162191, year = {2026}, author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y}, title = {Author Correction: Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.}, journal = {NPJ digital medicine}, volume = {9}, number = {1}, pages = {}, doi = {10.1038/s41746-026-02769-1}, pmid = {42162191}, issn = {2398-6352}, }
@article {pmid42162287, year = {2026}, author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T}, title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42162287}, issn = {1432-8798}, support = {ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; }, mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation &amp; purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; }, abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.}, }
@article {pmid42162448, year = {2026}, author = {Bharadava, K and Makarani, N and Kaushal, RS}, title = {Co-selection of antimicrobial and heavy metal resistance in aquatic microbial communities at the water interface.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {8}, pages = {}, pmid = {42162448}, issn = {1573-2983}, mesh = {*Metals, Heavy/pharmacology/toxicity ; *Water Microbiology ; *Drug Resistance, Bacterial ; *Water Pollutants, Chemical ; Wastewater/microbiology ; *Drug Resistance, Microbial ; Humans ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; }, abstract = {Antimicrobial resistance (AMR) and heavy metal resistance (HMR) in aquatic ecosystems are increasing global health concerns driven by anthropogenic pollution of water systems. Municipal wastewater, hospital effluents, industrial discharge, agricultural runoff, and aquaculture activities contribute to the persistence and dissemination of resistant microorganisms and resistance genes in aquatic environments. Clinically important waterborne pathogens, including Escherichia coli, Salmonella Typhi, Shigella spp., and Vibrio cholerae, readily acquire resistance under continuous environmental stress conditions. Heavy metals further enhance AMR persistence through co-selection and cross-resistance mediated by mobile genetic elements carrying both antimicrobial and heavy metal resistance genes. This review summarizes the major environmental drivers, molecular mechanisms, and dissemination pathways associated with AMR-HMR interactions in aquatic systems. Recent advances in wastewater-based epidemiology, metagenomic surveillance, and resistance monitoring are highlighted as emerging tools for environmental and public health assessment. Current mitigation approaches, including advanced oxidation processes, membrane bioreactors, nanomaterial-based filtration, and microbial bioremediation, are also evaluated. A multidisciplinary One Health framework is essential for limiting environmental resistance dissemination and protecting human, animal, and ecosystem health.}, }
@article {pmid42162574, year = {2025}, author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E}, title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.}, journal = {Asian journal of anesthesiology}, volume = {63}, number = {1}, pages = {20-29}, doi = {10.6859/aja.202503_63(1).0003}, pmid = {42162574}, issn = {2468-824X}, mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; }, abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.<br><br>METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.<br><br>RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.}, }
@article {pmid42162897, year = {2026}, author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J}, title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.}, journal = {Veterinary journal (London, England : 1997)}, volume = {318}, number = {}, pages = {106706}, doi = {10.1016/j.tvjl.2026.106706}, pmid = {42162897}, issn = {1532-2971}, abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.}, }
@article {pmid42163161, year = {2026}, author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM}, title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-08132-8}, pmid = {42163161}, issn = {1471-244X}, abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.<br><br>METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.<br><br>RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p&#x2009;<&#x2009;0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.<br><br>CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).}, }
@article {pmid42163620, year = {2026}, author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y}, title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.}, journal = {Combinatorial chemistry &amp; high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073460107260407065758}, pmid = {42163620}, issn = {1875-5402}, abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.<br><br>METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl&#x2081;. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&amp;E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.<br><br>RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.<br><br>DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.<br><br>CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.}, }
@article {pmid42164149, year = {2026}, author = {Scutari, R and Fox, V and Mastropaolo, M and Fini, V and Mussa, M and Bigliano, P and Colagrossi, L and Vrenna, G and Perinzano, A and Scabini, S and Perno, CF and Calcagno, A}, title = {Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1791094}, pmid = {42164149}, issn = {2296-858X}, abstract = {Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1), Candida albicans, Enterococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for Mycobacterium species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of Fusarium pseudograminearum, Mycobacterium canettii, and Ralstonia sp., alongside low-level viral sequences [Epstein-Barr virus (EBV) and HSV-1]. These results reflected the patient's severe immune deficiency, characterized by a marked depletion of CD8[+] T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.}, }
@article {pmid42164154, year = {2026}, author = {Wang, S and Wang, X and Sun, K and Jin, Z and Ma, J}, title = {Pulmonary sarcoidosis complicated with pulmonary cryptococcosis: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1822801}, pmid = {42164154}, issn = {2296-858X}, abstract = {Pulmonary sarcoidosis is an idiopathic granulomatous disorder primarily affecting the lungs and mediastinal lymph nodes. Pulmonary cryptococcosis, an opportunistic mycosis caused by Cryptococcus species, may occur concurrently with sarcoidosis, presenting substantial diagnostic challenges, particularly in treatment-naïve patients. A 63-years-old previously healthy female presented with insidious-onset dyspnea and low-grade fever. Chest computed tomography (CT) showed mediastinal and hilar lymphadenopathy, accompanied by small nodules in the right lower lobe. She was diagnosed with pulmonary sarcoidosis at a local hospital and started on prednisone, with symptomatic improvement. However, follow-up imaging showed enlargement and cavitation of the right lower lobe nodules. Admission laboratory tests, including inflammatory markers and fungal serology, were all unremarkable. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified sequences of Cryptococcus neoformans. Histopathological examination of mediastinal lymph node specimens confirmed the presence of non-necrotizing granulomas, which is consistent with a diagnosis of sarcoidosis. Meanwhile, the right lower lobe lung biopsy revealed positive staining for Cryptococcus. The patient was treated with fluconazole, resulting in radiological resolution. This case highlights the importance of considering pulmonary cryptococcosis as a potential complication in treatment-naïve sarcoidosis patients who present with abnormal chest shadows. Underlying immune dysregulation in sarcoidosis may obscure both clinical and radiological findings, thereby complicating the diagnostic process.}, }
@article {pmid42164315, year = {2026}, author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG}, title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag105}, pmid = {42164315}, issn = {2730-6151}, abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.}, }
@article {pmid42164317, year = {2026}, author = {Domínguez-Huerta, G and Cabello, AM and Santos-Bruña, JJ and Mercado, JM and Ferrera, I}, title = {Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag110}, pmid = {42164317}, issn = {2730-6151}, abstract = {Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon's prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.}, }
@article {pmid42164318, year = {2026}, author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A}, title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag106}, pmid = {42164318}, issn = {2730-6151}, abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.}, }
@article {pmid42164663, year = {2026}, author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J}, title = {What a pickle-a metagenomic perspective on the cucumber fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809866}, pmid = {42164663}, issn = {1664-302X}, abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.}, }
@article {pmid42164669, year = {2026}, author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z}, title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1670904}, pmid = {42164669}, issn = {1664-302X}, abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.}, }
@article {pmid42165181, year = {2026}, author = {Zhang, B and Zhang, J and Duan, F and Xuan, Z and Sun, T and Lu, L}, title = {Enzymatic Galactosylation of Erythritol Enhances Antibacterial Activity against Cariogenic Streptococcus mutans.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {21}, pages = {16527-16538}, doi = {10.1021/acs.jafc.5c14195}, pmid = {42165181}, issn = {1520-5118}, mesh = {*Streptococcus mutans/drug effects/genetics/physiology/growth &amp; development ; *Erythritol/chemistry/pharmacology/metabolism ; *beta-Galactosidase/genetics/metabolism/chemistry ; *Anti-Bacterial Agents/pharmacology/chemistry/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Dental Caries/microbiology ; Biofilms/drug effects ; *Galactose/metabolism ; Escherichia coli/genetics/metabolism ; }, abstract = {Erythritol is a widely used sweetener with beneficial properties and bioactivities, including the inhibition of Streptococcus mutans, a bacterium that induces dental caries. Galactosylation of compounds is an attractive method for improving antimicrobial activity. In this study, a novel metagenomic β-galactosidase gene, bga7, was successfully expressed in Escherichia coli. The recombinant enzyme was used to galactosylate erythritol, generating a high yield (93.6%) of galactoside product at a concentration of 2 U/mL upon incubation with 20 mM o-nitrophenyl-β-d-galactopyranoside and 0.5 M erythritol at 40 °C and pH 9.0 for 4 h. The product was confirmed to be β-galactosyl-erythritol by MS and NMR analysis. This galactoside demonstrated significantly enhanced inhibition of both the planktonic growth of S. mutans and biofilm formation compared to erythritol alone. Further investigation into the mechanism revealed that the galactoside suppressed the transcriptional levels of four important genes (gtfB, ftf, srtA, and spaP) associated with bacterial adhesion and biofilm formation.}, }
@article {pmid42165232, year = {2026}, author = {Nap, B and Thinnes, CC and Thiele, I}, title = {Whole-body metabolic modelling and its prospects in precision nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/S0029665126103061}, pmid = {42165232}, issn = {1475-2719}, abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.}, }
@article {pmid42165805, year = {2026}, author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM}, title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42165805}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; }, abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.}, }
@article {pmid42165964, year = {2026}, author = {Chen, S and Hua, Y and Chen, D and Jiang, X}, title = {Laboratory diagnosis of brucellosis: evolving synergy between serological testing and next-generation sequencing.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42165964}, issn = {1435-4373}, abstract = {BACKGROUND: Brucellosis is an animal‑to‑human infection that is hard to identify in practice; its signs are vague and the laboratory tools used in routine care have clear limits. Bacterial culture is regarded as the reference test; the procedure is slow and has modest sensitivity, and in many hospitals clinicians rely mainly on serologic assays when they make a diagnosis. Over the past decade clinical microbiology laboratories have increasingly used next‑generation sequencing (NGS) as a tool for pathogen identification, especially metagenomic NGS (mNGS). In patients with suspected bru-cellosis clinicians and laboratory staff often see a mismatch between test results, with serological assays suggesting infection but NGS reports failing to detect Brucella, a gap between serology and sequencing that remains a frequent and unresolved problem in routine diagnosis.<br><br>OBJECTIVE: This review brings together available data on how serological tests and sequencing-based methods in both metagenomic and targeted formats contribute to the laboratory diagnosis of human brucellosis and where they fall short.<br><br>CONCLUSION: It describes biological and technical sources of false-positive serology and false-negative sequencing and sets out a practical integrated way to judge and confirm mismatched findings so that laboratories and clinicians can use conventional and molecular tools together and reach sound decisions when brucellosis is suspected.}, }
@article {pmid42166146, year = {2026}, author = {Besteman, MS and Alaux, E and Doloman, A and Tahon, G and Ettema, TJG and Sousa, DZ}, title = {Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42166146}, issn = {1574-6941}, support = {0.24.002.002//Ministry of Education, Culture and Science, Netherlands/ ; VI.C.192.016/NWO_/Dutch Research Council/Netherlands ; 817834/ERC_/European Research Council/International ; }, mesh = {*Metagenomics ; Anaerobiosis ; *Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; Fatty Acids/metabolism ; *Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/metabolism ; }, abstract = {Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate, and acetate. This analysis identified multiple interesting novel targets, including the families DTU052 and CALXsZ01 (class Syntrophomonadia) as potential butyrate oxidizers; the families UBA6807, PHBD01, FEN-1087, and FEN-1099 (class Syntrophia) as potential propionate oxidizers; and genus DTU068 (family Thermacetogeniaceae) together with the family-level lineage 4572-78 (phylum Chloroflexota) as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.}, }
@article {pmid42166340, year = {2026}, author = {Sato, M and Kanaly, RA and Mori, JF}, title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42166340}, issn = {1465-2080}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth &amp; development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth &amp; development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; }, abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.}, }
@article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; }, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, }
@article {pmid42166998, year = {2026}, author = {Wu, Q and Zheng, Y and Xia, Y and Ge, C and Deng, H and Zhao, Y and Luo, J and Feng, D}, title = {Decoding the seagrass plastisphere: Metagenomic insights into biogeochemical cycling of biogenic elements and ecological consequences.}, journal = {Environment international}, volume = {212}, number = {}, pages = {110311}, doi = {10.1016/j.envint.2026.110311}, pmid = {42166998}, issn = {1873-6750}, mesh = {Carbon/metabolism ; Ecosystem ; *Metagenome ; Metagenomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Sulfur/metabolism ; Aquatic Organisms ; *Water Pollutants/metabolism ; *Hydrocharitaceae/genetics/metabolism ; Plastics/metabolism ; *Water Microbiology ; }, abstract = {Seagrass meadow, a crucial blue carbon ecosystem, is increasingly threatened by plastic pollution. Plastic debris in this sensitive ecosystem creates a new microbial habitat known as "plastisphere". However, the functional role of plastisphere, particularly in driving the cycling of key biogenic elements, remains poorly understood. This knowledge gap raises concerns over potential disruptions to elemental fluxes and subsequent ecological consequences. Here, metagenomic analysis was employed to investigate the metabolic profile of in-situ plastisphere in seagrass meadow, with particular focus on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) biotransformation. The obtained results revealed that plastisphere microbes were taxonomically distinct from those in natural environments of the seagrass meadow, and these inhabitants were capable of driving diverse metabolic pathways. However, >75% functional gene similarity indicated a significant functional overlap between the plastisphere and natural environments. This niche enriched genes related to heterotrophic organic C degradation (27.71% ± 3.28%) and oxidation (17.86% ± 2.04%) pathways, organic N metabolism (62.18% ± 8.57%) mainly through GS-GOGAT pathways and denitrification (8.70% ± 4.06%), polyphosphate degradation (22.89% ± 2.20%) and organic P mineralization (17.50% ± 1.70%), as well as assimilatory/dissimilatory sulfate reduction (30.60% ± 3.49%) and thiosulfate disproportionation (13.57% ± 2.89%) metabolic pathways. Metabolic linkage within seagrass plastisphere was facilitated by highly connected taxa including Silicimonas and Erythrobacter, which linked electron-donating processes (including organic C degradation and S oxidation) to electron-accepting pathways (e.g., sulfate/nitrate reduction, C fixation). These interactions established the plastisphere as a potential biogeochemical hotspot, potentially amplifying the risks of CO2/N2O emission, H2S accumulation, nutrient competition with seagrass and potential eutrophication from imbalanced P mobilization, ultimately threatening the health and stability of seagrass ecosystem.}, }
@article {pmid42167281, year = {2026}, author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC}, title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70327}, doi = {10.1111/1462-2920.70327}, pmid = {42167281}, issn = {1462-2920}, support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; }, mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; }, abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.}, }
@article {pmid42167521, year = {2026}, author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L}, title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {402}, number = {}, pages = {128381}, doi = {10.1016/j.envpol.2026.128381}, pmid = {42167521}, issn = {1873-6424}, mesh = {*Wetlands ; *Anti-Bacterial Agents/analysis ; *Waste Disposal, Fluid/methods ; Wastewater/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; *Genes, Bacterial ; Bacteria/genetics ; }, abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.}, }
@article {pmid42167540, year = {2026}, author = {Wang, W and Liu, H and Jiang, K and Posum, W and Lu, Z and Chen, X}, title = {A rare case of Porphyromonas endodontalis lung abscess mimicking lung cancer on imaging: the diagnostic value of postoperative metagenomic next-generation sequencing.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {169}, number = {}, pages = {108821}, doi = {10.1016/j.ijid.2026.108821}, pmid = {42167540}, issn = {1878-3511}, mesh = {Humans ; Male ; *Lung Abscess/microbiology/diagnosis/diagnostic imaging/surgery ; *Lung Neoplasms/diagnosis/diagnostic imaging ; Aged ; Diagnosis, Differential ; High-Throughput Nucleotide Sequencing ; *Bacteroidaceae Infections/diagnosis/microbiology/diagnostic imaging ; *Porphyromonas endodontalis/genetics/isolation &amp; purification ; Metagenomics ; Tomography, X-Ray Computed ; }, abstract = {This case highlights the diagnostic challenge of a Porphyromonas endodontalis lung abscess mimicking lung cancer. A 67-year-old male presented with a right lower lobe mass suggestive of malignancy. Following wedge resection, pathology confirmed an abscess. Metagenomic next-generation sequencing (mNGS) of the tissue revealed a microbial profile dominated by oral anaerobes of Porphyromonas endodontalis. Postoperative mNGS identified the oral origin of infection and prompted periodontal treatment, leading to full recovery. This report reveals the decisive value of postoperative mNGS in correcting a diagnosis of infection mimicking lung cancer. It emphasizes that oral anaerobic infections can present as "tumor-like" pulmonary lesions. This case suggests that oral infection sources should be considered in the differential diagnosis of challenging pulmonary lesions and highlights the potential value of a multidisciplinary approach that includes dental evaluation.}, }
@article {pmid42167986, year = {2026}, author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S}, title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.}, journal = {Journal of the World federation of orthodontists}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ejwf.2026.03.003}, pmid = {42167986}, issn = {2212-4438}, abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.<br><br>METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.<br><br>RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri&#x2011;implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).<br><br>CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri&#x2011;implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.}, }
@article {pmid42168196, year = {2026}, author = {Bowie, KR and Luhung, I and Burke, TR and Roberts, SC and Martinello, RA and Gerstein, M and Peccia, J and Healy, HG}, title = {Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73533-y}, pmid = {42168196}, issn = {2041-1723}, support = {1S10OD030363-01A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas. Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.}, }
@article {pmid42168704, year = {2026}, author = {Zhang, X and Mallick, H and Rahnavard, A}, title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {42168704}, issn = {2730-664X}, support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.<br><br>METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.<br><br>RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.<br><br>CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.}, }
@article {pmid42168837, year = {2026}, author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T}, title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05157-7}, pmid = {42168837}, issn = {1471-2180}, support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; }, abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.}, }
@article {pmid42168845, year = {2026}, author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P}, title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05168-4}, pmid = {42168845}, issn = {1471-2180}, support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; }, abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.}, }
@article {pmid42169289, year = {2026}, author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I}, title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119324}, doi = {10.1016/j.foodres.2026.119324}, pmid = {42169289}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; }, abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.}, }
@article {pmid42169351, year = {2026}, author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S}, title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119400}, doi = {10.1016/j.foodres.2026.119400}, pmid = {42169351}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; *Metagenomics/methods ; Fermentation ; *Whey/microbiology ; *Food Microbiology ; Biogenic Amines/analysis ; China ; Milk/microbiology ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.}, }
@article {pmid42169753, year = {2026}, author = {Song, D and Zhong, X and Zhang, G and Chen, J and Xue, Y and Yang, L}, title = {Linking geographic flavor signatures to microbial origin in high-temperature Daqu: An integrated metaproteomics and metabolomics approach.}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103952}, pmid = {42169753}, issn = {2590-1575}, abstract = {Elucidating the molecular architecture of microbial terroir is vital for precision fermentation, yet functional decoupling between taxonomic abundance and in situ expression remains a fundamental challenge. To resolve this "abundance-activity paradox," we integrated metaproteomics, metabolomics, and metagenomics across the Chishui River gradient. We identified distinct chemosensory fingerprints: upstream thermotolerant consortia (Bacillus and Oceanibacillus) specialize in 2,3,5,6-tetramethylpyrazine biosynthesis mediated by bacterial acetolactate decarboxylase, while downstream microbiota (Weissella and Debaryomyces) prioritize alcohol and ester formation. Crucially, metaproteomic profiling unmasked the "rare biosphere" as a primary driver of core metabolic fluxes. While Bacillus was genomically dominant, keystone functional taxa-specifically low-abundance fungi like Hyphopichia and Paecilomyces-were the actual executors of rate-limiting starch hydrolysis. Furthermore, functional resilience was uniquely maintained through robust fungal co-occurrence networks despite geographic constraints. This study challenges abundance-centric paradigms, providing an activity-based framework for the rational design of synthetic microbial consortia to standardize flavor while preserving regional identity.}, }
@article {pmid42169756, year = {2026}, author = {Chen, Y and Yu, K and Sun, Y and Yan, Y and Yin, G and Wang, J and Li, X and Tang, S and Pronyk, P and Xia, Y}, title = {Plastic leachates drive conjugative transfer of antibiotic resistance genes.}, journal = {Environmental science and ecotechnology}, volume = {31}, number = {}, pages = {100705}, pmid = {42169756}, issn = {2666-4984}, abstract = {Plastic pollution pervades aquatic ecosystems worldwide, releasing leachates that interact intimately with microbial communities. Antibiotic resistance genes (ARGs) disseminate rapidly through horizontal gene transfer via plasmid conjugation, posing a severe and accelerating threat to public health and environmental stability. While microplastic particles are known to promote ARG exchange within biofilms, the influence of soluble chemical leachates derived from degrading plastics has remained unclear. Here we show that photodegraded leachate from polyvinyl chloride (PVC)-a widely used material in water infrastructure-substantially enhances conjugative transfer of ARGs in both laboratory model systems and natural aquatic microbiomes. Exposure increased transconjugant abundance up to 26.4-fold and conjugation efficiency up to 44.6-fold, with non-monotonic responses modulated by leachate concentration and microbial community diversity. Characterization of the leachate revealed high proportions of biolabile dissolved organic matter alongside additives; mechanistic assays demonstrated that these effects arise through elevated intracellular reactive oxygen species (21% increase), activation of the SOS response and DNA-repair pathways, increased extracellular protein production facilitating cell-cell contact, and compensatory adjustments in the electron transport chain that maintain ATP homeostasis. These results demonstrate that plastic leachates act as potent but previously overlooked facilitators of ARG dissemination beyond the physical effects of microplastics. Our findings reveal a critical synergy between plastic pollution and the global antimicrobial-resistance crisis, underscoring the urgent need for targeted regulations on plastic additives and degradation products in aquatic systems.}, }
@article {pmid42170025, year = {2026}, author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H}, title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag129}, pmid = {42170025}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.<br><br>RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210&#xa0;000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.<br><br>PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.}, }
@article {pmid42170880, year = {2026}, author = {Ershova-Menze, E and Westgaard, JI and Hjellnes, H and Falkenhaug, T}, title = {Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70149}, doi = {10.1111/1755-0998.70149}, pmid = {42170880}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Zooplankton/genetics/classification ; Animals ; Biodiversity ; DNA/genetics/isolation &amp; purification ; *Metagenomics/methods ; Electron Transport Complex IV/genetics ; }, abstract = {DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.}, }
@article {pmid42171141, year = {2026}, author = {Tagliamonte, S and Neill, HR and Murphy, B&#xd3; and Pourshahidi, KL and De Filippis, F and Ercolini, D and Gill, CIR and Natalia, K and Curran, B and Nicole, M and Mary, S and Dobani, S and Fontana, M and Vitaglione, P}, title = {Dietary N-acylethanolamines are bioaccessible in the small intestine and modulate postprandial hormonal responses: a randomized crossover trial in subjects with ileostomy.}, journal = {Food &amp; function}, volume = {17}, number = {11}, pages = {5106-5117}, doi = {10.1039/d5fo03328d}, pmid = {42171141}, issn = {2042-650X}, mesh = {Humans ; Female ; Postprandial Period ; Male ; Cross-Over Studies ; *Ileostomy ; Double-Blind Method ; Middle Aged ; *Ethanolamines/metabolism/administration &amp; dosage ; *Intestine, Small/metabolism ; Adult ; Aged ; Endocannabinoids ; Blood Glucose/metabolism ; *Gastrointestinal Hormones/metabolism ; }, abstract = {N-Acylethanolamines (NAEs) are bioactive lipid mediators involved in the regulation of appetite, inflammation, and gut-brain signaling. This study investigated the metabolic fate of dietary NAEs following the consumption of two test meals with differing NAE contents in subjects with ileostomy and evaluated their effects on gastrointestinal hormones, glycaemia, and appetite regulation. An acute, double-blind, randomized, crossover postprandial study was conducted in ileostomy patients who consumed either a high-NAE meal (HNM) or a low-NAE meal (LNM) on two separate occasions. Ileal fluid and plasma samples were collected over an 8-hour postprandial period for analysis of NAEs and endocannabinoids (ECs). Baseline ileal microbiota composition was assessed. At the end of the 8-hour period, participants completed a buffet meal test to evaluate ad libitum energy intake. Dietary NAEs were significantly recovered in ileal fluids after HNM intake, with concentrations approximately 3-fold higher than those after LNM, suggesting partial digestion and release from the food matrix. No significant differences in postprandial plasma NAE concentrations were observed between meals. HNM consumption led to higher postprandial levels of plasma insulin, C-peptide, and glucose-dependent insulinotropic polypeptide, despite no differences in glycemic response or subsequent ad libitum energy intake. Metagenomic analysis identified clusters of ileal microbial taxa associated with circulating lipid profiles, suggesting a role of the small intestinal microbiota in the metabolism of NAEs and ECs. Dietary NAEs reach the small intestine at active concentrations and may influence local signaling via GPR119, with microbiota composition influencing their release from food.}, }
@article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030526}, doi = {10.1128/msystems.00305-26}, pmid = {42171373}, issn = {2379-5077}, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, }
@article {pmid42171625, year = {2026}, author = {Paietta, EN and Johnston, RA and Kraberger, S and Randrianarisoa, SF and Razanamahenina, TT and Ramboninarimalala, A and Velontsara, JB and Raherinirina, TG and Raveloson, L and Finley, NL and Baitchman, E and McAdoo, BG and Yoder, AD and Varsani, A}, title = {Mammal-infecting DNA viruses identified in lemurs and rodents in Madagascar mirror the evolutionary history of their hosts.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42171625}, issn = {2057-5858}, mesh = {Animals ; Madagascar ; *Lemur/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Rodentia/virology ; Rats/virology ; Metagenomics ; Genome, Viral ; }, abstract = {Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, Parvoviridae and Polyomaviridae and assessed their phylogenetic relationships to known viruses. Endemic lemurs and tufted-tailed rats displayed particularly novel DNA viral diversity mirroring the geographic isolation and subsequently rich evolutionary history of their hosts. Notably, we provide the first coding-complete sequences in lemurs of herpesviruses, polyomaviruses, adeno-associated viruses and circoviruses. In contrast, the DNA viral communities of black rats in Madagascar were similar to those found in globally distributed black and brown rat populations, given their broad geographic spread and relatively recent introduction to the island. Given the scarcity of viral research in natural populations of lemurs and rodents in Madagascar despite the island's exceptional biodiversity and escalating anthropogenic pressures, this study provides a genomic and phylogenetic foundation for DNA viruses infecting Malagasy lemurs and rodents.}, }
@article {pmid42171661, year = {2026}, author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R}, title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42171661}, issn = {1751-7370}, support = {BBX011089/1//UK Research and Innovation/ ; NE/S005137/1//UK Research and Innovation/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/classification/genetics ; Grassland ; Metagenomics ; United Kingdom ; Ecosystem ; Biodiversity ; }, abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions towards metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterized by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.}, }
@article {pmid42171933, year = {2026}, author = {Xu, Y and Sun, X and Xu, S and Deng, S and Zhang, Y}, title = {Clinical profile of microsporidial keratoconjunctivitis in healthy individuals of China -new species and neglected risk factors.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00596-9}, pmid = {42171933}, issn = {1869-5760}, abstract = {OBJECTIVE: To characterize microsporidial keratoconjunctivitis (MKC) in immunocompetent individuals in Mainland China, including novel etiologies and risk factors.<br><br>METHODS: A prospective analysis of 20 MKC patients in 2025, including clinical features, pathogens (via corneal scrapings and metagenomic sequencing), risk factors and etc. RESULTS: All patients were misdiagnosed for a median of 1 month. Patients (mean age 28.5 years, 13 F) showed Encephalitozoon hellem (65.0%), E. bieneusi (15.0%, first reported in MKC), and Vittaforma corneae (15.0%). Key risks included bird contact (70.0%, mostly psittacines), contact lens use (40.0%), and water exposure (15.0%). The most common symptom was redness (85.0%); limbal fluorescein positivity occurred in 65.0%. Topical 0.02% PHMB cured 90.0% of 20 cases; one recurrence followed treatment stop. Some E. hellem cases linked to parrots showed potential zoonotic transmission.<br><br>CONCLUSION: MKC in China involves E. bieneusi and parrot-associated E. hellem. Limbal staining aids diagnosis; PHMB is effective. Zoonotic risks related to Psittacine birds and contact lens use require clinical attention.}, }
@article {pmid42172047, year = {2026}, author = {Delgado, LF and Ortís Sunyer, J and Laczny, CC and Hickl, O and May, P and Wilmes, P}, title = {PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {42172047}, issn = {2047-217X}, support = {C23/BM/18091896//Luxembourg National Research Fund/ ; ERC-CoG 863664/ERC_/European Research Council/International ; }, mesh = {*Virulence Factors/genetics ; *Multigene Family ; *Metagenome ; *Software ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; *Computational Biology/methods ; Bacterial Toxins/genetics ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.<br><br>FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGCs) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting BGCs.<br><br>CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.}, }
@article {pmid42172141, year = {2026}, author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S}, title = {Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42172141}, issn = {1758-0463}, support = {/CA/NCI NIH HHS/United States ; U24CA289073/NH/NIH HHS/United States ; 3U24CA180996-10S1/NH/NIH HHS/United States ; }, mesh = {*Metadata/standards ; Humans ; *Data Curation/methods ; *Neoplasms/genetics ; *Databases, Genetic ; *Metagenomics ; *Genomics ; }, abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective harmonization. We performed comprehensive manual curation and harmonization of metadata, such as participant characteristics and study conditions, from 212 027 omics samples across 468 studies in two repositories: curatedMetagenomicData (93 studies, 22 588 samples) and cBioPortal (375 studies, 189 438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into far fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions during this large-scale metadata harmonization. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.}, }
@article {pmid42172324, year = {2026}, author = {Freschlin, CR and Yang, KK and Romero, PA}, title = {Scalable and cost-efficient custom gene library assembly from oligopools.}, journal = {Science advances}, volume = {12}, number = {21}, pages = {eady2279}, pmid = {42172324}, issn = {2375-2548}, support = {R01 GM150929/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Library ; Software ; *Oligonucleotides/genetics ; Computational Biology/methods ; }, abstract = {Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.}, }
@article {pmid42172586, year = {2026}, author = {Singh, R and Gupta, P and Singh, R and Basant, N}, title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/etojnl/vgag115}, pmid = {42172586}, issn = {1552-8618}, abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.}, }
@article {pmid42172842, year = {2026}, author = {Chen, X and Tan, QG and Pan, K and Xiao, A and Cheng, H and Wang, X}, title = {Vegetation of exotic fast-growing species Sonneratia apetala increases the potential of methylmercury production: Insights from carbon bioavailability, microbial metabolism and mercury methylators.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142469}, doi = {10.1016/j.jhazmat.2026.142469}, pmid = {42172842}, issn = {1873-3336}, mesh = {*Methylmercury Compounds/metabolism ; *Carbon/metabolism ; Geologic Sediments/microbiology/chemistry ; Methylation ; Bacteria/metabolism/genetics ; China ; }, abstract = {Mangrove sediments are hotspots for neurotoxic methylmercury (MeHg) production, with litter-derived organic carbon strongly affecting mercury (Hg) methylation. However, the specific role of carbon bioavailability in regulating net MeHg production remains unclear. This study investigated sediments vegetated by exotic fast-growing Sonneratia apetala (SA) and native Kandelia obovata (KO) in southern China. Contrary to the expectation that larger carbon pools enhance methylation, MeHg levels were 2.1-2.6 times higher in SA sediments despite KO containing 1.2-4.2 times more total organic carbon. This disparity was driven by carbon bioavailability: SA sediments exhibited a significantly higher proportion of available carbon (34-50%) compared to KO (28-36%), which stimulated microbial activity and enriched Hg-methylating microbes (1.4-3.3 times higher in hgcAB gene abundance). Metagenomics showed that SA not only promoted key Hg-methylating taxa (e.g., Desulfobacterales, Syntrophobacteria) but also upregulated their metabolic pathways for labile carbon use and methyl transfer to Hg. Our results demonstrate that carbon bioavailability, governed by species-specific litter chemistry, is the key driver of net MeHg production. The findings provide an in-depth understanding of Hg biogeochemistry by linking soil carbon quality to microbial metabolic networks, and offer novel insights for evaluating the ecological risks associated with exotic species in mangrove restoration.}, }
@article {pmid42172844, year = {2026}, author = {Xu, Y and Xie, T and Zhong, W and Yang, G and Zhang, W}, title = {Probable disseminated Mycobacterium avium complex infection in an apparently immunocompetent patient: A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {7}, pages = {103245}, doi = {10.1016/j.jiph.2026.103245}, pmid = {42172844}, issn = {1876-035X}, mesh = {Humans ; *Mycobacterium avium-intracellulare Infection/diagnosis/drug therapy/microbiology/pathology ; *Mycobacterium avium Complex/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; Osteomyelitis/microbiology/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Immunocompetence ; Skin Ulcer/microbiology ; Male ; }, abstract = {Disseminated Mycobacterium avium complex (MAC) infection is rare in immunocompetent hosts. This often leads to diagnostic delays. We report a challenging case of an apparently immunocompetent patient with pulmonary lesions, osteomyelitis, and skin ulcers. While routine cultures were pending, metagenomic next-generation sequencing (mNGS) rapidly identified MAC, enabling timely treatment. Subsequent culture and species identification confirmed the pathogen as Mycobacterium colombiense. Systematic reviews since 2000 have shown that skeletal and pulmonary involvement are common in this population. Diagnosis has gradually incorporated molecular biological techniques, and with timely treatment, patient outcomes are generally favorable. Our findings highlight the limitations of traditional microbiology and demonstrate that mNGS is a vital adjunctive tool for slow-growing pathogens. We conclude that disseminated MAC should be considered in refractory multifocal infections, even without recognized immunodeficiencies. Early molecular diagnosis, individualized multidrug therapy, and rigorous follow-up are essential for clinical remission.}, }
@article {pmid42172850, year = {2026}, author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R}, title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130036}, doi = {10.1016/j.jenvman.2026.130036}, pmid = {42172850}, issn = {1095-8630}, mesh = {Tibet ; *Wastewater/microbiology ; RNA, Ribosomal, 16S ; *Waste Disposal, Fluid ; *Microbiota ; Bacteria ; Altitude ; Metagenomics ; }, abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.}, }
@article {pmid42172982, year = {2026}, author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C}, title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158288}, doi = {10.1016/j.phymed.2026.158288}, pmid = {42172982}, issn = {1618-095X}, mesh = {Animals ; Homeostasis/drug effects ; Male ; *Zonula Occludens-1 Protein/metabolism ; *Bile Acids and Salts/metabolism ; Liver/drug effects/metabolism ; Rats ; Rats, Sprague-Dawley ; *Quinazolines/pharmacology ; *Cholestasis/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Liver Diseases/drug therapy/metabolism ; }, abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.<br><br>OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.<br><br>METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and &#x3b1;-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.<br><br>RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.<br><br>CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.}, }
@article {pmid42173380, year = {2026}, author = {Du, S and Ding, S and Zhao, Y and Wang, Y and Ju, F and Wu, D}, title = {Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134949}, doi = {10.1016/j.biortech.2026.134949}, pmid = {42173380}, issn = {1873-2976}, mesh = {*Oxygen/metabolism/pharmacology ; *Acetates/toxicity ; *Composting/methods ; Aerobiosis ; Germination/drug effects ; *Metagenomics/methods ; }, abstract = {Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.}, }
@article {pmid42173516, year = {2026}, author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A}, title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {331}, number = {1}, pages = {G38-G59}, doi = {10.1152/ajpgi.00056.2026}, pmid = {42173516}, issn = {1522-1547}, support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Tumor Escape/drug effects ; Male ; Mice ; *Bile Acids and Salts ; Dysbiosis/chemically induced ; STAT1 Transcription Factor/metabolism ; Wnt1 Protein/genetics/metabolism ; STAT3 Transcription Factor/metabolism ; Disease Progression ; B7-H1 Antigen/metabolism ; Humans ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Mice, Inbred C57BL ; Interferon-gamma/metabolism ; }, abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes tumorigenesis, we evaluated the effects of HFD + ABS ± ABx treatment on tumor immune evasion in mice. In HFD + ABS + ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1, and programmed cell death-ligand 1 (PD-L1) was observed, along with apoptosis suppression. Protein expressions of interferon-gamma (IFNγ) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD + ABS + ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFNγ stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1, and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD + ABS + ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFNγ-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.NEW &amp; NOTEWORTHY Coadministration of antibiotics with a high-fat diet and acid bile salts exacerbated dysbiosis, insulin resistance, and systemic inflammation, thereby promoting tumor progression via tumor immune evasion at the squamocolumnar junction (SCJ) in K19-Wnt1/C2mE mice. In the tumor, interferon-gamma-induced programmed death-ligand 1 through the activation of signal transducer and activator of transcription 1 (STAT1) and STAT3. Understanding the link between dysbiosis and tumor immunity might aid in the development of new immunotherapies for SCJ tumors.}, }
@article {pmid42173938, year = {2026}, author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE}, title = {Metagenomic survey of pathogen prevalence in the infant gut.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47440-7}, pmid = {42173938}, issn = {2045-2322}, support = {101039583//ERC Starting Grant/ ; }, abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.}, }
@article {pmid42174003, year = {2026}, author = {Kumari, R and Ghosh, C and Kumar, R and Shakya, R and Kumar, S and Saini, AK}, title = {Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53672-4}, pmid = {42174003}, issn = {2045-2322}, support = {project grant MH-32/2024//R&amp;D cell, Miranda House, University of Delhi, India/ ; }, abstract = {Lack of regular monitoring of water sources may lead to undetected contamination, posing serious health risks and necessitating regular water quality assessments. Sampling for physicochemical, microbial analyses, and online surveys across three higher education institutions was done to evaluate water quality. Spatiotemporal variations among physicochemical parameters showed that the pH, EC, and TDS decreased during the wet season, reflecting the dilution effect of rain. However, DO increased from 0.67 to 4.83 ppm, indicating better aeration. PCA showed seasonal variability, whereas the correlation matrix highlighted both positive and negative interrelationships between temperature-pH (- 0.25), DO-ORP (0.11), and TDS-EC (1.00). Potentially toxic metals were either negligible or not detected. Metagenomics revealed the presence of 29 bacterial phyla, 61 classes, 124 orders, 241 families, and 457 genera. Canonical correspondence analysis showed the influence of Mo, EC, salinity, and TDS on Bacteroidota, Chloroflexota, Cyanobacteriota, and Planctomycetota, whereas Verrucomicrobiota, Acidobacteriota, Chlamydiota, Candidatus Melainabacteria, Bdellovibrionota, and Deinococcota were affected by Ni, pH, and COD. Pathogen mapping revealed the presence of Vibrio, Pseudomonas, Enterobacter spp., etc., responsible for diseases such as cholera, diarrhea, and typhoid. Also, occupants' perception about the water quality emphasizes the need for better management of drinking water in HEIs.}, }
@article {pmid42174021, year = {2026}, author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W}, title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53556-7}, pmid = {42174021}, issn = {2045-2322}, abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.}, }
@article {pmid42174437, year = {2026}, author = {van Bemmelen, J and Nika, I and Baaijens, JA}, title = {Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12874-w}, pmid = {42174437}, issn = {1471-2164}, abstract = {BACKGROUND: Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by selecting a subset of genomes as references, insights regarding the impact of different reference genome selection methods across taxonomic classification tools are lacking.<br><br>RESULTS: We systematically evaluate genome selection and dereplication methods on bacterial and viral datasets using simulated metagenomic samples and a bacterial mock community. For bacterial species-level profiling, incorporating all available genomes generally yields the highest accuracy, while having a limited impact on computational resource usage. In contrast, for highly similar bacterial strain-level and SARS-CoV-2 lineage-level datasets we find that selection significantly improves abundance estimation accuracy. Incorporating location-based metadata further enhances viral profiling performance by prioritizing locally relevant genomes. Across viral experiments, smaller reference sets significantly reduce memory and runtime requirements during both indexing and profiling, although this comes at an additional pre-processing cost.<br><br>CONCLUSIONS: Reference genome selection influences both accuracy and computational efficiency in taxonomic profiling, but its benefits seem context- and resolution-dependent. Our results demonstrate that reference set design does not have a one-size-fits-all solution, and that selection strategies should be adapted based on the biological and computational setting.}, }
@article {pmid42174665, year = {2026}, author = {Nolan, S and Trego, A and Waters, N and Thorn, C and Fenton, O and Richards, KG and O'Flaherty, V and Ijaz, UZ and Abram, F}, title = {Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00902-x}, pmid = {42174665}, issn = {2524-6372}, support = {14 F847//Irish Department of Agriculture, Food and Marine/ ; }, abstract = {BACKGROUND: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L[-1] d[-1] was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L[-1] d[-1] OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.<br><br>RESULTS: After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (<&#x2009;1000&#xa0;CFU&#xa0;g[-1]). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.<br><br>CONCLUSIONS: Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts in microbial pathways, underpinning the simultaneous improvement in methane production and E. coli removal. While further research is required to assess the impact of the observed microbial community dynamics on system stability, our findings suggest that full scale on-farm AD operators could explore the effects of feeding intervals on their process performance.}, }
@article {pmid42175291, year = {2026}, author = {Dicko, A and Barro, SG and Somda, NS and Sombie, S and Bandaogo, O and Sanou, G and Esona, MD and Bonkoungou, JIO}, title = {Application of Metagenomics and Artificial Intelligence for Pathogen Characterization in Domestic Animals and Epizootic Prediction: A Systematic Review and Meta-Analysis.}, journal = {Studies in health technology and informatics}, volume = {336}, number = {}, pages = {2095-2096}, doi = {10.3233/SHTI260622}, pmid = {42175291}, issn = {1879-8365}, mesh = {Animals ; *Metagenomics/methods ; *Artificial Intelligence ; *Animals, Domestic/microbiology ; *Disease Outbreaks/veterinary/prevention &amp; control ; *Animal Diseases/diagnosis/microbiology ; }, abstract = {Sub-Saharan Africa suffers devastating animal health losses exceeding $20 billion each year. By combining metagenomics with artificial intelligence (AI), a promising path emerges for faster diagnostics and proactive disease prediction. Our PRISMA-guided review of 1,225 studies reveals that metagenomics achieves 94.2% diagnostic sensitivity (compared to 67.3% with conventional methods), while AI dramatically shortens turnaround from 48-72h to just 4-8h, offering a valuable 14-18 day early warning window for epizootics.}, }
@article {pmid42175403, year = {2026}, author = {Tang, R and Wang, R and Han, Y}, title = {Mycobacterium avium complex pulmonary disease in rheumatoid arthritis-associated interstitial lung disease under non-biologic immunomodulatory therapy: A case report.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48801}, pmid = {42175403}, issn = {1536-5964}, mesh = {Humans ; Male ; *Lung Diseases, Interstitial/complications/drug therapy/etiology ; Aged ; *Arthritis, Rheumatoid/complications/drug therapy ; *Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology ; Mycobacterium avium Complex/isolation &amp; purification ; }, abstract = {RATIONALE: Rheumatoid arthritis (RA) is a well-recognized risk factor for nontuberculous mycobacterial infections, especially among patients receiving glucocorticoids or biological disease-modifying antirheumatic drugs. However, cases of Mycobacterium avium complex (MAC) pulmonary disease in RA patients without such immunosuppressive therapies are rarely reported, which challenges the conventional risk stratification.<br><br>PATIENT CONCERNS: A 78-year-old male with a 3-year history of RA and interstitial lung disease (ILD) presented with progressive dyspnea and chest tightness. He had no fever, joint swelling, or typical infection flares. Before admission, he was treated with Tripterygium Glycosides and Iguratimod (non-biologic, non-glucocorticoid agents).<br><br>DIAGNOSIS: The patient had chest tightness and weight loss. Chest high-resolution computed tomography showed asymmetric progression of ILD, along with tree-in-bud signs, centrilobular nodules, and suspicious fibrocavities. Bronchoscopy revealed necrotizing granulomatous inflammation, and quantitative metagenomic sequencing of bronchoalveolar lavage fluid confirmed MAC (no drug-resistant genes detected).<br><br>INTERVENTIONS: The patient was put on a 4-drug anti-MAC regimen (rifampicin, azithromycin, ethambutol, amikacin). However, he was lost to follow-up after being transferred to a tuberculosis specialist hospital. He eventually died of unknown causes, and there were prior reports of his nonadherence to treatment.<br><br>OUTCOMES: For RA patients with ILD who show asymmetric imaging progression or discordant inflammatory markers, it is crucial to actively screen for atypical pathogens like MAC, even in the absence of glucocorticoid or biologic exposure. This case highlights the necessity of expanding nontuberculous mycobacterial infection risk assessment beyond traditional immunosuppressive therapies in RA-ILD patients.<br><br>LESSONS: For patients with autoimmune disease-associated interstitial pneumonia, particularly those with progressive interstitial lung disease (ILD) despite stable autoimmune serology, proactive screening for atypical pathogens such as nontuberculous mycobacteria is critical. When imaging shows asymmetric lesions, tree-in-bud opacities, centrilobular nodules, or fibrocavitary changes, clinicians should prioritize comprehensive etiological evaluation - including bronchoscopy and histopathology - to avoid misdiagnosing these opportunistic infections.}, }
@article {pmid42175735, year = {2026}, author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X}, title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70408}, doi = {10.1111/mec.70408}, pmid = {42175735}, issn = {1365-294X}, support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; }, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; }, abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.}, }
@article {pmid42175741, year = {2026}, author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z}, title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70929}, doi = {10.1111/gcb.70929}, pmid = {42175741}, issn = {1365-2486}, support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; }, mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.}, }
@article {pmid42176010, year = {2026}, author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E}, title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42176010}, issn = {1432-184X}, mesh = {Animals ; *Isopoda/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; *Hepatopancreas/microbiology ; Metagenome ; Metagenomics ; Lignin/metabolism ; Phylogeny ; Italy ; }, abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.}, }
@article {pmid42176043, year = {2026}, author = {Khan, I and Naeem, I and Ali, S and Gulbin, M and Iqbal, A and Shafiq, M}, title = {Metagenomic surveillance identifies a high-risk antibiotic resistance profile in community wastewater: a pilot study from Pakistan.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {42176043}, issn = {1432-1912}, abstract = {Environmental antimicrobial resistance surveillance in low- and middle-income countries (LMICs) faces critical data gaps, particularly in Pakistan, where approximately 90% of municipal wastewater is discharged untreated. In the absence of systematic monitoring in regions like Khyber Pakhtunkhwa, we conducted a pilot shotgun metagenomic sequencing study on two strategically selected community wastewater sites in Mardan. To translate complex metagenomic data into actionable public health intelligence, we developed the Antibiotic Resistance Risk Index (ARRI), a novel framework integrating antibiotic resistance gene (ARG) proportional abundance, pathogen taxonomic expansion, and WHO priority weighting. Our analysis revealed that the urban site (MCW2) exhibited a "critical" resistance profile, characterized by a 54% increase in ARG allelic richness (628 unique variants) despite a 19.9% decline in total relative ARG abundance. Taxonomic compositional changes consistent with an aerobic shift, including a 34-fold decline in Thermodesulfobacteria and a 46% increase in Pseudomonadota, were observed alongside an increased proportion of WHO priority pathogens, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. This site served as a reservoir for last-resort resistance determinants, including blaNDM, blaIMP, blaCTX-M, and mcr, which emerged exclusively in the urban drainage environment. The resistome contained 159 ARG families and 26 MGE types. Network analysis showed that 90.8% of ARG-MGE pairs exhibited coordinated increase in relative abundance, with all carbapenemase-linked pairs showing parallel trends. Consequently, ARRI scores escalated from 8.7 (moderate risk) to 34.2 (critical risk) at the urban site. These findings reveal the environmental circulation of hospital-associated resistance through decentralized sanitation infrastructure, representing a convergence of hospital-associated and community resistance profiles in LMIC settings. This study demonstrates that risk-weighted surveillance enables high-resolution, actionable AMR monitoring, providing a baseline methodology for environmental AMR surveillance in resource-limited settings.}, }
@article {pmid42176229, year = {2026}, author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB}, title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag134}, pmid = {42176229}, issn = {1751-7370}, abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress (Y-A-S) life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.}, }
@article {pmid42176246, year = {2026}, author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M}, title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42176246}, issn = {1867-1314}, support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; }, abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.}, }
@article {pmid42176375, year = {2026}, author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D}, title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.}, journal = {Water research}, volume = {302}, number = {}, pages = {126129}, doi = {10.1016/j.watres.2026.126129}, pmid = {42176375}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Phosphorus/metabolism ; *Freezing ; *Microbiota ; Geologic Sediments ; }, abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.}, }
@article {pmid42176511, year = {2026}, author = {Li, K and Jin, F and Tan, S and Zeng, X and Yuan, D and Shu, F and Chen, J and Ouyang, JM and Zhang, L and Li, C and Zhu, J}, title = {Cinchonain Ia inhibits uric acid reabsorption by binding to the TRP-459 residue of the GLUT9 protein.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158292}, doi = {10.1016/j.phymed.2026.158292}, pmid = {42176511}, issn = {1618-095X}, mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism ; *Uric Acid/metabolism/blood ; Male ; *Plant Extracts/pharmacology/chemistry ; *Polygonum/chemistry ; *Glucose Transport Proteins, Facilitative/metabolism/chemistry ; Rats ; Kidney/drug effects/metabolism ; Rats, Sprague-Dawley ; Mice ; Liver/drug effects/metabolism ; Humans ; }, abstract = {BACKGROUND: Hyperuricemia, a chronic metabolic disorder resulting from purine metabolism abnormalities, imposes a substantial burden on patients, their families, and society. Consequently, discovering more efficient prevention strategies and treatment drugs is of crucial importance. Polygonum capitatum (Buch.-Ham. ex D. Don) H. Gross is a plant belonging to the Polygonaceae family and Polygonum genus. Polygonum capitatum can reduce uric acid levels and alleviate gouty arthritis; However, whether its aqueous extract contains other uric acid-lowering active components besides quercetin and gallic acid still requires further research.<br><br>PURPOSE: This study aims to investigate the protective effects and potential mechanisms of Polygonum capitatum aqueous extract on liver and kidney function, while also identifying new potential pharmacologically active components for hyperuricemia within the extract.<br><br>METHODS: This study established a hyperuricemia rat and mice model and a uric acid-induced renal injury cell model. Liquid chromatography-tandem mass spectrometry was employed to analyze the active components of Polygonum capitatum aqueous extract. The target was analyzed by proteomics. Metagenomics and spatial metabolome were used to analyze gut microbes and metabolites associated with liver and kidney injury. Finally, SPR, DARTS, and CETSA were used to assess the binding potential of active components to targets. Additionally, mutant plasmids were constructed to analyze the binding sites between pharmacologically active components and their targets.<br><br>RESULTS: The aqueous extract of Polygonum capitatum significantly reduced serum uric acid levels and alleviated renal injury in the hyperuricemia rat model, with no apparent damage on liver tissue morphology or hepatic function indicators. Metagenomic and spatial metabolomics analyses demonstrated that the extract increased the relative abundance of beneficial gut microbiota and decreased that of harmful bacteria. It also modulated the levels and distribution of renal metabolites such as l-arginine and N-acetylglucosamine, reduced lipid oxidation in the kidney. Proteomics analysis suggests that renal GLUT9 may be one of the action targets of this extract. LC-MS/MS analysis indicated that the chemical composition of the extract underwent significant changes after entering rat blood and undergoing renal metabolism. Specifically, serves as a new active component in Polygonum capitatum aqueous extract, Cinchonain Ia was found to bind to the TRP-459 residue of GLUT9, inhibiting its expression and thereby reducing uric acid reabsorption in vivo and in vitro, and alleviated oxidative stress, inflammation, and tissue damage. However, overexpression of GLUT9 markedly reversed the inhibitory effects of Cinchonain Ia on inflammation and injury.<br><br>CONCLUSIONS: The aqueous extract of Polygonum capitatum prevents liver damage and alleviates kidney injury by regulating gut microbiota and renal metabolites. Furthermore, Cinchonain Ia, as one of its active components, can bind to the TRP-459 residue of the GLUT9 protein and inhibit its expression, thereby suppressing uric acid reabsorption and lowering serum uric acid levels.}, }
@article {pmid42176589, year = {2026}, author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q}, title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128552}, doi = {10.1016/j.micres.2026.128552}, pmid = {42176589}, issn = {1618-0623}, mesh = {*Phosphorus/metabolism ; Soil Microbiology ; *Trichoderma/physiology/metabolism ; Rhizosphere ; *Pseudomonas/metabolism/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pyrus/microbiology/growth &amp; development/metabolism ; Biomass ; Microbiota ; Metagenome ; Plant Roots/microbiology ; }, abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.}, }
@article {pmid42176630, year = {2026}, author = {Wu, Y and Ma, W and Sun, Y and Tang, J and Xu, X and Zhu, J and Miao, J and Li, M and Zeng, J and Gou, K and Song, Y and Zou, J}, title = {From active defense to cross-kingdom alarm: Rhizosphere microenvironment remodeling in soybean under polylactic acid nanoplastics and cadmium Co-stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142470}, doi = {10.1016/j.jhazmat.2026.142470}, pmid = {42176630}, issn = {1873-3336}, mesh = {*Rhizosphere ; *Glycine max/drug effects/metabolism/genetics ; *Cadmium/toxicity ; *Polyesters/toxicity ; *Soil Pollutants/toxicity ; Plant Roots/drug effects/metabolism ; Stress, Physiological ; Flavonoids/biosynthesis ; Soil Microbiology ; }, abstract = {As foundational components of the food web, plants face significant environmental threats caused by the coexistence of micro/nanoplastics (MNPs) and heavy metals. This study investigates the combined effects of cadmium and biodegradable polylactic acid nanoplastics on soybean. Under co-exposure conditions, toxicity progressively diminishes from the roots to the leaves of soybeans. By integrating root transcriptomics, root exudate metabolomics, rhizosphere soil metagenomics, and soil physicochemical analyses within a Bayesian structural equation modeling framework, we identified the Flavonoid biosynthesis pathway as a central mediating hub in the rhizosphere microenvironment under combined stress. Soybean roots modulated this pathway as a response strategy, which concurrently served as a signal for rhizosphere microbes to downregulate energy-intensive processes such as Methane metabolism, facilitating microbial adaptation. The down-regulation of the Flavonoid biosynthesis pathway in root exudates further altered rhizosphere soil properties, creating a feedback loop that amplified the expression of stress-related genes in soybean roots.}, }
@article {pmid42176697, year = {2026}, author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J}, title = {Artificial reefs alter viral communities and functional traits in coastal waters.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108131}, doi = {10.1016/j.marenvres.2026.108131}, pmid = {42176697}, issn = {1879-0291}, abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.}, }
@article {pmid42176766, year = {2026}, author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM}, title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.}, journal = {Neuroscience and biobehavioral reviews}, volume = {187}, number = {}, pages = {106775}, doi = {10.1016/j.neubiorev.2026.106775}, pmid = {42176766}, issn = {1873-7528}, mesh = {Humans ; *Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology ; *Oxidative Stress/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/immunology/metabolism ; *Neuroinflammatory Diseases/immunology/metabolism ; Probiotics ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.}, }
@article {pmid42176818, year = {2026}, author = {Dorofeev, A and Pelevina, A and Gruzdev, E and Beletsky, A and Berestovskaya, Y and Litti, Y and Mardanov, A and Pimenov, N}, title = {Development of an Azonexus- and Competibacter-enriched phosphate-accumulating community in the anaerobic/anoxic sequencing batch reactor: Cooperative denitrification.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134959}, doi = {10.1016/j.biortech.2026.134959}, pmid = {42176818}, issn = {1873-2976}, mesh = {*Denitrification ; *Bioreactors/microbiology ; Anaerobiosis ; *Phosphates/metabolism ; Sewage/microbiology ; *Rhodocyclaceae/metabolism ; *Batch Cell Culture Techniques ; }, abstract = {Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.}, }
@article {pmid42176923, year = {2026}, author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y}, title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.}, journal = {International journal of biological macromolecules}, volume = {368}, number = {}, pages = {152668}, doi = {10.1016/j.ijbiomac.2026.152668}, pmid = {42176923}, issn = {1879-0003}, mesh = {Animals ; *Atractylodes/chemistry ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism/pathology ; *Carbon/metabolism ; *Fatty Liver/drug therapy/metabolism ; Disease Models, Animal ; }, abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat and methionine/choline-deficient diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/d) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.}, }
@article {pmid42177038, year = {2026}, author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K}, title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00121}, pmid = {42177038}, issn = {1876-2891}, abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.}, }
@article {pmid42177062, year = {2026}, author = {Adamek, M and Yılmaz, TM and Erdogmus, S and Moore, S and Ziemert, N}, title = {The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {35-60}, doi = {10.1016/bs.mie.2025.08.023}, pmid = {42177062}, issn = {1557-7988}, mesh = {*Multigene Family ; *Software ; Genome, Bacterial ; Genome, Fungal ; Fungi/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Computational Biology/methods ; Biological Products/metabolism ; Data Mining/methods ; Genomics/methods ; Metagenome ; }, abstract = {Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.}, }
@article {pmid42177063, year = {2026}, author = {Sélem-Mojica, N and Magaña-Lemus, M&#xc1; and Rosiles-Loeza, PY and Barona-Gómez, F}, title = {Bringing CORASON to Windows: Exploring fungal natural products through biosynthetic gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {61-73}, doi = {10.1016/bs.mie.2026.03.001}, pmid = {42177063}, issn = {1557-7988}, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Fusarium/genetics/metabolism ; Phylogeny ; *Software ; Genome, Fungal ; *Biosynthetic Pathways/genetics ; *Computational Biology/methods ; }, abstract = {Biosynthetic gene clusters (BGC) are genomic regions that encode the production of specialized metabolites, including antibiotics, pigments, and toxins. While BGC are traditionally classified into broad categories such as NRPS, PKS, and terpene clusters, these classes often overlook finer relationships among gene clusters that produce structurally or functionally related compounds. Tools like BiG-SCAPE and BiG-SLiCE have been developed to address this issue by organizing BGC into gene cluster families (GCFs). CORASON complements these tools by enabling phylogenetic reconstruction of BGC, identifying conserved core genes, and visualizing GFCs as a continuum of variation in gene presence/absence and sequence identity. Although CORASON is incorporated in BiG-SCAPE visualization, it is also a standalone tool initially designed for bacterial genomes annotated via RAST and implemented through Docker in Linux environments. Here, we demonstrate CORASON's broader applicability using fungal GenBank files and its installation via Conda on Windows. As a case study, we examine metagenome-assembled genomes (MAGs) from Fusarium domesticum, a lesser-known member of the Fusarium genus, which is often present in food-associated microbiomes. Unlike its pathogenic relatives (F. oxysporum, F. graminearum), F. domesticum remains understudied, making it an interesting target for genomic mining. This work expands the accessibility of CORASON for fungal genome analysis and highlights its potential in uncovering novel biosynthetic potential in overlooked microbial taxa.}, }
@article {pmid42177457, year = {2026}, author = {Zhang, H and Abbas, Z and Li, H and Zhu, Y and Hu, X and Si, D}, title = {Synergistic fungal-enzymatic fermentation of corn straw enhances nutritional value, microbial stability, and bio-feed quality.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05190-6}, pmid = {42177457}, issn = {1471-2180}, support = {2024TSYCTD0016//Xinjiang Uygur Autonomous Region "Tianshan Talents" Cultivation Program/ ; }, abstract = {Valorizing mature, dry corn straw into nutritional animal feed is constrained by its recalcitrant lignocellulosic matrix, while conventional silage methods face stability and logistical limitations. Existing enzymatic and bacterial approaches often lack synergistic efficacy and fail to mitigate pathogen risk in dry biomass systems. We engineered a two-stage fungal-enzymatic fermentation strategy employing a consortium of Aspergillus niger LFB-AN14, Coriolopsis trogii LFB-F1, Bacillus subtilis LFB-BS7, and Pediococcus acidilactici A62, integrated with cellulase, xylanase, and laccase under optimized conditions (1% inoculation, 5:5:1:1 ratio, 37 °C, 21 days). Our results demonstrated that the bacterial-enzyme co-treatment (Group A3) significantly reduced fiber content, with neutral detergent fiber (NDF) and acid detergent fiber (ADF) decreasing by 22.6% and 29.1%, respectively, compared to the control (p < 0.001). Lignin degradation was enhanced, accompanied by a 4.5-fold increase in water-soluble carbohydrates (WSC). The metabolic profile revealed elevated lactic acid production (36.54 g/kg FM) and the suppression of undesirable byproducts such as propionic and butyric acids. Microbial community analysis revealed a dominant shift toward Pediococcus (> 50% abundance) and inhibition of pathogenic Enterobacter spp. Structural analyses (SEM, FTIR) confirmed extensive lignocellulose deconstruction, particularly through carbonyl and hydroxyl functional groups. Metagenomic analysis revealed upregulated Auxiliary Activity (AA) enzymes and cellulosome modules, elucidating the mechanistic basis for enhanced degradation. KEGG enrichment highlighted enhanced aromatic compound metabolism and yeast proliferation, reflecting superior metabolic efficiency. This integrated fungal-enzymatic approach establishes a safe, scalable, and metabolically efficient strategy for transforming agricultural residues into high-quality bio-feed, resolving key challenges in fiber digestibility, pathogen control, and storage stability for sustainable livestock production.}, }
@article {pmid42178356, year = {2026}, author = {Chen, S and Xu, S and Muhammad, ZUA and Wang, X and Guo, K and Tao, J and Li, M and Wang, H and Zhang, C and Hou, S}, title = {Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07491-x}, pmid = {42178356}, issn = {2052-4463}, support = {JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; 4241003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Planktonic microbial and viral communities are fundamental drivers of biogeochemical cycling and energy flow in marine ecosystems. These communities display substantial variability in their composition at daily to sub-daily scales, which cannot be captured by conventional low-frequency monthly or weekly sampling. To reveal these high-resolution dynamics, we performed a time-series sampling of planktonic microbial and viral communities in the subtropical Daya Bay at 2-hour intervals over 3 days. Seawater samples were subjected to metagenomic and metatranscriptomic sequencing for the cellular size fraction (>0.2 μm) and metagenomic sequencing for the viral size fraction (0.02-0.2 μm). This approach enabled us to capture fine-scale temporal variations in the genomic composition and transcriptional activities of microbial and viral communities. The resulting comprehensive dataset, including 700 metagenome-assembled genomes (MAGs) and 118,242 viral operational taxonomic units (vOTUs), provides a valuable resource for investigating the metabolic potentials and dynamic interactions within natural planktonic microbial-viral assemblages in subtropical bay ecosystems, offering insights into their ecological roles that are inaccessible through low-temporal-resolution sampling.}, }
@article {pmid42178395, year = {2026}, author = {Sharaf, H and Bobay, LM}, title = {MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {6}, pages = {}, pmid = {42178395}, issn = {1367-4811}, support = {R01GM132137//National Institutes of Health (NIGMS)/ ; }, mesh = {*Metagenomics/methods ; Genotype ; *Software ; *Bacteria/genetics/classification ; Algorithms ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging.<br><br>RESULTS: Here we present MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.<br><br>AVAILABILITY: MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at www.github.com/lbobay/MetaStrainer and on Zenodo: 10.5281/zenodo.17872331.}, }
@article {pmid42178569, year = {2026}, author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T}, title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42178569}, issn = {2049-2618}, support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; }, abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.<br><br>RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67&#xa0;mg CO2 per g dry weight in a year.<br><br>CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.}, }
@article {pmid42178714, year = {2026}, author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2676162}, pmid = {42178714}, issn = {1949-0984}, mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; }, abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.}, }
@article {pmid42178721, year = {2026}, author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M}, title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2675078}, pmid = {42178721}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology/immunology/etiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Immunoglobulin A, Secretory/immunology/genetics ; *Transplant Recipients ; Tacrolimus/adverse effects ; Bacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Immunosuppressive Agents/adverse effects/therapeutic use ; *Organ Transplantation/adverse effects ; Feces/microbiology ; Child, Preschool ; Liver Transplantation/adverse effects ; }, abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.}, }
@article {pmid42180198, year = {2026}, author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B}, title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.}, journal = {ACS environmental Au}, volume = {6}, number = {3}, pages = {435-448}, pmid = {42180198}, issn = {2694-2518}, abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.}, }
@article {pmid42180259, year = {2026}, author = {He, J and Ning, Y and Liang, H and Qin, J and Wei, Y and Liang, S and He, Z and Yin, S}, title = {Special pathogen infections presenting with neck mass as the initial manifestation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1767591}, pmid = {42180259}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Neck/pathology/microbiology ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/pathology/drug therapy ; *Mycoses/diagnosis/microbiology/pathology/drug therapy ; *Talaromyces/isolation &amp; purification ; Nontuberculous Mycobacteria/isolation &amp; purification ; China ; Lymphadenopathy/microbiology ; }, abstract = {BACKGROUND: The etiology of neck masses is complex. Infections caused by Talaromyces marneffei (TM) and nontuberculous mycobacteria (NTM) are uncommon but often present with insidious clinical manifestations, leading to frequent misdiagnosis.<br><br>METHODS: We collected and analyzed data from 13 patients with TM/NTM infections presenting with neck masses at The First Affiliated Hospital of Guangxi Medical University and The Second Affiliated Hospital of Guangxi Medical University. Clinical manifestations, laboratory findings, infection sites, pathogen types, treatments, and outcomes were described and analyzed.<br><br>RESULTS: Of the 13 patients, six were male and seven female, with a median age of 57 years (range, 27-73 years). All patients were residents of Guangxi and tested positive for anti-interferon-&#x3b3; autoantibodies (AIGAs), with titers of 1:2500 in 12 patients and 1:500 in one. The median time from symptom onset to diagnosis was 5 months (range, 1-19 months). Common clinical features included lymphadenopathy (13/13), fever (11/13), respiratory symptoms (10/13), and rash or skin ulceration (8/13). Frequent laboratory abnormalities included leukocytosis (11/13), neutrophilia (11/13), elevated erythrocyte sedimentation rate (12/13), and elevated C-reactive protein (13/13). Coinfection with two or more pathogens was observed in 12 patients. The lungs and lymph nodes were involved in all 13 patients, followed by bone (11/13), skin or soft tissue (8/13), bloodstream or bone marrow (3/13), and nasopharynx (3/13). Neck mass specimens yielded NTM in nine cases and TM in four. NTM was most frequently identified by metagenomic next-generation sequencing (mNGS), whereas TM was detected by culture. The median follow-up duration was 28 months (range, 1-86 months). During follow-up, 6 patients (46.2%) experienced disease exacerbations. Among the 13 patients, 12 achieved clinical improvement after pathogen-directed antimicrobial therapy, while one patient died.<br><br>CONCLUSION: Neck masses have diverse etiologies. TM and NTM infections presenting initially as neck masses are rare and easily misdiagnosed as tuberculosis, malignancy, or lymphoma. Culture and mNGS are crucial diagnostic tools for TM and NTM, respectively. Clinicians should maintain a high index of suspicion for these infections, particularly in immunocompromised patients in endemic regions.}, }
@article {pmid42180316, year = {2026}, author = {Chen, X and Zhang, M and Yang, L and Chen, Y and Chi, Y and Zhao, Y and Ma, Z and Li, Y and Wang, X}, title = {CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated with Streptococcus Mutans.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2674332}, pmid = {42180316}, issn = {2000-2297}, abstract = {BACKGROUND: Streptococcus mutans is a key cariogenic bacterium. Current antimicrobials lack species specificity, while phage-based approaches remain experimental and require more S. mutans phage isolates.<br><br>OBJECTIVE: To profile the diversity of S. mutans-associated phages and strain-level heterogeneity in phage exposure using genome-informed CRISPR spacer and prophage analyses.<br><br>MATERIALS AND METHODS: We compiled 944 publicly available S. mutans genomes and dereplicated them into 735 non-redundant strains. CRISPR-Cas systems, spacers, spacer targets, and putative prophages were identified, quality-assessed, and functionally annotated. Phylogenetic relationships of (pro)phages were evaluated using terminase large subunit proteins, and comparative genomics compared spacer-positive and spacer-negative strains.<br><br>RESULTS: CRISPR systems were detected in 548/735 strains, yielding 14,263 spacers, 1,864 phage-targeting spacers mapped to 110 viral genomes, including 41 cultured isolates, 51 metagenome-assembled phages, and 18 uncultured viral genomes. The most frequently targeted cultured phage was phiKSM96, whereas metagenome-assembled Caudoviricetes ctNo011 showed broader targeting. Prophage mining identified 186 regions in 130 strains, including 37 of &#x2265; medium quality and elements related to ctNo011 and phiKSM96. TerL phylogeny showed that most high-quality endogenous prophages clustered with phiKSM96 and ctNo011.<br><br>CONCLUSION: These findings reveal a vast, uncultivated phage repertoire targeting S. mutans, providing a critical genomic roadmap to guide the future isolation of novel phages for caries prevention.}, }
@article {pmid42180431, year = {2026}, author = {Mallawaarachchi, V and Bouras, G and Wick, RR and Grigson, SR and Papudeshi, B and Edwards, RA}, title = {agtools: a software framework to manipulate assembly graphs.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag126}, pmid = {42180431}, issn = {2635-0041}, abstract = {MOTIVATION: Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragments. Apart from their core use in assemblers, assembly graphs have become increasingly important in a range of downstream applications such as metagenomic binning, plasmid detection, viral genome resolution, and haplotype phasing. However, there is a need for a comprehensive tool that allows programmatic access to manipulate assembly graphs (e.g. parse, convert, filter, and analyze) across different assembly graph formats.<br><br>RESULTS: Here we present agtools, an open-source Python framework to manipulate assembly graphs produced by commonly used assemblers. agtools provides a command-line interface for tasks such as assembly graph format conversion, segment filtering, and component extraction. It also exposes a Python package interface to load, query, and analyze assembly graphs from popular genome and metagenome assemblers. This enables streamlined assembly-graph-based analyses that can be integrated into other bioinformatics software and workflows.<br><br>The source code of agtools is hosted on GitHub at https://github.com/Vini2/agtools and the documentation is available at https://agtools.readthedocs.io/. agtools can also be installed from Bioconda (https://anaconda.org/bioconda/agtools) and PyPI (https://pypi.org/project/agtools/).}, }
@article {pmid42180728, year = {2026}, author = {Wang, T and Wang, M and Zhao, L and Tang, G and Hou, L}, title = {Case Report: Pulmonary brucellosis presenting as multiple cavitary lung lesions on imaging.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1814731}, pmid = {42180728}, issn = {2296-858X}, abstract = {Pulmonary brucellosis is a rare focal manifestation of human brucellosis with non-specific clinical features. Predominant imaging findings include pneumonia, pleural effusion, pulmonary nodules, abscesses, and interstitial changes. Multiple cavitary lesions are exceptionally rare. Herein, we report a case of bilateral multiple pulmonary cavities in a 76-year-old man with a 2-year history of intermittent cough, sputum production, and progressive dyspnea that acutely worsened 10 days prior to admission with intermittent fever, anorexia, and fatigue. Chest computed tomography (CT) revealed bilateral upper lobe irregular mass-like opacities and multiple nodules with heterogeneous density, punctate calcifications, and cavitation; multiple microcavitations in the right middle and lower lobes and the left lower lobe; and enlarged, calcified hilar and mediastinal lymph nodes. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Brucella species, which was confirmed by positive serology. After 3 days of doxycycline (0.1 g bid po) and rifampicin (0.6 g qd po), followed by 140 days of doxycycline (0.1 g bid po), rifapentine (0.6 g biw po), and levofloxacin (0.5 g qd po), along with silibinin meglumine tablets 0.1 g tid po for hepatoprotective therapy, the patient became afebrile with significant symptomatic improvement. Repeat chest CT demonstrated reduction in the right upper lobe consolidation/cavity and left upper lobe consolidation, resolution of the right lower lobe cavity, and complete resolution of the microcavitations. This case underscores that pulmonary brucellosis should be considered in the differential diagnosis of cavitary lung lesions in patients with livestock exposure and that prolonged combination antibiotic therapy can achieve favorable clinical and radiological outcomes.}, }
@article {pmid42181109, year = {2026}, author = {Wunderer, M and Mullaymeri, A and Wagner, AO and Prem, EM}, title = {Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42181109}, issn = {2516-8290}, abstract = {The genome of the methylotrophic methanogen Methanomethylovorans thermophila L2FAW is not included in the Genome Taxonomy Database (GTDB) so far, even though the strain was first described in 2005. To evaluate its genomic characteristics and placement in the GTDB, we sequenced the genome of M. thermophila L2FAW via Illumina shotgun and Oxford Nanopore sequencing and subsequently did hybrid assembly. The assembled genome consists of 2.25 Mbp (contigs ≥500 bp) with a G+C content of 40 mol%. The quality of the genome is good, which is already apparent from the low L50 (=1) and L90 (=2) metrics. Our assembled genome was highly similar to the metagenome-assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity of 99.9%. Even though KEGG Mapper Reconstruction results revealed that M. thermophila L2FAW harbours all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis and gapseq predicted formate as a potential substrate for M. thermophila L2FAW, no metabolic activity could be observed on acetate, H2-CO2 (80:20 vol/vol, 2,000 mbar) and on a mixture of H2-CO2 and formate in lab tests; thus, the obligate methylotrophic lifestyle of the phenotype was confirmed.}, }
@article {pmid42181159, year = {2026}, author = {Bressuire, C and Thirion, F and Chiaravano, L and Ngom, SI and Marion, R and Gilles, M and Quinquis, B and Mathieu, E and Berland, M and Blottière, HM and Le Bourgot, C and Béra-Maillet, C}, title = {Short-chain fructo-oligosaccharides modulate gut microbiota composition and metabolism: dose-response assessment in an ex vivo gut model.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2674335}, pmid = {42181159}, issn = {2993-3935}, abstract = {Short-chain fructo-oligosaccharides (scFOS) are prebiotic fiber rapidly fermented in the colon and known to stimulate beneficial bacteria, such as Bifidobacterium spp. and Lactobacillaceae. While their overall effects on the gut microbiota are established, the dose-response relationship remained only partially characterized. This study aimed to determine the minimum effective dose of scFOS required to modulate gut microbiota composition and functions. An ex vivo chemostat model was used to simulate colonic fermentation with different doses of scFOS (1 to 10 g/d). Microbiota composition and metabolic activity were assessed by qPCR, short-chain fatty acid (SCFA) quantification, and shotgun metagenomics. An increase in scFOS dose led to higher SCFA levels, particularly acetate and butyrate, along with a modification in microbial composition, with a minimum significant effective dose of 2.5 g/d. Significant increase in Bifidobacterium adolescentis, Anaerostipes hadrus, and Clostridium innocuum was observed at the same dose. Functional analysis revealed an enrichment of GH32 genes in the pangenomes of species positively impacted by scFOS. These findings demonstrate that low doses of scFOS can effectively modulate the gut microbiota and enhance SCFA production, supporting their use in dietary interventions aimed at improving intestinal health.}, }
@article {pmid42182002, year = {2026}, author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y}, title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1839764}, pmid = {42182002}, issn = {1664-302X}, abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.<br><br>METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.<br><br>RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum &#x3b2;-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.<br><br>DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.}, }
@article {pmid42182003, year = {2026}, author = {Li, F and Liu, X and Hou, W and Dong, H and Hu, J and Chen, H and Zhong, Y and Wu, Y and Xu, X and Ding, Y}, title = {Archaeal communities as indicators of hydrothermal influence in the Tianxiu vent field, Northwest Indian Ocean.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1837947}, pmid = {42182003}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal sediments represent critical zones for archaea-driven biogeochemical cycling, yet the ecological differentiation of archaeal communities across hydrothermal gradients remains poorly understood. Here, we used 16S rRNA gene amplicon sequencing of sediment cores from two contrasting sites in the Tianxiu hydrothermal field of the Northwest Indian Ocean, and performed metagenomic analysis on the near-vent BC12 sediments, to investigate archaeal community composition, co-occurrence patterns, and metabolic potential in response to the hydrothermal activity. Comparative analysis revealed marked divergence between near-vent site BC12 and far-vent site JL218P. The site BC12, under stronger hydrothermal influence, was enriched in Hydrothermarchaeia, along with Nanoarchaeia and Thermoplasmata, and exhibited a more complex, highly connected co-occurrence network. Correlation analyses further showed that Hydrothermarchaeia abundance was significantly associated with hydrothermal-related geochemical gradients, supporting this lineage as a potential indicator of hydrothermal influence. Metagenomic analysis of BC12 further revealed Hydrothermarchaeia genomes encoding the Wood-Ljungdahl carbon fixation pathway, while genome-centric functional inference suggested enhanced potential for methanogenesis and hydrogen oxidation. In contrast, JL218P was dominated by Nitrososphaeria, showed limited vertical variation, and formed a simpler network structure, with predicted functional profiles more closely associated with nitrification and aerobic ammonia oxidation. Together, these findings identify hydrothermal-related geochemical heterogeneity as a major driver of archaeal community composition, ecological organization, and metabolic differentiation in deep-sea sediments, and advance our understanding of the ecological drivers structuring deep-sea hydrothermal ecosystems.}, }
@article {pmid42182018, year = {2026}, author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M}, title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829529}, pmid = {42182018}, issn = {1664-302X}, abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.<br><br>METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.<br><br>RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.<br><br>DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.}, }
@article {pmid42182023, year = {2026}, author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K}, title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798902}, pmid = {42182023}, issn = {1664-302X}, abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.<br><br>METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.<br><br>RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.<br><br>DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.}, }
@article {pmid42182035, year = {2026}, author = {Qian, W and Han, A and Al Hatmi, AMS and Wang, Y and Rafiq, M and Cui, G and Zhou, S and Li, S and Kang, Y}, title = {Concordance between environmental resistomes and pathogenic phenotypes: a case study of multidrug-resistant Klebsiella pneumoniae in a drinking water source in Guizhou, China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1810806}, pmid = {42182035}, issn = {1664-302X}, abstract = {INTRODUCTION: The persistence of antibiotic resistance in aquatic environments poses a public health concern, particularly when drinking water sources act as reservoirs for multidrug-resistant opportunistic pathogens. However, the linkage between environmental resistomes and the resistance phenotypes of cultivable bacteria remains under-characterized. This case study investigated this relationship in a karst drinking water source in Guizhou, China.<br><br>METHODS: Surface water samples from seven sites were analyzed for antibiotic residues using LC-MS/MS. Metagenomic sequencing was conducted on selected contamination hotspots to characterize microbial communities and antibiotic resistance genes (ARGs). Cultivable bacteria were isolated, identified via 16S rRNA sequencing, and tested for antimicrobial susceptibility. To validate resistance mechanisms, a multidrug-resistant Klebsiella pneumoniae isolate was analyzed for tetA expression using RT-qPCR.<br><br>RESULTS: Antibiotic residues were detected across all sites, with sulfonamides and tetracyclines being the most prevalent. Consistent with this chemical pressure, metagenomic analysis identified corresponding ARGs, including sul1 and tet(Q), which functionally clustered with mobile genetic elements. From the contaminated matrix (sample W2), a multidrug-resistant Klebsiella pneumoniae strain (B8) was recovered. Mechanistic validation revealed a 2.78-fold upregulation of the tetA efflux pump gene in this strain.<br><br>DISCUSSION: These findings demonstrate a concordance among chemical selection pressures, environmental resistomes, and active resistance phenotypes. The results indicate that drinking water sources can harbor and maintain clinically relevant resistant bacteria, supporting the implementation of integrated surveillance strategies to evaluate biological risks.}, }
@article {pmid42182110, year = {2026}, author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G}, title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42182110}, issn = {2692-8205}, abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.}, }
@article {pmid42182295, year = {2026}, author = {Kumar, A and Keerthipati, P and Lotana, H and White, T and Jones, E and Prescrille, J and Webb, T and Zhu, Y and Somakhin, A and Johnson, D and Tsymbalyuk, O and Simard, M and Qin, X and Ge, Y and Zhang, H and Dilipkumar, S and Gonzalez-Juarbe, N and Drake, WP}, title = {The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725489}, pmid = {42182295}, issn = {2692-8205}, abstract = {Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP- E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP- E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP- E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.}, }
@article {pmid42182444, year = {2026}, author = {Wright, JT and Yendluri, S and Thomas, NC and Butterfield, CN and Dangerfield, TL and Taylor, DW}, title = {Structural and kinetic insights into a metagenomics-derived Cas12a with high specificity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.724879}, pmid = {42182444}, issn = {2692-8205}, abstract = {CRISPR-Cas12a nucleases provide an attractive alternative to Cas9 due to their compact RNA scaffold, T-rich PAM requirement, and improved target specificity. However, the mechanistic features that govern activity and discrimination across Cas12a orthologs remain incompletely understood. Here, we characterize Cas12a-MG29-1, a highly active and specific nuclease identified through metagenomic mining, using cryogenic electron microscopy, mutational analysis, and kinetic modeling. The Cas12a-MG29-1 structure reveals repositioned flexible loops near the distal end of the R-loop, including reduced engagement of one loop region and additional contacts formed by a second distal loop. Structure-guided mutagenesis and loop-swap experiments indicate that distal R-loop architecture modulates target discrimination in a context-dependent manner. Single-turnover cleavage and stopped-flow measurements show that Cas12a-MG29-1 and AsCas12a form reversible R-loops with similar kinetics but differ in strand cleavage following R-loop formation. Global kinetic modeling demonstrates that Cas12a-MG29-1 exhibits accelerated non-target strand cleavage, shifting kinetic partitioning toward product formation. This faster irreversible commitment provides a mechanistic explanation for enhanced activity and specificity without altering initial target interrogation. Together, these findings identify distal R-loop interactions and catalytic commitment as key determinants of Cas12a function and provide a framework for interpreting and engineering next-generation Cas12a orthologs.}, }
@article {pmid42182637, year = {2026}, author = {Cai, X and Pang, S and Tang, C and Li, S}, title = {Relationship between airway stents and airway microorganisms: a literature review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {4}, pages = {418}, pmid = {42182637}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.<br><br>METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.<br><br>KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.<br><br>CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.}, }
@article {pmid42182855, year = {2026}, author = {Jia, Y and Zhu, Y and Cai, H}, title = {Polymicrobial Multidrug-Resistant Infection and Fatal Bowel Ischemic Perforation After Urgent Heart Transplantation in a VA-ECMO-Bridged Recipient: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {604688}, pmid = {42182855}, issn = {1178-6973}, abstract = {Post-transplant infection caused by multidrug-resistant organisms (MDROs) is a major challenge in heart transplantation, especially in recipients requiring veno-arterial extracorporeal membrane oxygenation (VA-ECMO) before surgery. We describe a 52-year-old man with non-ST-elevation myocardial infarction and refractory cardiogenic shock who required VA-ECMO, intra-aortic balloon pump support, continuous renal replacement therapy, and mechanical ventilation before urgent heart transplantation. Before transplantation, he had active pneumonia. Donor respiratory culture grew Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus, whereas donor blood culture and blood metagenomic next-generation sequencing (mNGS) were negative. After transplantation, serial mNGS and conventional cultures revealed rapidly progressive polymicrobial infection involving Stenotrophomonas maltophilia, Burkholderia multivorans, carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Klebsiella pneumoniae, and vancomycin-resistant Enterococcus faecium. Antimicrobial therapy was repeatedly adjusted, and VA-ECMO was successfully discontinued on postoperative day 13. However, on postoperative day 16, the patient developed bowel ischemia with gastrointestinal perforation, followed by feculent peritonitis, persistent septic shock, progressive multiorgan dysfunction syndrome, and death on postoperative day 24. This case shows that perioperative infection control in VA-ECMO-bridged urgent heart transplant recipients requires more than broad-spectrum antimicrobial escalation. It requires careful assessment of preoperative infection controllability, interpretation of mNGS in conjunction with culture-based susceptibility testing, and early investigation of occult abdominal ischemia when clinical deterioration is unexplained.}, }
@article {pmid42183063, year = {2026}, author = {Zhang, J and Chen, C and Hu, Y and Jia, S and Li, B and Hu, W and Jia, Y and Li, D and Liu, Y}, title = {Interaction between microorganisms and flavour products during cigar fermentation promoted by citrus Reticulata-"Chenpi" derived Enterobacter G5Z-2: based on multi-omics studies and microbial profiles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1785975}, pmid = {42183063}, issn = {2296-4185}, abstract = {INTRODUCTION: Cigar fermentation is crucial for developing its characteristic aroma, exogenous microorganisms can be used to enhance fermentation. It is reported that the citrus reticulata 'Chachi' (Chenpi, a traditional fermented ingredient) extract can improve the flavor of cigarette. However, there is no report on the influence of Chenpi-derived microorganisms on the fermentation process and flavor quality of cigar tobacco leaves (CTLs) till now.<br><br>METHODS: A fermentation strain (Enterobacter hoffmannii, G5Z-2) was isolated from Chenpi, and it was applied as a bioaugmentation agent in CTLs fermentation. A multi-omics approach, including metagenomics and metabolomics, was employed to investigate its impact.<br><br>RESULTS: Inoculation with G5Z-2 significantly altered the microbial community structure, suppressing native Pseudomonas and reducing overall alpha diversity while enriching beneficial genera like Aspergillus and Staphylococcus. Metabolomic analysis revealed substantial restructuring of metabolic pathways, particularly the enrichment of amino acid metabolism (such as arginine biosynthesis and phenylalanine metabolism) and nicotinate/nicotinamide metabolism. This led to accelerated degradation of proteins and amino acids, providing precursors for Maillard reaction, and a marked increase (57.5%) in total volatile flavour compounds, including key aroma constituents from carotenoid and cembranoid degradation.<br><br>CONCLUSION: The Chenpi-derived E. hoffmannii G5Z-2 optimises the fermentation process by modulating the microbial consortium and driving metabolic shifts towards favourable flavour development, demonstrating significant potential for improving the quality of Chinese-style cigars.}, }
@article {pmid42184066, year = {2026}, author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A}, title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42184066}, issn = {1573-0972}, support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration &amp; dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; }, abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.}, }
@article {pmid42184159, year = {2026}, author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C}, title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42184159}, issn = {1574-6941}, support = {//Scientific Committee on Antarctic Research/ ; 542264307//German Research Foundation/ ; 569718716//German Research Foundation/ ; }, mesh = {Antarctic Regions ; *Phytoplankton/metabolism/genetics/classification ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Diatoms ; Seawater/microbiology ; Polysaccharides/metabolism ; *Microbiota ; }, abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.}, }
@article {pmid42184529, year = {2026}, author = {Wang, R and Chen, H}, title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142479}, doi = {10.1016/j.jhazmat.2026.142479}, pmid = {42184529}, issn = {1873-3336}, mesh = {Manure ; Animals ; *Fertilizers ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Cattle ; *Agricultural Irrigation ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Soil/chemistry ; Chickens ; Metals, Heavy/analysis ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; }, abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.}, }
@article {pmid42184535, year = {2026}, author = {Ma, B and Li, F and Zhang, C and Deng, Y and Sekar, R and Chen, Z and Wang, M and Zamyadi, A and He, S and Huang, T and Guo, J and Zhang, H}, title = {Multivalent manganese-mediated synergistic aerobic denitrification boost nitrogen removal in oligotrophic aquatic systems: Insight into microbial functional and metabolic complementarity.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142496}, doi = {10.1016/j.jhazmat.2026.142496}, pmid = {42184535}, issn = {1873-3336}, mesh = {*Manganese/chemistry/metabolism ; *Denitrification ; *Nitrogen/metabolism ; Bioreactors ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; Water Purification/methods ; }, abstract = {Efficient nitrogen removal from oligotrophic lakes and reservoirs necessitates the development of innovative, eco-friendly strategies to mitigate the limitation of organic electron donors. We engineered four multivalent manganese (Mn) composite-functionalized bioreactors for oligotrophic water remediation, which demonstrated a sustained total nitrogen removal efficiency exceeding 97.66% over five operational cycles. Manganese powder-doped activated carbon achieved the highest nitrate removal rate, ranging from 0.29956 to 0.39831 mg/L/d. Immobilization with sodium alginate has mitigated manganese oxidative corrosion, thereby resulting in more sustained long-term reactive performance. Furthermore, denitrifying bacteria synergistically promote the enrichment of phosphorus-accumulating microorganisms and manganese-oxidizing bacteria (Burkholderiaceae, Methylophilaceae, and Azospirillaceae), which play pivotal roles in denitrification and manganese cycling, within Mn addition (MNA) reactors. Correlation analyses revealed stronger co-occurrence patterns between denitrification genes and manganese-oxidizing genes in the MNA reactors compared to the control. The abundance of ATP-binding cassette transporter genes, particularly encoding lipopolysaccharide transport (wzt) and lipoprotein release (lolD), increased by 1.37-1.90-fold and 1.31-1.80-fold, respectively, in the MNA reactors relative to the control reactor. Furthermore, the metabolic complementarity network suggested that MNA not only promoted community metabolic competition and complementarity effects but also enhanced higher energy production and respiratory activity. These findings establish a manganese-driven microbial enhancement strategy for sustainable nitrogen removal from polluted surface waters, offering new opportunities for eco-engineered water treatment.}, }
@article {pmid42184563, year = {2026}, author = {Hull, R}, title = {RNA viruses are an integral part in evolution of all organisms.}, journal = {Virology}, volume = {621}, number = {}, pages = {110950}, doi = {10.1016/j.virol.2026.110950}, pmid = {42184563}, issn = {1096-0341}, mesh = {*RNA Viruses/genetics/physiology/classification ; Symbiosis ; *Evolution, Molecular ; *Biological Evolution ; Animals ; Genome, Viral ; Host-Pathogen Interactions ; Virus Replication ; Humans ; Retroviridae/genetics/physiology ; }, abstract = {RNA viruses are intracellular symbiotic obligate parasites, needing host factors and energy for their replication with forms of symbiosis ranging from antagonism (pathogenic, not contributing to host metabolism) to mutualism (contributing benefits to the host as well as making demands on host metabolism). As a group, they have several unusual features: a) metagenomic studies suggest that they are probably are the most common group of viruses infecting all organism species and are the most abundant biological entity on earth; b) they have existed ever since the Last Universal Common Ancestor from which all living organisms have evolved; c) a high proportion of their species have + strand RNA genomes, or are retroviruses, that replicate without proof-reading creating many variants (quasispecies); d) they replicate in organelles within the endoplasmic reticulum and other membranes which connect to other organelles and to membrane and metabolic network systems. This paper brings together these facts presenting the hypothesis that RNA viruses and retroviruses form host/mutualistic virus symbionts as an evolutionary unit with the viral responses to evolutionary stresses being rapid and linking closely with the slower host genomic responses. The hypothesis is presented with a background of evolution of organisms and viruses, drivers of evolution, and the evolutionary natural selection pathway from the sources of stresses to impact and molecular reactions to stresses entering the basic organism body, the cell.}, }
@article {pmid42184767, year = {2026}, author = {Chen, D and Ibrar, M and Yan, F and Sun, G and Xue, R and Jia, A and Zhou, J and Gao, Y and Ma, C and Wang, M and Zhang, J and Ma, Z and Liu, L}, title = {The rising power of females: Dioecious shrub enhances soil organic carbon sequestration via fungal necromass in chronosequence of desertified alpine grassland restoration.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130022}, doi = {10.1016/j.jenvman.2026.130022}, pmid = {42184767}, issn = {1095-8630}, mesh = {*Grassland ; *Soil/chemistry ; *Soil Microbiology ; *Carbon Sequestration ; Carbon ; *Fungi ; Rhizosphere ; Tibet ; }, abstract = {Desertification-induced soil organic carbon (SOC) loss poses a major environmental threat to the alpine grasslands of the Qinghai-Tibet Plateau, jeopardizing ecological security and sustainability. While pioneer shrub introduction has yielded positive ecological outcomes, the mechanisms of SOC recovery remain poorly understood. We investigated the effects of a widely used dioecious shrub on rhizosphere SOC dynamics across a 20-year restoration chronosequence, employing a comprehensive framework that combined root exudation measurements, soil physicochemical analysis, metagenomics, and biomarker profiling to decipher the mechanism. Our results reveal that microbial-derived carbon dominated rhizosphere SOC accrual, contributing 20.1-22.0% to the total SOC pool, over 50 times more than plant-derived carbon (0.1-0.4%). The microbial pool was predominantly fungal necromass (>93%), correlated with declining root exudation and suppressed carbon-degrading gene abundance during restoration. In the 20th year after recovery, a striking divergence in the effects of male and female shrubs on rhizosphere SOC became apparent, with female shrubs sustaining 15% more microbial necromass and 47% more lignin phenols than males. Our findings highlight that SOC restoration in the rhizosphere of pioneer shrubs is predominantly driven by a fungal-mediated microbial carbon pump. Moreover, the preferential use of female shrubs offers a dual benefit: enhancing long-term rhizosphere SOC sequestration and controlling shrubs encroachment. This sex-informed strategy therefore provides a scalable framework for degraded alpine grasslands and serves as a transferable model for other drylands undergoing warming-wetting transitions, where alleviated water limitation increasingly enables vegetation-microbe-mediated carbon stabilization.}, }
@article {pmid42184943, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Zhang, J}, title = {In situ assembly of the humic acid-protein conductive network facilitates chain elongation for medium-chain fatty acids anaerobic production from waste activated sludge.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134964}, doi = {10.1016/j.biortech.2026.134964}, pmid = {42184943}, issn = {1873-2976}, mesh = {*Sewage/microbiology/chemistry ; *Humic Substances ; *Fatty Acids/biosynthesis ; Anaerobiosis ; *Proteins/metabolism ; }, abstract = {Biosynthesis of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) is primarily limited by intracellular reductive stress (NADH accumulation) and energy shortages. This work demonstrates that humic acid (HA), functioning as a redox mediator, effectively enhances the carbon chain elongation (CE) process. Optimal HA supplementation (1000 mg/L) increased the peak MCFAs yield by 98.3%, driving a fundamental shift in the dominant product spectrum from short-chain fatty acids (SCFAs) to MCFAs. Combined metagenomic and electrochemical analyses reveal that this enhancement originates from HA-mediated spatial and metabolic integration across multiple scales. Macroscopically, HA complexes with proteins to construct a conductive biopolymer network. Functioning as a highly efficient extracellular electron sink, this network significantly accelerates transmembrane electron discharge to consume excess intracellular electrons. This rapid electron extrusion alleviates reductive stress and relieves product feedback inhibition on dehydrogenases, concurrently inducing an elevated cellular energy charge (ATP surge). Subsequently, feedback regulation driven by this high-energy state suppresses the competitive acetogenic branch (Pta-ackA pathway), effectively preventing carbon loss. Dominated by the highly enriched CE taxon Candidatus_Microthrix, the microbial consortium exhibits a robust metabolic potential to channel carbon into synergistic RBO and FAB pathways. This metabolic shift, fueled by abundant precursors and energy, effectively circumvents acidic toxicity by rapidly consuming SCFAs. These findings elucidate the critical role of HA in reshaping microbial redox homeostasis, providing a robust mechanistic foundation for high-value carbon recovery engineering from complex solid wastes.}, }
@article {pmid42185267, year = {2026}, author = {Zhou, YL and Feng, JC and Lu, R and Chen, Z and Mara, P and Tao, X and Liu, J and Huang, Y and Hu, J and Yao, J and Edgcomb, VP and Teske, A and Wang, X and Zhang, S}, title = {Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73573-4}, pmid = {42185267}, issn = {2041-1723}, support = {42494884//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42325603//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly understood. Here we analyse the phylogenomic diversity at the species and strain levels of clade ANME-1 from deep-sea cold seeps, as a model system with a well-studied phylogenetic framework. We reconstruct high-quality circular metagenomic-assembled genomes (cMAGs) and identify highly variable genomic hotspots that distinguish them. Genomic differentiation and diversification in ANME-1 is associated with genes involved in prokaryotic defense systems, transport mechanisms and methane metabolism. In addition, heterologous expression of ANME-1 hicAB operons supports their proposed role as toxin/antitoxin systems, possibly involved in mediating responses to environmental stresses.}, }
@article {pmid42185302, year = {2026}, author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R}, title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01021-8}, pmid = {42185302}, issn = {2055-5008}, support = {2020/06077-9//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.}, }
@article {pmid42185318, year = {2026}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR}, title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73524-z}, pmid = {42185318}, issn = {2041-1723}, support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.}, }
@article {pmid42185326, year = {2026}, author = {Hoggard, M and Gios, E and Tee, HS and Geoghegan, JL and Handley, KM}, title = {DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73439-9}, pmid = {42185326}, issn = {2041-1723}, abstract = {Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and traits of environmental adaptation, we analyse metagenomic and metatranscriptomic data from an estuarine salinity gradient, including water and sediment. We then expand our analysis to globally-distributed viral genomes. Viral distributions vary by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, are largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, viruses feature osmoadaptive traits similar to their prokaryote hosts. These include slightly elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities, particularly in virus major tail and capsid proteins, which are not solely explained by reliance on host machinery. Further studies are needed to determine the primary driver of these modifications in viruses (e.g. environment or host) and whether these traits restrict virus distributions beyond host-range limitation. Overall, our findings indicate that successful proliferations of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) are rare, with viruses constrained to specific ecological niches.}, }
@article {pmid42185942, year = {2026}, author = {Wang, Y and Peng, Y and Wang, B and Di, M and Xi, M and Yao, Z and Shi, C and Feng, Q and Yin, D and Li, J and Xu, X and Zhang, R and Peng, X}, title = {A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42185942}, issn = {1674-9782}, abstract = {BACKGROUND: Under high-concentrate feeding conditions, ruminants often experience rumen microecological imbalance and dysfunction, which can impair growth performance and increase the risk of antibiotic resistance gene (ARG) dissemination.<br><br>RESULTS: To evaluate the ameliorative effects of Aspergillus niger (A. niger) cultures, fattening sheep were randomly allocated into the following five groups: a control group (CON), a control diet supplemented with 250, 500, or 1,000 mg/kg A. niger cultures (designated as LA, MA, and HA, respectively); and an antibiotic group supplemented with 5,000 mg/kg chlortetracycline premix (AN). Microbial community analysis indicated that several bacterial taxa, including Succinivibrio sp900317105, Prevotella sp002353485, Quinella sp017515635, Quinella sp015206805, and Prevotella sp900320255, were significantly enriched in the A. niger culture-supplemented groups (P&#x2009;<&#x2009;0.05). ARG profiling showed that the abundance of tetracycline resistance genes was significantly lower in all A. niger groups compared with the CON and AN groups (P&#x2009;<&#x2009;0.05), while &#x3b2;-lactam resistance genes were significantly reduced in the HA group (P&#x2009;<&#x2009;0.05). Furthermore, the abundances of Rank I and Rank II ARGs were significantly higher in the AN group than in the other groups, whereas the abundances of Rank II and Rank IV ARGs were significantly lower in the A. niger culture groups than in the CON and AN groups. Metabolomic analysis further demonstrated that supplementation with A. niger cultures significantly decreased the concentration of N-decanoyl-L-homoserine lactone (P&#x2009;<&#x2009;0.05) while increasing the levels of N-3-oxotetradec-7Z-enoyl-L-homoserine lactone, indole-3-methyl acetate, and indole-3-propionic acid (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest that A. niger cultures can reduce the abundance of ARGs and mitigate the risk of ARG dissemination by modulating the rumen microbial community and associated metabolites.}, }
@article {pmid42185948, year = {2026}, author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P}, title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12986-3}, pmid = {42185948}, issn = {1471-2164}, support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.<br><br>RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.<br><br>CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.}, }
@article {pmid42186028, year = {2026}, author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y}, title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01335-5}, pmid = {42186028}, issn = {1475-2891}, abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.<br><br>METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10&#xa0;years) and 133 adolescents (11-17&#xa0;years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.<br><br>RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.<br><br>CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.}, }
@article {pmid42186092, year = {2026}, author = {Wang, L and Li, F and Ma, Z and Ungerfeld, EM and Zhang, T and Zhang, Z and Liu, X and Zhang, Q and Zhang, X}, title = {Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02436-3}, pmid = {42186092}, issn = {2049-2618}, support = {32308686//The National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.<br><br>METHODS: We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.<br><br>RESULTS: The YC treatment increased the lambs' final body mass (P&#x2009;=&#x2009;0.02), average daily gain (P&#x2009;=&#x2009;0.03), digestibilities of&#xa0;neutral detergent fiber (P&#x2009;<&#x2009;0.001) and&#xa0;acid detergent fiber (P&#x2009;<&#x2009;0.001), and rumen pH (P&#x2009;<&#x2009;0.05), and tended to increase organic matter digestibility (P&#x2009;=&#x2009;0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6&#xa0;h post-morning feeding (P&#x2009;=&#x2009;0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.<br><br>CONCLUSION: Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H2. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.}, }
@article {pmid42186552, year = {2026}, author = {Méndez-Sánchez, D and Pomahač, O and Valt, M and Bourland, WA and Čepička, I}, title = {An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).}, journal = {Marine life science &amp; technology}, volume = {8}, number = {2}, pages = {289-323}, pmid = {42186552}, issn = {2662-1746}, abstract = {UNLABELLED: Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species-including three newly described-across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00352-x.}, }
@article {pmid42186601, year = {2026}, author = {Zhang, Z and Jia, Z and Zhang, X and Zou, W and Chen, J}, title = {Late-onset cytomegalovirus pneumonia after autologous stem cell transplantation for angioimmunoblastic T-cell lymphoma: a case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261450721}, pmid = {42186601}, issn = {2049-9361}, abstract = {This case report illustrates a diagnostic and therapeutic challenge in a highly immunocompromised host: severe pneumonia occurring late after autologous hematopoietic stem cell transplantation (auto-HSCT). A 57-year-old male with angioimmunoblastic T-cell lymphoma (AITL) presented with hypoxemic respiratory failure 1 year post-auto-HSCT, a timeline extending beyond the typical high-risk period for opportunistic infections. A profoundly low CD4+ T-cell count (172/µL) was identified as the key predisposing factor. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) enabled rapid, unbiased pathogen detection, confirming cytomegalovirus (CMV) pneumonia (viral load: 3.0 × 10[4] copies/mL) with Klebsiella pneumoniae coinfection. An integrated management strategy was instituted, comprising early empiric coverage for Pneumocystis jirovecii pneumonia, targeted therapy with ganciclovir and levofloxacin, and adjunctive immunomodulation using intravenous immunoglobulin and corticosteroids. This comprehensive approach resulted in full recovery, highlighting that the severity of immune suppression-rather than time since transplantation alone-determines infection risk. This case challenges the conventional time-based risk paradigm and supports immune-guided surveillance. It underscores the transformative role of mNGS in diagnosing complex infections in immunocompromised patients and advocates for a management paradigm that concurrently addresses pathogen eradication and host immune dysfunction.}, }
@article {pmid42186944, year = {2026}, author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F}, title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70160}, doi = {10.1111/1755-0998.70160}, pmid = {42186944}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; }, abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.}, }
@article {pmid42187250, year = {2026}, author = {Liu, X and Kwok, L-Y and Zhang, W}, title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0024426}, doi = {10.1128/spectrum.00244-26}, pmid = {42187250}, issn = {2165-0497}, abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.<br><br>IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.}, }
@article {pmid42187318, year = {2026}, author = {Tang, Y and Lin, Z and Liu, Z and Guo, J and Yang, C and Feng, L and Wang, Y and Zhang, P and Chen, Y}, title = {Impact of Corneal Microbial Latency Detected by Metagenomic next-generation sequencing on Postoperative Recovery Following Keratorefractive lenticule extraction.}, journal = {Journal of cataract and refractive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/j.jcrs.0000000000001979}, pmid = {42187318}, issn = {1873-4502}, abstract = {PURPOSE: To investigate the microbial species latent in corneas of healthy individuals and determine whether small incision lenticule extraction (SMILE) serves as a risk factor for pathogen reactivation.<br><br>SETTING: The Ophthalmology Department of Peking University Third Hospital, Beijing, China.<br><br>DESIGN: Prospective Cohort Study.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was employed to analyze the microbial composition of corneal lenticules from SMILE. Based on the results, patients were categorized into Viral Group (VG) and Non-Viral Pathogen Group (NVPG). Two Matched Groups (MG1 and MG2) were established by selecting pathogen-negative individuals at a 1:4 ratio relative to two positive groups. Using SPSS to analyze baseline characteristics, preoperative ocular parameters and postoperative ocular parameters among groups.<br><br>RESULTS: Among the detected pathogens, latent Herpesviruses were identified in 9 cases (4.31%), Papillomavirus were 4 cases (1.91%), and non-viral pathogens were 20 cases (9.57%). Both VG and NVPG groups showed no significant differences in baseline characteristics or preoperative ocular parameters compared with MG groups. In postoperative ocular parameters, no significant differences were found between VG and MG1, though intergroup variations in intraocular pressure and corneal thickness were observed (p>0.05). However, NVPG demonstrated significantly poorer results than MG2 in 1 month-spherical equivalent (p=0.033) and corneal epithelial staining (p=0.044).<br><br>CONCLUSION: These findings indicate pathogen latency does not affect ocular status and SMILE surgery is unlikely to reactivate latent viruses or exerts minimal influence. Viral latency has almost no impact on postoperative recovery, while latent non-viral pathogens may interfere with postoperative recovery.}, }
@article {pmid42187703, year = {2026}, author = {Sun, Q and Li, J and Xu, G and Zhou, C and Lei, K and Jiang, W}, title = {Source-Specific Nitrogen Inputs Are Associated with Pathway Partitioning Between Denitrification and DNRA in River Water.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187703}, issn = {2079-7737}, support = {Lishui City Key R&amp;D Program Projects.(2023zdyf03)//Lishui Ecological and Environmental Monitoring Center of Zhejiang Province/ ; }, abstract = {Understanding how external nitrogen sources regulate nitrogen fate in river water is critical for improving nitrogen removal and reducing greenhouse-gas risk. Here, short-term microcosm incubations were conducted using source water as the background matrix and seven representative source inputs. By integrating hydrochemical analyses, bacterial community profiling, metagenomics, RT-qPCR, and process-rate measurements, we evaluated source-dependent shifts in nitrogen-cycling pathways. Manure-related inputs generated the highest organic and nitrogen loading, suppressed nitrification, enhanced nrfA (cytochrome c nitrite reductase) abundance and transcription, and promoted DNRA, indicating a shift toward nitrogen retention via ammonium regeneration. In contrast, sewage-related inputs maintained relatively high NO3[-] availability, elevated nirS (cytochrome cd1 nitrite reductase) and nosZ (nitrous oxide reductase) expression, and enhanced denitrification, but also increased N2O production. Metagenomic, transcriptional, and rate-based evidence consistently identified 12 h as a critical window for source-dependent pathway redistribution, highlighting the importance of short-term monitoring for detecting rapid nitrogen-cycle responses following pollution inputs. These findings support source-oriented nitrogen management that considers both nitrogen loading and hydrochemical controls on nitrate fate.}, }
@article {pmid42187710, year = {2026}, author = {Singh, S and Tiwari, H and Singh, M and Gautam, V and Gautam, A and Gautam, HK}, title = {Expanding the Microbial Genomic Landscape and Biotechnological Applications of CRISPR-Cas Systems.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187710}, issn = {2079-7737}, support = {(File No.: ANRF/IRG/2025/000135/LS)//Anusandhan National Research Foundation (ANRF)/ ; CST/D-1187//Council of Science and Technology, Uttar Pradesh, India (CST-UP)/ ; }, abstract = {The CRISPR-Cas systems, identified initially as adaptive immune mechanisms in bacteria and archaea against viral threats, have rapidly evolved into transformative tools in genetic engineering and biotechnology. These RNA-guided systems are broadly classified into Class 1, comprising multi-subunit complexes, and Class 2, characterized by compact single-effector protein, such as Cas9, Cas12, and Cas13. Their remarkable structural and functional diversity enables microorganisms to adapt to diverse ecological niches, offering a vast repertoire of genome-editing strategies. Beyond their natural role in maintaining genome integrity and defense, CRISPR-Cas systems have been extensively repurposed for precise genome modification, transcriptional regulation, epigenetic editing, and nucleic acid detection. Recent advances in computational mining of microbial genomes and metagenomes have uncovered a broad range of novel CRISPR effectors with unique properties, distinct protospacer adjacent motif (PAM) requirements, RNA-targeting capabilities, miniature architectures, and promiscuous cleavage activities that significantly expand the molecular biology toolkit. The development of CRISPR-based technologies such as base editing, prime editing, gene knock-in/out, and live-cell DNA/RNA imaging exemplifies the versatility of these systems. Despite the challenges associated with delivering complex Class 1 systems, both classes are now being actively harnessed across diverse microbial platforms. Concurrently, the CRISPR-Cas research, particularly for guide RNA (gRNA) design and activity prediction, has revolutionized target specificity and editing efficiency. This review presents a comprehensive overview of CRISPR-Cas system diversity, their genomic landscape in microorganisms, and their cutting-edge biotechnological applications. It also emphasizes the transformative potential of CRISPR in synthetic biology, therapeutics, diagnostics, environmental remediation, and agriculture, while also addressing the ethical and biosafety considerations surrounding its deployment. As CRISPR-Cas systems continue to evolve, they stand at the forefront of innovations that bridge natural microbial immunity with engineered precision tools for next-generation biotechnology.}, }
@article {pmid42187714, year = {2026}, author = {Peng, D and Huang, T and Kang, W}, title = {Evolutionary Strategies for Heavy Metal Resistance: Genomic Plasticity in Pseudomonas Versus Stability in Aeromonas and Bacillus.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187714}, issn = {2079-7737}, support = {2025QT02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2024FY100200//Science &amp; Technology Fundamental Resources Investigation Program/ ; }, abstract = {Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)-three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R[2] > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.}, }
@article {pmid42187862, year = {2026}, author = {Mills, N and Mills, N and Suwannarach, N and Noirungsee, N and Kumla, J and Inwongwan, S and Yongsawas, R and Saksunwiriya, C and Domethong, V and Shoocongdej, R and Disayathanoowat, T}, title = {Fungal Communities Associated with Wooden Coffins in a Prehistoric Burial Cave.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {42187862}, issn = {2309-608X}, support = {2021//U.S. Ambassador's Fund for Cultural Preservation/ ; }, abstract = {Phi Man Long Long Rak Cave, located in Mae Hong Son Province, northern Thailand, is a prehistoric burial site containing ancient wooden coffins that have undergone biodeterioration, likely due to fungal activity. Both culture-dependent and culture-independent approaches were employed to characterize fungal communities and assess their roles in wood degradation. Culture-dependent analysis identified five Aspergillus isolates from the wooden coffins, most of which produced cellulolytic and hemicellulolytic enzymes; some isolates also produced organic acids, indicating significant degradative potential. Culture-independent analysis revealed a community dominated by Aspergillus, together with additional taxa such as Penicillium and Ceriporia that were not detected by cultivation, highlighting greater community diversity and demonstrating the complementarity of the two methods. Functional prediction indicated a predominance of saprotrophic fungi. The presence of shared dominant taxa between soil and coffin-associated substrates suggests ecological connectivity at the soil-coffin interface, although the direction of dispersal cannot be determined from the present data. All tested fungicides inhibited fungal growth, with the highest efficacy observed in the formulation containing the highest proportion of active components. Taken together, these findings provide insights into fungal biodeterioration processes and inform conservation strategies.}, }
@article {pmid42188011, year = {2026}, author = {Li, X and Deng, W and Zhang, Z and Tong, H and Cao, Y}, title = {Revealing the Formation Mechanism of Key Metabolites During Japonica Rice Storage Driven by Microbial Functional Genes.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188011}, issn = {2218-1989}, support = {2023010714-JH3/107//Liaoning Provincial Science and Technology Plan Project General Project/ ; 254358.//China Postdoctoral Science Foundation Project/ ; }, abstract = {BACKGROUND: To elucidate the evolution of metabolites and fungal communities during storage of fragrant japonica rice (Liaoxiangjing 1396), and to investigate the biosynthetic mechanisms of key compounds and their association with quality deterioration, this study examined rice samples stored under simulated conditions for 16 months.<br><br>METHOD: Samples were collected at 4-month intervals (designated R20, R14, R13, R12, and R11). Metabolites were identified using GC-MS non-targeted metabolomics, while fungal community structure was analyzed through metagenomics. Core mechanisms were further elucidated via PLS-DA, KEGG pathway enrichment, and multiomics association analysis.<br><br>RESULT: Results demonstrated that the fatty acid content of rice increased initially and then stabilized (from 12.24 mg/g in R20 to 17.63 mg/g in R12). A total of 263 metabolites were identified, with oxygenated organic compounds (38 species) and lipids/lepidid molecules (24 species) as the predominant categories. Twelve key differential metabolites were screened from the R20 and R12 groups, involving five major metabolic pathways, including amino acid metabolism and lipid metabolism. In the fungal community, Pseudomonas (60.2%) and Pantoea (38.19%) were dominant taxa, with a specific Pantoea species (Pantoea sp.) identified as a core potential biomarker. Multiomics association analysis revealed that Klebsiella dominated the ndhB energy metabolism pathway, while multiple bacteria cooperatively regulated the mcp chemotaxis pathway, interacting with monosaccharide and amino acid accumulation.<br><br>CONCLUSIONS: This study reveals that the storage quality deterioration of fragrant japonica rice is driven by the "metabolite-microbe-pathway" chain regulation, and the dynamic changes in key metabolites and fungal communities can serve as quality early warning targets.}, }
@article {pmid42188051, year = {2026}, author = {Deng, H and Zhang, R}, title = {TCM-Derived Natural Compounds Targeting the Gut Microbiota in Metabolic Dysfunction-Associated Steatotic Liver Disease: Gut-Liver Axis Mechanisms, Safety Considerations, and Translational Challenges.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188051}, issn = {2218-1989}, abstract = {The occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD) are closely related to intestinal flora imbalance, intestinal barrier damage, and gut-liver axis dysfunction. Due to their multi-target regulatory effects and advantages in intestinal microecological intervention, Chinese herbal monomers have shown promising application prospects in the prevention and treatment of MASLD. However, basic research on their toxicity still lags behind, and issues related to safety and clinical translation urgently need attention. This article systematically reviews the research progress on how flavonoids, triterpenoids, alkaloids, and polysaccharides improve hepatic steatosis, inflammatory responses, and metabolic disorders from a toxicological perspective by reshaping the intestinal microbiota, repairing the intestinal mucosal barrier, regulating short-chain fatty acid and bile acid metabolism, and synergistically acting on signaling pathways such as TLR4/NF-kB, FXR, TGR5, SIRT1, and the NLRP3 inflammasome. Furthermore, by combining methods such as 16S rRNA sequencing, metagenomics, metabolomics, and multi-omics integration, the article analyzes their application value and limitations in toxicological mechanism research, and discusses the translational bottlenecks faced by Chinese herbal monomers in pharmacokinetics, bioavailability, quality standardization, targeted delivery, and toxicological safety. Existing evidence indicates that Chinese herbal monomers have a three-in-one intervention advantage of microecological remodeling-metabolic regulation-inflammation inhibition, but their long-term medication safety, toxic target organs, dose-effect/toxicity relationships, and potential drug interactions still need further clarification. This article aims to provide a systematic reference for the safety evaluation and clinical translational research of Chinese herbal monomers in the prevention and treatment of MASLD.}, }
@article {pmid42188128, year = {2026}, author = {Sontigun, N and Thanawan, N and Fungwithaya, P}, title = {Epidemiology and Antimicrobial-Resistant Genes of Family Staphylococcaceae in Musca domestica: Case Studies from Chicken Farm, Pig Farms, and Residential Areas in Southern Thailand.}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, pmid = {42188128}, issn = {2075-4450}, support = {KREF186729//King Mongkut's Institute of Technology Ladkrabang Research Fund/ ; }, abstract = {The major Staphylococcaceae family is recognized as opportunistic pathogens colonizing human and animal skin, mucous membranes, and environments. Musca domestica, the house fly, plays a role in the transmission of AMR bacteria. This study focused on examining the epidemiology and antimicrobial-resistant genes of the family Staphylococcaceae in M. domestica through metagenomic analysis, using samples collected from three animal farms and two residential areas in southern Thailand. Fifty M. domestica were collected from five places surrounding Walailak University, including one chicken farm (CF1), two pig farms (PF2 and PF3), and two residential areas (H1 and H2). All samples were dispatched for analysis using shotgun metagenomic sequencing and analyzed using FastQC, MultiQC, FASTQ, MEGAHIT, QUAST, ABRicate, AMRFinderPlus, ResFinder, ARG-ANNOT, MEGARES, PlasmidFinder, VFDB, Kraken2, Krona and Python. Our findings describe the taxonomic composition of Staphylococcaceae taxa in M. domestica from different environments; the representation of the family Staphylococcaceae in CF1, PF2, PF3, H1, and H2 was recorded at 2%, 0.7%, 0.2%, 0.2%, and 2% of this phylum, respectively. The average populations discovered were Staphylococcus (37.4%), Mammaliicoccus (17.4%), and Macrococcus (10.3%), respectively. Trimethoprim-resistant genes (dfrG and dfrE) were found only in CF1, PF2, and H1. Interestingly, fosfomycin-resistant genes were found only in M. domestica within residential areas. Our findings pertain to the Staphylococcaceae population in M. domestica within residential areas, which exhibited varying multidrug-resistance genes, particularly those resistant to fosfomycin.}, }
@article {pmid42188162, year = {2026}, author = {Tao, M and Zhang, J and Fan, Y}, title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, pmid = {42188162}, issn = {2075-4450}, support = {Grant No. 32402469//National Natural Science Foundation of China/ ; }, abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.}, }
@article {pmid42188886, year = {2026}, author = {Yi, C and Nicolas, CS and Sun, Z and Wang, Q and Dong, T and Wu, Y}, title = {Effects of a Novel Prebiotic and Postbiotic Dietary Supplement on Gut Microbiota, Intestinal Barrier Markers, and Inflammation in Healthy Dogs.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188886}, issn = {2306-7381}, support = {202404810411350//Virbac China/ ; }, abstract = {Although prebiotics and postbiotics support gastrointestinal health, evidence for their combined effects in dogs remains limited. This study evaluated a novel prebiotic and postbiotic supplement in healthy dogs undergoing a dietary transition. Thirty-six healthy adult dogs were randomly assigned to control group (CON, high-protein basal diet with placebo chew) or treatment group (TRT, the same basal diet with chew containing prebiotics [baobab fruit pulp and acacia gum] and postbiotics [inactivated Lactobacillus acidophilus and selected yeast fractions]) for a 28-day formal trial following a 7-day adaptation period. The primary outcomes evaluated included clinical fecal scores, specific biomarkers of intestinal barrier function and inflammation, fecal short-chain fatty acids, and microbiota structure. Following the 7-day adaptation, formal trial baseline, fecal scores were already within the healthy range and remained optimal without differing between groups throughout the study. Compared with CON, the TRT group showed lower fecal calprotectin and serum diamine oxidase levels, and higher fecal butyrate (p < 0.05). Metagenomic analysis revealed increased abundances of Bacteroidota, Oscillospiraceae, Prevotellaceae, and Prevotella in TRT (p < 0.05). Overall, in healthy dogs, this supplementation was associated with favorable microbiota modulation and modulated biomarkers of intestinal barrier and inflammation within normal ranges, without altering clinical fecal endpoints.}, }
@article {pmid42188905, year = {2026}, author = {Yao, Y and Yang, Z and Xie, T and Zhang, Y and Huang, F and Meng, C and Wu, Y}, title = {Multi-Omics Analyses of the Gut Microbiota and Metabolism in Cats with Different Body Conditions and the Effects of Fecal Microbiota Transplantation.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188905}, issn = {2306-7381}, abstract = {Obesity is increasingly recognized in domestic cats and is associated with metabolic disturbances such as insulin resistance and dyslipidemia. The gut microbiota is considered an important regulator of host metabolism, yet its role in feline obesity remains unclear. In this study, a multi-omics approach was used to investigate gut microbiota composition and metabolic profiles in cats with different body conditions and to evaluate the effects of fecal microbiota transplantation (FMT) on the feline gut microbiota and overall metabolism. In Experiment 1, twenty-four cats were classified as obese, normal, or lean, and their gut microbiota and serum metabolites were analyzed. In Experiment 2, fecal microbiota from obese or lean donors were transplanted into recipient cats. Although overall microbial diversity and community structure did not differ significantly among groups, Coriobacteriaceae and Collinsella were enriched in obese cats, whereas Enterobacteriaceae-related taxa were more abundant in normal-weight cats. Serum metabolomics revealed alterations mainly related to amino acid and antioxidant metabolism, including O-acetylcarnitine, glutathione, and tryptophan metabolism. FMT shifted the recipient gut microbial communities toward their respective donor profiles (obese or lean) but did not significantly affect body weight or routine serum biochemical parameters during the experimental period. These findings suggest that gut microbiota remodeling may influence metabolic processes prior to detectable phenotypic changes in cats.}, }
@article {pmid42189102, year = {2026}, author = {Zheng, H and Xie, X and Zhang, L and Cai, Y and Zhang, Q and Yang, F and Liu, X and Basitere, M and Wei, C and Qiu, G}, title = {Intralineage Diversity and Global Biogeography of Ca. Phosphoribacter.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {22}, pages = {15964-15976}, doi = {10.1021/acs.est.5c18078}, pmid = {42189102}, issn = {1520-5851}, mesh = {*Metagenome ; *Phosphorus/metabolism ; Phylogeny ; *Actinobacteria/genetics/metabolism ; Sewage/microbiology ; }, abstract = {In wastewater treatment plants (WWTPs), the newly defined polyphosphate-accumulating organism (PAO) "Candidatus Phosphoribacter" demonstrated important contributions to phosphorus removal. However, their phylogenetic and metabolic diversity, as well as ecological distributions, remain largely uncharacterized. By sequencing 81 activated sludge samples from 34 provinces in China and integrating 747 WWTP metagenomes from six continents, we recovered 166 metagenome-assembled genomes (MAGs) of this genus, expanding the number of Ca. Phosphoribacter MAGs by 17 times and identifying 12 novel species. Biogeographical analysis demonstrated their distinct intercontinental distribution. The coexistence of cosmopolitan species and regionally dominant ones was observed globally as a result of metabolic differentiation. Ancestral gene family reconstruction indicated that this genus underwent a streamlining process dominated by gene loss. Vertically inherited ppk2 and horizontally acquired phoU jointly underpinned the genetic basis of a PhoU-dysregulation-driven polyphosphate phenotype. Comparative genomics revealed broad metabolic potential, including versatile carbon utilization, α-glucan metabolism, and three complementary denitrifying phenotypes. Metatranscriptomic analyses further supported glucose uptake and potential α-glucan cycling as a carbon storage polymer. Overall, this study establishes the most comprehensive genomic framework of Ca. Phosphoribacter, elucidates their functional metabolisms, ecological roles, and global distributions, providing new insights into Ca. Phosphoribacter-mediated enhanced biological phosphorus removal (EBPR) for improved engineering implementation and system sustainability.}, }
@article {pmid42189287, year = {2026}, author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M}, title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00262-026-04432-w}, pmid = {42189287}, issn = {1432-0851}, support = {PE00000019//NextGenerationEU/ ; }, abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.}, }
@article {pmid42189388, year = {2026}, author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G}, title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42189388}, issn = {1869-1889}, abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.}, }
@article {pmid42189604, year = {2026}, author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC}, title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.}, journal = {Kidney360}, volume = {}, number = {}, pages = {}, doi = {10.34067/KID.0000001219}, pmid = {42189604}, issn = {2641-7650}, abstract = {BACKGROUND: On the one hand, dietary interventions are known for their pivotal role in regulating diversity, composition as well as function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.<br><br>METHODS: Three protective dietary regimens - a fasting mimicking diet, a diet depleted in sulfur containing amino acids and caloric restriction - were examined in parallel in a rodent model of ischemia-reperfusion injury. To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage we used comparative shotgun metagenomics for taxonomic as well as functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.<br><br>RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary-preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial derived short chained fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed towards the metabolic use of these bacterial derived short-chained fatty acids in kidneys of protected mice.<br><br>CONCLUSIONS: As proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism and molecular nephrology.}, }
@article {pmid42190464, year = {2026}, author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A}, title = {Age, strain, and gut section shape the microbiome of commercial laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107152}, pmid = {42190464}, issn = {1525-3171}, abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.}, }
@article {pmid42190784, year = {2026}, author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM}, title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.}, journal = {International journal of biological macromolecules}, volume = {370}, number = {}, pages = {152693}, doi = {10.1016/j.ijbiomac.2026.152693}, pmid = {42190784}, issn = {1879-0003}, abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.}, }
@article {pmid42190825, year = {2026}, author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J}, title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124845}, doi = {10.1016/j.envres.2026.124845}, pmid = {42190825}, issn = {1096-0953}, mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis/chemistry ; *Geologic Sediments/chemistry/microbiology ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Molecular Weight ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Microbiota ; }, abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.}, }
@article {pmid42190956, year = {2026}, author = {Xia, R and Cui, B and Li, G and Zhou, H and Luo, W and Xu, Z}, title = {Integrated metagenomics unravels the microbial mechanisms driving greenhouse gas and odor emissions during composting.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {134984}, doi = {10.1016/j.biortech.2026.134984}, pmid = {42190956}, issn = {1873-2976}, mesh = {*Metagenomics/methods ; *Greenhouse Gases/analysis/metabolism ; *Composting ; Methane ; *Odorants/analysis ; *Bacteria/metabolism/genetics ; Nitrous Oxide/analysis ; Hydrogen Sulfide ; Temperature ; }, abstract = {While composting is widely used for the resource recovery of organic waste, it is complicated by greenhouse gas and odor emissions. An integrated analysis of emission characteristics and elemental metabolism mechanisms is essential for targeted control strategies. Using integrated metagenomics and modular network analysis, this study identified the biotic and abiotic factors driving gaseous emissions. Results showed that methane (CH4) and nitrous oxide (N2O) emissions mainly occurred during the mesophilic and cooling stages, whereas ammonia (NH3) and hydrogen sulfide (H2S) peaked at the thermophilic stage. Initially, acidogens (e.g. Klebsiella) and methanogens (e.g. Methanobacterium) promoted CH4 production via aceticlastic (e.g. ackA gene) and hydrogenotrophic (e.g. frhB gene) pathways. Meanwhile, nitrate-reducing bacteria and denitrifiers converted nitrate nitrogen to N2O via assimilatory/dissimilatory reduction and denitrification pathways, respectively. As temperature increased into the thermophilic stage, CH4 and N2O production decreased due to the thermal inhibition of acidogens and nitrate-reducing bacteria. However, intense mineralization of organic nitrogen/sulfur compounds released ammonium and sulfate ions, leading to NH3 volatilization and microbial H2S production by sulfate-reducing bacteria (e.g. Desulfitibacter) via synergistic assimilatory/dissimilatory sulfate reduction pathways. Reduced thermal inhibition at the cooling stage restored activity of acidogens and methanogens, which drove CH4 emission via all four pathways. Denitrifiers (e.g. Pusillimonas) with nirS and norC genes and nitrifiers (e.g. Devosia) with hao genes were also enriched, increasing N2O production. Nevertheless, N2O was ultimately reduced to N2 by denitrifiers carrying nosZ at the mature stage. These findings provide fundamental insights for developing targeted strategies to mitigate gaseous emissions during composting.}, }
@article {pmid42191017, year = {2026}, author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Barra Caracciolo, A and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V}, title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.}, journal = {New biotechnology}, volume = {94}, number = {}, pages = {121-135}, doi = {10.1016/j.nbt.2026.05.013}, pmid = {42191017}, issn = {1876-4347}, abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - such as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.}, }
@article {pmid42192344, year = {2026}, author = {Liu, L and Su, P and Gong, F and Wang, A and Wang, X and Yang, L and Mo, W and Jiang, T}, title = {Diagnosis and management of mixed Chlamydia abortus and psittaci pneumonia guided by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13691-y}, pmid = {42192344}, issn = {1471-2334}, support = {2023SK4077//the China Hunan Provincial Clinical Medical Technology Demonstration Base for Cardiac Arrest Diseases/ ; }, abstract = {BACKGROUND: Chlamydia abortus primarily causes abortion and stillbirth in animals and is associated with pregnancy-related complications in humans. However, it is an extremely rare cause of pneumonia in humans. While Chlamydia psittaci is a well-established respiratory pathogen, pneumonia resulting from a co-infection with both species has not been previously reported.<br><br>CASE PRESENTATION: A 57-year-old male presented with fever, cough, and shortness of breath. Imaging revealed extensive pulmonary inflammation and consolidation, which rapidly progressed to respiratory failure. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed a mixed infection with Chlamydia abortus and Chlamydia psittaci. Following the early initiation of targeted doxycycline therapy, the patient's clinical symptoms and pulmonary imaging showed significant improvement, leading to a full recovery and hospital discharge.<br><br>CONCLUSIONS: To our knowledge, this study reports the first case of atypical pneumonia caused by a mixed Chlamydia abortus and Chlamydia psittaci infection in a male patient, thereby expanding the clinical spectrum of these zoonotic pathogens. The case exhibited a "clinical-imaging dissociation," characterized by severe radiographic changes alongside relatively mild clinical symptoms. When conventional diagnostic methods failed to identify the pathogens, mNGS provided a rapid and precise diagnosis. Guided by this result, early targeted therapy with doxycycline achieved a marked therapeutic effect, preventing progression to severe disease and an adverse outcome.<br><br>TRIAL REGISTRATION: Not applicable.}, }
@article {pmid42192666, year = {2026}, author = {Liu, L and Wang, M and Wang, X and Liu, Y and Li, Z}, title = {Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192666}, issn = {2079-6382}, support = {242300420230//Natural Science Foundation of Henan Province/ ; }, abstract = {Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation.}, }
@article {pmid42192676, year = {2026}, author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW}, title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192676}, issn = {2079-6382}, support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; }, abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.}, }
@article {pmid42192677, year = {2026}, author = {Carneiro, PAM and Santos, LRD and Jardim, R and Silva, CBDGE and Araújo, FR and Dávila, AMR}, title = {Resistome and Mobilome Profiling of Raw Cow and Buffalo Milk from the Brazilian Amazon via Shotgun Metagenomics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192677}, issn = {2079-6382}, support = {408696/2024-9//Beef Cattle National Science and Technology Institute/CNPq/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.}, }
@article {pmid42192724, year = {2026}, author = {Skotareva, AE and Sokolova, EA and Voronina, EN}, title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192724}, issn = {2079-6382}, support = {125012300671-8//Russian state-funded project/ ; }, abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.}, }
@article {pmid42193165, year = {2026}, author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42193165}, issn = {2076-3921}, support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.}, }
@article {pmid42193259, year = {2026}, author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL}, title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42193259}, issn = {2076-3921}, support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; }, abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.}, }
@article {pmid42193752, year = {2026}, author = {Guo, T and Wan, B and Ye, Y and Zhang, Y and Mao, M and Li, R and Fang, Y and Lu, Y and Shao, R and Wu, Y and Wang, Y and Wu, J and Yang, H}, title = {A Prevotella-Rich Gut Microbiota and Microbial CAZymes Are Associated with Half-Diving Length in Ducks.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193752}, issn = {2076-2615}, support = {2024YFF1000900//National Key Research and Development Program of China/ ; 32302739//National Natural Science Foundation of China/ ; 32360830//National Natural Science Foundation of China/ ; 20243BCE51147//Ganpo Juncai Support Program/ ; QN2023015//Ganpo Juncai Support Program/ ; 20232ACB215003//Natural Science Foundation of Jiangxi Province/ ; }, abstract = {The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe-phenotype association in waterfowl.}, }
@article {pmid42193766, year = {2026}, author = {Qiu, G and Bai, H and Shi, J and Xue, Y and Wang, T and Qin, S and Zhou, X and He, K}, title = {Metagenomic and Metabolomic Analysis of Intestinal Excrement Differences Between Natural Hatching and Artificial Peeling out of the Shell in Nipponia nippon.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193766}, issn = {2076-2615}, support = {ZJXRDQ-2025-JC28//the Project for Enhancing the Reproductive Capacity of the Red-crowned Crane/ ; }, abstract = {The Nipponia nippon is a critically endangered species, and its breeding efforts are of vital importance for its conservation. Although artificial shell removal is sometimes employed in current breeding programs to increase survival rates, it may also have unknown impacts on chicks' development. To investigate the influence of artificial shell removal on the gut microbiota composition in Nipponia nippon, metagenomic sequencing and untargeted LC-MS/MS analyses were performed. Samples from the early, mid, and late stages of natural hatching (ZE, ZM, ZL) and artificial shell removal (RE, RM, RL) were compared. Results indicated that the natural hatching groups formed a unique, highly diverse, and stable community by the late stage (ZL). Conversely, artificial peeling caused the microbial community succession to stagnate at an intermediate state. The RL group experienced a sharp decline in alpha diversity and a significant enrichment of opportunistic pathogens, such as Edwardsiella, Clostridium, and Fusobacterium. Functionally, the microbial community in the RL group remained in a stage of expanding basic functions rather than reaching an advanced equilibrium state. Metabolomic analysis confirmed this developmental arrest, revealing abnormal accumulations of organic acids, such as citric acid, and indole derivatives in the RL group. This indicates metabolic dysregulation, stress, and altered microbial-host chemical signaling. Furthermore, the significant biomarker Edwardsiella was strongly correlated with multiple differential metabolites in the RL group. Ultimately, these results indicate that artificial peeling intervention disrupts environmental adaptation and induces metabolic alterations in the intestinal development of the Nipponia nippon chicks.}, }
@article {pmid42193830, year = {2026}, author = {Zhou, K and Shi, H and Kong, X and Ma, W and Kang, J and Che, H and Hua, Y}, title = {Wuwei Jianpi San Improves Growth Performance and Immune Status in Yaks Through Modulation of Rumen Microbiota and Host Metabolism.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193830}, issn = {2076-2615}, support = {CARS-37, CARS-07G-13//China Agriculture Research System of MOF and MARA/ ; No. Gaufx-03J01//Fuxi Foundation of Gansu Agricultural University/ ; 24YFNA016//Gansu Provincial Key Research and Development Program - Agriculture Field/ ; KJZC-2025-14//Modern Cold and Drought Characteristic Agricultural Science and Technology Sup-port Project of Gansu Province/ ; }, abstract = {To investigate the effects of Wuwei Jianpi San (WJPS), a Chinese herbal compound feed additive, on rumen microecology, host metabolism, and immune function in healthy yaks (Bos grunniens), and to determine the optimal supplementation level, 32 yaks with similar initial body weight were randomly assigned to four groups: a control group and three groups receiving 0.5%, 1.0%, or 2.0% WJPS for 90 days. Growth performance, hematological indices, serum antioxidant and immune parameters, tryptophan metabolites, ruminal short-chain fatty acids (SCFAs), and rumen microbiota were analyzed. WJPS supplementation improved growth performance, as shown by a reduced feed-to-gain ratio in all treated groups and tended to increase average daily gain in the 2.0% group. It also enhanced hematological, antioxidant, and immune status, evidenced by increased white blood cell (WBC) and lymphocyte (Lym) counts and elevated interleukin-2 (IL-2), immunoglobulin G (IgG), and superoxide dismutase (SOD) levels. Moreover, 2.0% WJPS increased total SCFAs, acetate, and n-butyrate, while WJPS reduced kynurenine pathway metabolites, including kynurenine, 3-hydroxykynurenine, and quinolinic acid. Metagenomic analysis showed that WJPS tended to shape rumen microbial composition by increasing Bacillota and decreasing Bacteroidota, and these microbial changes were associated with host immune indices and tryptophan metabolism. Overall, 2.0% WJPS showed the best comprehensive effect.}, }
@article {pmid42195821, year = {2026}, author = {Wang, X and Liu, X and Han, G and Erdene, K and Bai, C and Cao, Q and Zheng, Y and Hai, L and Ao, C}, title = {Allium mongolicum Regel-Mediated Rumen Microbiota Intervention Modulates Hepatic Metabolome to Reduce 4-Alkyl Branched-Chain Fatty Acids in Lamb Longissimus Thoracis Muscle.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195821}, issn = {2304-8158}, support = {32260839//National Natural Science Foundation of China/ ; }, abstract = {Deposition of three key 4-alkyl branched-chain fatty acids (KBCFA), including 4-methyloctanoic acid (MOA), 4-ethyloctanoic acid (EOA), and 4-methylnonanoic acid (MNA), causes the gamey flavor in sheep meat. This study integrated metagenomics and metabolomics to evaluate how Allium mongolicum Regel (AMR) supplementation (15 g/d) and rumen fluid transplantation (RFT) modulate rumen microbiota and hepatic metabolism to reduce KBCFA in lamb longissimus thoracis muscle. The experiment consisted of two phases. In Phase I, twelve 3-month-old male Dorper × Small Tailed Han sheep (25 ± 1 kg) were selected as the rumen donor group. These sheep were supplemented with 15 g/d/head of AMR powder in their basal diet until the end of the experiment. In Phase II, thirty 3-month-old male Dorper × Small Tailed Han sheep (23 ± 2 kg) were randomly assigned to one of three groups (n = 10 per group): the control group (STG), which was fed the basal diet and received a physiological saline transplant; the AMR group, which was fed the basal diet supplemented with 15 g/d/head of AMR powder and received a physiological saline transplant; and the rumen fluid transplant group (RTG), which was fed the basal diet and received a rumen fluid transplant from the donor group. Compared to the STG, results showed that the MOA, EOA, and MNA in the AMG decreased by 64.51%, 54.72%, and 49.34%, respectively. Similarly, the MOA, EOA, and MNA in the RTG were reduced by 63.13%, 56.17%, and 49.60%, respectively (p < 0.001). For the rumen metagenome, AMR enriched the genus Prevotella, while RFT increased Butyrivibrio. Hepatic metabolomics revealed a distinct shift where AMR elevated amino acid derivatives and RFT enhanced carnitine-related metabolites. These alterations indicate a potential metabolic shift associated with amino acid metabolism and mitochondrial β-oxidation, rather than lipid elongation. We postulate that this coordinated regulation across the rumen-liver-muscle axis may alter the availability of lipogenic precursors for KBCFA synthesis, ultimately contributing to improved meat flavor.}, }
@article {pmid42195847, year = {2026}, author = {Song, D and Yang, L and Zhang, C}, title = {Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195847}, issn = {2304-8158}, support = {32460269//National Natural Science Foundation of China/ ; MTXYTD202501//The Science and Technology Innovation Team of Moutai Institute/ ; Qiankehe Platform Talent-ZDSYS [2023] 007//Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation industry/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd./ ; }, abstract = {Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.}, }
@article {pmid42195939, year = {2026}, author = {Chen, P and Du, G and Chen, J and Fang, F}, title = {Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195939}, issn = {2304-8158}, support = {32172182//National Natural Science Foundation of China/ ; }, abstract = {Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce.}, }
@article {pmid42196007, year = {2026}, author = {Duo, Q and Zhao, Y and Osman, H and Shao, W and Zhao, Y}, title = {Correlation Between Microbial Communities and Volatile Organic Compounds in Camel Milk at Different Lactation Stages in Xinjiang, China.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42196007}, issn = {2304-8158}, support = {2023B02034-1//Xinjiang Academy of Agricultural Sciences/ ; XJARS-11-09//Xinjiang Academy of Agricultural Sciences/ ; xjnkywdzc-2026002-10//Xinjiang Academy of Agricultural Sciences/ ; }, abstract = {The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.}, }
@article {pmid42196140, year = {2026}, author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL}, title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196140}, issn = {1422-0067}, support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth &amp; development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; }, abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.}, }
@article {pmid42196196, year = {2026}, author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L}, title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196196}, issn = {1422-0067}, support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; }, abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.}, }
@article {pmid42196214, year = {2026}, author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT}, title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196214}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; }, abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.}, }
@article {pmid42196222, year = {2026}, author = {Zhang, X and Cai, L and Bai, Y and Peng, F}, title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196222}, issn = {1422-0067}, support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&amp;D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; }, abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.}, }
@article {pmid42196433, year = {2026}, author = {Zeng, Y and Lau, EYT and Ye, S and Lu, J and Zhang, R and Hu, R and Liang, JQ}, title = {Fecal Cloacibacillus porcorum Improves Non-Invasive Diagnosis of Colorectal Adenoma in the Hong Kong Population.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196433}, issn = {1422-0067}, support = {MRP/058/20//ITF-MRP, Hong Kong/ ; N/A//Hong Kong Ph.D. Fellowship Scheme (HKPFS)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; *Feces/microbiology ; Female ; Hong Kong/epidemiology ; Male ; Middle Aged ; Aged ; Biomarkers, Tumor/genetics ; Metagenomics ; ROC Curve ; }, abstract = {We previously developed a four-marker panel for the diagnosis of colorectal cancer (CRC) and adenoma. This study aimed to identify novel bacterial markers to improve adenoma detection using metagenomics and qPCR. Candidate markers were identified from metagenomic data (n = 492) using ANCOM-BC2 and Spearman's rank correlation analysis and were subsequently validated in an independent cohort (n = 426). Diagnostic performance was assessed both individually and in combination with our previously identified markers and FIT. Metagenomic analysis identified 21 candidate markers that increased along the normal-adenoma-carcinoma axis. Two top candidates, Cloacibacillus porcorum (Cp) and Intestinimonas butyriciproducens, were validated via qPCR and showed significant correlations with metagenomic abundances (both p < 0.0001). ROC analysis demonstrated that Cp levels significantly distinguished CRC and adenoma from controls, whereas I. butyriciproducens distinguished only CRC. The prevalence of Cp was significantly higher in adenoma and CRC than in controls (all p < 0.05). Multivariate analysis confirmed that Cp was independently associated with CRC and adenoma diagnoses. Adding Cp to the four-marker panel improved diagnostic sensitivity from 44.8% to 58.7% for adenoma and from 85.7% to 88.6% for CRC (specificity = 85%). When further combined with FIT, Cp improved sensitivity from 47.6% to 64.3% for adenoma and from 95.2% to 96.2% for CRC (specificity = 84.6%). C. porcorum is a novel bacterial marker that may aid in the non-invasive diagnosis of colorectal adenoma.}, }
@article {pmid42196657, year = {2026}, author = {Zafar, I and Shafiq, S and Khan, MS}, title = {Wastewater Treatment Challenges and Circular Reuse for One Health Sustainability: A Review.}, journal = {International journal of environmental research and public health}, volume = {23}, number = {5}, pages = {}, pmid = {42196657}, issn = {1660-4601}, mesh = {*Wastewater/analysis ; *One Health ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Humans ; *Recycling ; Environmental Monitoring ; }, abstract = {Wastewater is a complex and dynamic issue, particularly at the human-animal-environment interface, bearing biological and chemical hazards that may serve as a resource for transmission pathways for pathogens, antimicrobial resistance (AMR) determinants, heavy metals, pharmaceutical residues, per- and polyfluoroalkyl substances (PFAS), and microplastics. Rising global health issues necessitate effective wastewater treatment and advanced research to support risk-informed circular management within a one health framework, incorporating wastewater-based epidemiology (WBE), multi-omics approaches, nanobiotechnology, and green technologies. Inadequate wastewater treatment and uncontrolled discharge result in the generation of more than 380 billion cubic meters of wastewater annually worldwide, contributing to ecological degradation, the spread of AMR, and long-term toxicological risks. Despite significant advances in wastewater treatment, several challenges remain, including complex contaminant mixtures, limited detection and monitoring technologies, variable treatment efficiency, and weak regulatory and governance frameworks. This review highlights key wastewater treatment issues and presents recent advances in WBE and multi-omics approaches, such as metagenomics, resistome profiling, virome analysis, and chemical fingerprinting for contaminant monitoring and public health risk assessment. This review also examines circular reuse strategies focused on water reclamation, nutrient recovery, bioenergy production, and resource recovery, with particular emphasis on nature-based systems, hybrid biological-physicochemical treatment platforms, and green nanobiotechnology as promising approaches to improve treatment performance while minimizing environmental impacts. In conclusion, this review highlights the importance of integrated and sustainable wastewater management approaches within the One Health framework to address emerging challenges and promote environmental resilience, public health protection, and circular resource recovery.}, }
@article {pmid42197004, year = {2026}, author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH}, title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197004}, issn = {2072-6643}, support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.<br><br>METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.<br><br>RESULTS: The results showed that the a-FMT group recovered &#x3b1; diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.<br><br>CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.}, }
@article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, }
@article {pmid42197087, year = {2026}, author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y}, title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197087}, issn = {2072-6643}, support = {2020YFC2002902//Beijing Sport University/ ; }, mesh = {Aged, 80 and over ; Female ; Humans ; Male ; *Exercise/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Malnutrition/microbiology/therapy ; Nursing Home Residents ; Nursing Homes ; Nutrition Assessment ; *Nutritional Status ; }, abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.<br><br>METHODS: A total of 129 nursing home residents (&#x2265;80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF &#x2265; 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.<br><br>RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.<br><br>CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.<br><br>CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).}, }
@article {pmid42197123, year = {2026}, author = {Rojas-Flores, SJ and Liza, R and Nazario-Naveda, R and Díaz, F and Delfin-Narciso, D and Cardenas, MG and Cabanillas-Chirinos, L}, title = {Mapping the Convergence of Frontier Technologies for Major Environmental Challenges: A Chemical and Molecular Perspective on the Use of AI for Climate Action and Antimicrobial Resistance.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {10}, pages = {}, pmid = {42197123}, issn = {1420-3049}, mesh = {*Artificial Intelligence ; *Climate Change ; Metagenomics ; Humans ; *Drug Resistance, Microbial ; }, abstract = {The planet faces the critical interconnected challenges of climate change and antimicrobial resistance (AMR); these two crises mutually reinforce each other, threatening global health and ecosystem stability. This study conducts a systematic documentary analysis to map the convergence and identify the structural gaps between two key technological domains: artificial intelligence (AI) for climate action and molecular methods for AMR. The methodology was based on a corpus of 179 scientific documents indexed in Scopus (2010-2025), analyzed with data science tools to identify trends, collaborations, and impact. Quantitative results revealed clear leadership by the United States, accounting for 37.4% of publications, followed by China (26.8%); this leadership reflects the concentration of high-throughput molecular surveillance infrastructure and data science clusters essential for monitoring the environmental resistome. In terms of scientific impact, Spain showed the highest average, with 32.8 citations per article. The most influential work, a review on food security and sustainability, accumulated 275 citations. Network analysis identified authors such as Zhu, Yongguan, with 240 citations in total, as central nodes in international collaborations. Thematically, metagenomics and machine learning emerged as mature and interconnected research cores. This analysis confirms a solid yet still fragmented relationship between the two fields. The analysis reveals that, while metagenomic tools dominate the current literature, a gap persists in correlating genotypic resistance potential with functional phenotypic expression under changing climatic stressors. The results confirm a solid yet still fragmented foundation, highlighting the need for hybrid platforms that transition from descriptive bibliometrics to functional integration for designing systemic solutions. Future work should prioritize the development of hybrid platforms, such as intelligent biosensors, and collaborative governance frameworks that accelerate effective responses to these dual crises.}, }
@article {pmid42197331, year = {2026}, author = {Manoharan, RK and Shin, HD and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and La, IJ and Lee, DH and Han, KI and Srinivasan, S}, title = {Shotgun Metagenomic Analysis of Gut Microbiota and Antibiotic Resistance Genes in a High-Fat Diet Mouse Model Treated with Heat-Killed Lactiplantibacillus plantarum beLP1.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197331}, issn = {2076-2607}, abstract = {The gut microbiota is a central regulator of metabolic function, and its disruption by a high-fat diet (HFD) is strongly linked to obesity and metabolic impairment. This study evaluated the potential of heat-killed Lactiplantibacillus plantarum beLP1 (beLP1[®]) in alleviating HFD-induced metabolic and microbial imbalances in mice. Male C57BL/6N mice were fed an HFD for 10 weeks, with or without daily oral supplementation of beLP1 (≥3 × 10[10] cells). Compared with untreated HFD mice, beLP1 supplementation reduced serum triglycerides by 35% and lowered liver enzymes AST and ALT by 17% and 36%, respectively. Blood glucose levels remained similar to the HFD group throughout the study period. Shotgun metagenomic analysis revealed that beLP1 restored gut microbial diversity, increased beneficial taxa such as Akkermansia and Faecalibaculum high. and reduced pro-inflammatory species including Streptococcus sp., Mucispirillum schaedleri and Clostridium cocleatum. These microbial changes were associated with partial normalization of the Firmicutes/Bacteroidota ratio and improvements in antibiotic resistance gene (ARG) profiles. Specifically, in silico analysis of the short-chain fatty acid (SCFA) synthesis pathways indicated that the potential for acetate and propionate production was maximized in the beLP1 group, resulting in the highest relative abundance among all groups. This functional enhancement directly correlated with the enrichment of key SCFA-producing taxa, particularly Akkermansia muciniphila, confirming that increased bacterial abundance suggests an enhanced functional potential for SCFA production. Furthermore, beLP1[®] induced a selective modulation of gut ARGs, significantly reducing specific subtypes such as tetracycline and multidrug efflux genes, despite a slight increase in vancomycin resistance markers. Overall, our findings suggest that beLP1[®] attenuated the rate of body weight gain during the initial weeks of HFD exposure and significantly improved markers of hepatic stress and lipid metabolism.}, }
@article {pmid42197333, year = {2026}, author = {Zhao, Z and Wang, X and Wen, F and Zhao, F and Zhang, M and Menghe, B}, title = {Integrated Metagenomic and Metabolomic Profiling Identifies Predictive Biomarkers for Overweight Status in a Mongolian Population.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197333}, issn = {2076-2607}, support = {2018YFE0123500//Special Funds for International Science and Technology Cooperation of China/ ; }, abstract = {Mongolians have high overweight prevalence linked to their nomadic lifestyle and diet, but gut microbiota studies in this population are scarce. This study used fecal metagenomic and serum metabolomic analyses of 96 Mongolian participants (normal-weight n = 55, overweight n = 41) to characterize gut microbiome alterations and identify weight-related biomarkers. The analyses revealed that Parabacteroides distasonis, Barnesiella intestinihominis, and Alistipes onderdonkii were significantly reduced in overweight individuals (p < 0.05). Concurrently, the metabolites such as beta-cryptoxanthin, p-cresol, and ribothymidine were significantly down-regulated in the overweight group (p < 0.05). Random forest models from the three datasets showed a strong diagnostic ability for microbial families (AUC > 0.70). A subsequent integrated multi-kingdom classifier that combined microbiota and metabolite data achieved the highest performance (AUC = 0.818). Key features with high predictive contributions were identified, including Lactobacillus crispatus, Alistipes onderdonkii, and Parabacteroides distasonis, and metabolites, such as beta-cryptoxanthin, p-cresol, and picolinic acid. These results show the random forest model has high predictive value for distinguishing normal weight and overweight individuals. In summary, this study identified specific gut microbiota and serum metabolomic profiles linked to overweight in Mongolians. Multi-omics integration established a diagnostic biomarker model, laying a theoretical basis for microbiome-targeted weight management interventions.}, }
@article {pmid42197335, year = {2026}, author = {Naranjo-Moran, J and Ratti, MF and Vera-Morales, M}, title = {Microorganisms from Antarctica: A Review of Their Potential in the Bioremediation of Hydrocarbon-Contaminated Soils.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197335}, issn = {2076-2607}, abstract = {Antarctica's extreme cryospheric conditions impose severe thermodynamic constraints on the natural attenuation of hydrocarbon pollutants. Despite the Antarctic Treaty System's protections, the footprint of human logistics has left persistent reservoirs of petroleum hydrocarbons that threaten endemic biodiversity. This review critically synthesizes the state-of-the-art in Antarctic bioremediation, moving beyond traditional culture-dependent studies to integrate recent multi-omics breakthroughs (2020-2025). We analyze the molecular mechanisms limiting bioavailability in frozen soils and highlight the adaptive strategies of psychrophilic consortia, including the modification of membrane fluidity and the expression of cold-active enzymes (e.g., RHDs, AlkB). Notably, we discuss emerging findings on novel long-chain alkane degradation genes (almA, ladA) identified in 2025, which challenge previous assumptions about recalcitrance. Furthermore, the review evaluates the engineering bottlenecks of in situ versus ex situ strategies, emphasizing the synergistic potential of bacterial-fungal co-cultures and the ecological necessity of "climate-smart" remediation to mitigate methane emissions from thawing permafrost. By bridging the gap between fundamental microbial genetics and applied field engineering, we propose a roadmap for the next generation of biotechnological solutions in the warming polar environment.}, }
@article {pmid42197351, year = {2026}, author = {Huang, W and Liang, J and Chan, P and Liu, Z and Guo, L}, title = {Probiotics Exert Colonization Resistance Against F. nucleatum subsp. polymorphum: Disruption by Antibiotics and Underlying Molecular Mechanisms.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197351}, issn = {2076-2607}, support = {81670982//National Natural Science Foundation of China/ ; }, abstract = {Fusobacterium nucleatum (F. nucleatum), a key oral pathogen, promotes colorectal cancer (CRC) progression via gut translocation. Although gut probiotics provide colonization resistance against pathogens, antibiotic-induced dysbiosis may facilitate F. nucleatum integration and increase the risk of CRC. The mechanisms underlying probiotic-F. nucleatum antagonism and antibiotic modulation remain unclear. A 33-strain probiotic consortium and F. nucleatum subsp. Polymorphum (F. polymorphum) ATCC 10953 were co-cultured. The inhibitory effects of probiotics on F. nucleatum and the impacts of antibiotics (ABXs) on the microbial community structure in the co-culture system and on the probiotic-mediated inhibition of F. nucleatum were evaluated using spent medium assays, plate confrontation tests, growth curves, qRT-PCR, metagenomic sequencing, and transcriptomics. Hydrogen peroxide/pH/lysine assays and coaggregation models were performed to probe the associated mechanisms. Probiotics strongly inhibited the growth of F. nucleatum in a dose-dependent manner, primarily via organic acids, while F. nucleatum enriched amino acid/vitamin biosynthesis pathways without major growth suppression. Antibiotics weakened probiotic antagonism, shifted species abundance (↓ L. plantarum, ↑ L. paracasei), induced adaptive stress responses in F. nucleatum (↑ nucleotide metabolism, propanediol degradation, pdxS), and reduced lysine biosynthesis. Lysine supplementation restored probiotic abundance and disrupted F. nucleatum coaggregation. Multi-strain probiotics exert potent colonization resistance effects against F. nucleatum, mainly through organic acids and metabolic interference. Antibiotic-induced dysbiosis impairs this protective effect and may promote the persistence of F. nucleatum, which has been implicated in CRC risk. Targeted probiotic strategies may offer novel preventive approaches.}, }
@article {pmid42197355, year = {2026}, author = {Feletti, R and Mori, A and Zaffagnini, A and Castilletti, C and Pomari, E}, title = {The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197355}, issn = {2076-2607}, support = {PE00000007, INF-ACT//EU funding within the MUR PNRR/ ; 5MIL-VISA L1P17//Italian Ministry of Health/ ; }, abstract = {The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral "dark matter"; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae-particularly torque teno virus-reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance.}, }
@article {pmid42197366, year = {2026}, author = {Huang, Z and Chen, S and Fan, A and Chen, Y and Cai, Q and Zeng, T and Zheng, W and Yang, Y}, title = {Iron-Containing Flocs Derived from Environmental Emergency Response Influenced Nitrogen Cycling Driven by Microorganisms in River Sediments.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197366}, issn = {2076-2607}, support = {PM-zx703-202204-155//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PM-zx097-202506-204//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl3), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl3 caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level.}, }
@article {pmid42197381, year = {2026}, author = {Li, X and Liang, X and Hao, P and Wu, J and Liu, D}, title = {Compound Yeast Culture Reshapes Gut Microbiota and Functional Pathways to Enhance Antioxidant Capacity and Immune Homeostasis in Suckling Calves.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197381}, issn = {2076-2607}, support = {2022YFDZ0051//Inner Mongolia Autonomous Region Science and Technology Project/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Autonomous Region/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; }, abstract = {Diarrhea in suckling calves is associated with impaired growth, oxidative stress, immune dysfunction, and intestinal microbial dysbiosis. This study evaluated the effects of compound yeast culture (CYC) supplementation on growth performance, fecal characteristics, antioxidant capacity, immune function, and gut microbiota in diarrheic Holstein calves. Thirty-six approximately 7-day-old calves were enrolled, including 12 healthy calves (CON) and 24 diarrheic calves randomly assigned to a diarrhea group (DIA) or a CYC-supplemented group (DIA-YC; 50 g/d for 30 days). The experimental period lasted 60 days. Compared with the DIA group, calves in the DIA-YC group showed significantly higher average daily feed intake and average daily gain (ADG) during days 31-60 and across the entire period (p < 0.05), with a trend towards increased body weight. Fecal scores were significantly elevated in diarrheic calves during the early and mid-stages but were markedly reduced by CYC supplementation from days 7 to 30; no significant difference was observed between DIA-YC and CON during days 16-30 (p > 0.05). Diarrheic calves exhibited oxidative stress, characterized by decreased total antioxidant capacity (T-AOC) and increased malondialdehyde (MDA). CYC supplementation significantly increased T-AOC, superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities, while reducing MDA levels (p < 0.05). Immune analysis showed higher serum IgG and IL-10 levels and lower TNF-α levels in the DIA-YC group, along with improved intestinal barrier indicators, including diamine oxidase (DAO) activity and endotoxin levels. Metagenomic analysis revealed that diarrhea reduced microbial richness and diversity and altered community structure, whereas CYC partially restored microbial diversity and increased beneficial genera such as Prevotella, Coprococcus, Ruminococcus, and Parabacteroides. Functional analysis indicated that CYC enhanced pathways related to immune regulation, energy metabolism, and antioxidant function. CYC supplementation alleviates oxidative stress and immune dysfunction by modulating gut microbiota, thereby improving growth performance and reducing diarrheal severity in calves.}, }
@article {pmid42197408, year = {2026}, author = {Qie, T and Lin, D and Fan, Q and Sun, G and Wang, H and Liu, Z and Liu, X}, title = {Responses of Soil Nitrogen-Cycling Microbial Communities and Functional Potential to Grazing Intensities in Alpine Meadows.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197408}, issn = {2076-2607}, support = {KLGE202209//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 32260354//National Natural Science Foundation of China/ ; KLGE-2024-01//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 2023-QN-46//Lanzhou Science and Technology Bureau/ ; 2500011004//Gansu Agricultural University/ ; }, abstract = {Although grazing is a key driver of nitrogen cycling in alpine meadow soils, a systematic understanding of how different grazing intensities shape the structure and functional potential of soil nitrogen-cycling microbial communities remains lacking. In this study, soil samples were collected under five grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing, and extreme grazing) and metagenomic sequencing was employed to analyze variations in nitrogen-cycling microbial communities and functional genes. The results showed that bacteria were the dominant group in nitrogen-cycling communities (relative abundance: 93.99-98.98%), with significant community differentiation across grazing intensities. Light grazing maintained relatively high microbial diversity, whereas moderate and heavy grazing led to more pronounced differences in community composition. Functional gene analysis identified 41 nitrogen-cycling-related genes, primarily involved in denitrification, nitrate reduction, and ammonia assimilation. Light grazing enhanced nitrate reduction and glutamate synthesis; moderate grazing exhibited the strongest ammonia assimilation potential; heavy grazing significantly increased denitrification activity, indicating an elevated risk of nitrogen loss; and under extreme grazing, both the number and abundance of nitrogen-cycling functional genes declined markedly, with functional composition becoming simplified. Collectively, light grazing is more conducive to maintaining the balance between soil microbial diversity and nitrogen-cycling function in alpine meadows, whereas overgrazing disrupts the equilibrium between microbial communities and nitrogen metabolism. This study provides a microbiological basis for the restoration of degraded alpine meadows and sustainable grazing management.}, }
@article {pmid42197422, year = {2026}, author = {Shaik, SM and Schiro, G and Laubitz, D and Madan, JC and Kelley, CP and Daines, M and Rice, SA and Ghishan, FK and Kiela, PR}, title = {Functional Shifts in Gut Microbiota and Associated Metabolites Suggest Gut-Brain Axis Dysregulation in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS).}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197422}, issn = {2076-2607}, support = {NA//Alex Manful Fund/ ; RFGA2022-010-23//Arizona Department of Health Services/ ; }, abstract = {Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host-microbiome interactions in modulating neuro-immune functions via gut-brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut-brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe-metabolite networks allied to gut-brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut-brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.}, }
@article {pmid42197470, year = {2026}, author = {Zheng, Y and Wu, R and Feng, H and Wu, X and Yang, Y}, title = {Temperature Elevation Alters the Gut Antibiotic Resistome and Carbohydrate-Active Enzymes in the Desert Lizard Eremias roborowskii.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197470}, issn = {2076-2607}, support = {32560265//National Natural Science Foundation of China/ ; 32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; XJAUGRI2025030//Xinjiang Agricultural University Graduate Research Innovation Program/ ; }, abstract = {In the context of global warming, the resulting persistent thermal stress has become a critical environmental factor influencing the structural and functional homeostasis of gut microbiota in reptiles. In this study, Eremias roborowskii, a desert lizard endemic to the extreme heat conditions of the Turpan Basin, was selected as an ideal model for evaluating the ecological impacts of global warming. Meanwhile, a 60-day controlled laboratory experiment was conducted, exposing the lizards to normal (30 °C ± 1 °C), elevated (37 °C ± 1 °C), and high (42 °C ± 1 °C) temperatures to reflect future climate scenarios. Using shotgun metagenomic sequencing, the gut microbiota was characterized to investigate the dynamics of the antibiotic resistance genes (ARGs) and carbohydrate-active enzymes (CAZymes) under heat stress. The results reveal that elevated temperature selectively promotes heat-tolerant gut microbiota, such as Tetragenococcus and Faecalicatena, by altering host energy metabolism and modulating heat stress adaptation to maintain intestinal homeostasis. Moreover, the observed increase in resistome diversity and richness under elevated temperature may be attributed to temperature-induced shifts in gut microbial composition, particularly the enrichment of heat-tolerant ARG-carrying bacterial taxa. Metabolic changes in CAZymes were caused by gut microbiota remodeling, which optimized carbon utilization and preferentially allocated cell wall synthesis and repair. Furthermore, the pentose phosphate pathway and amino acid biosynthesis pathways were upregulated, providing NADPH for antioxidant defense and precursors for protein synthesis, respectively, thereby contributing to the maintenance of microbial cellular homeostasis. Our study provides a theoretical basis for understanding functional gene adaptation strategies in wildlife microbiomes due to climate change.}, }
@article {pmid42197480, year = {2026}, author = {Duran Yunga, ER and Rodriguez Coyago, ML}, title = {Structure and Function of the Dental Plaque Microbiome in Eubiosis: A Systematic Review of Ethnic-Racial Influences.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197480}, issn = {2076-2607}, abstract = {While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient's biological heritage.}, }
@article {pmid42197517, year = {2026}, author = {Albastaki, A and Smith, J}, title = {Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197517}, issn = {2076-2607}, abstract = {Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the community is described. Three approaches now dominate soil microbiome research: short-read 16S rRNA amplicon sequencing on Illumina platforms, full-length 16S sequencing on Oxford Nanopore Technologies (ONT) platforms (particularly the R10.4.1 flow cell), and long-read shotgun metagenomics. Each has distinct biases that shape the recovered community, yet researchers routinely select a method based on cost, understanding, or local expertise rather than on a clear knowledge of what each approach methodically over- or under-represents. Here, we review head-to-head benchmarking studies that have applied two or more of these methods to the same soil or directly comparable samples. We show that while long-read and short-read 16S approaches generally converge on dominant taxa and on between-sample differences, they disagree substantially on alpha diversity estimates, rare taxon detection, and the relative abundances of entire phyla. The R10.4.1 flow cell chemistry has narrowed but not eliminated the accuracy gap with Illumina, and shotgun metagenomics reveals systematic biases in both short and long-read assembly that depend on population diversity within the sample. We synthesise this evidence into an evidence-based decision framework tied to specific research questions and recognise the gaps in soil-specific benchmarking that limit current methods. Rather than asking which platform is "best," we argue that method choice should be framed as an important part of study design, with the biases of the chosen method acknowledged and, where possible, controlled for.}, }
@article {pmid42197550, year = {2026}, author = {Zhang, S and Li, G and Zhu, E and Zhao, Y and Yang, X and Huang, S and Zheng, Z}, title = {Rhizosphere Microbial Community and Metagenomic Annotation Responses in a Vallisneria natans-Sediment Microcosm Exposed to Trifluenfuronate and Fluopyram.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197550}, issn = {2076-2607}, support = {2023YFD1700403//the National Key Research and Development Program of China/ ; 2024R054//Zhejiang Shuren University/ ; }, abstract = {Rhizosphere microorganisms play central roles in nutrient cycling and contaminant transformation in sediment-associated freshwater systems, yet their responses to newer pesticides remain insufficiently characterized. In this study, a 28-day Vallisneria natans-rhizosphere sediment microcosm was used to compare the effects of trifluenfuronate and fluopyram at nominal concentrations of 0.01, 0.1, and 1 mg L[-1]. Bacterial community composition was assessed using 16S rRNA gene sequencing, and shotgun metagenomic data were used to evaluate relative functional annotation patterns. Plant physiological traits and rhizosphere sediment enzyme activities were measured as ecological context for interpreting microorganism-associated responses. Fluopyram, particularly at 1 mg L[-1], produced clearer ordination-level shifts in rhizosphere bacterial community composition than trifluenfuronate, although pairwise treatment separation was not statistically resolved after multiple-testing correction. Annotation-based metagenomic profiles also differed between the two pesticides: stronger exposure was associated with reduced relative signals for several xenobiotic-, transport-, and regulation-related annotations, while high-dose fluopyram showed a methane-metabolism-related annotation signal and high-dose trifluenfuronate showed relative enrichment of secondary-metabolism-related annotations. These microbial and annotation-profile responses coincided with stronger inhibition of V. natans growth and greater suppression of rhizosphere sediment enzyme activities under fluopyram exposure. Overall, fluopyram induced more consistent microorganism-associated response patterns than trifluenfuronate in the tested rooted macrophyte-sediment microcosm. The results highlight the sensitivity of rhizosphere microbial communities and metagenomic annotation profiles to pesticide exposure in sediment-associated freshwater systems.}, }
@article {pmid42197616, year = {2026}, author = {Wang, W and Yang, W and Song, W and Huang, S and Lai, J and Zhou, Z and Wang, P and Wang, B}, title = {Rhizosphere Microbial Effects on Soil Quality of Pinus massoniana and Schima superba Mixed Plantations.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42197616}, issn = {2223-7747}, support = {2023YFD2200902//National R&amp;D Program of China/ ; CAFYBB2024ZA021//Fujian Sanming Demonstration and Model Construction Project of China/ ; }, abstract = {This study aimed to reveal the rhizosphere microbial community structure, carbon-nitrogen-phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality improvement, providing a theoretical basis in soil microbiology for the cultivation of these mixed forests. The research subjects included pure P. massoniana plantations (CLPs), pure S. superba plantations (CLSs), and individual P. massoniana (HJP) and S. superba (HJS) trees within mixed plantations (HJLs). We collected rhizosphere and bulk soil samples to analyze their physicochemical properties and enzyme activities. Metagenomic sequencing was employed to profile the rhizosphere microbial communities and functional genes involved in C-N-P cycling. Furthermore, by integrating a functional gene co-occurrence network analysis with structural equation modeling (SEM), we systematically elucidated the coupling relationships among the stand types, soil properties, microbial communities, and nutrient cycling. Mixed planting significantly improved soil quality; compared to the CLP and CLS forests, the nitrate nitrogen (NO3[-]-N) content in the mixed forest soils increased by 121.01% and 120.10% (p < 0.05), and the activity of urease (URE) also significantly increased by 123.99% and 49.56%, respectively. Mixing significantly altered the microbial community structure. In the bacterial community of the mixed forests, the abundance of nitrogen-fixing and potentially phosphorus-solubilizing bacteria from the genera Paraburkholderia and Burkholderia increased. In the fungal community, the arbuscular mycorrhizal fungus Rhizophagus, which possesses a nutrient absorption advantage, exhibited absolute dominance, with its relative abundance ranging from 14.84% to 88.81%. The abundances of genes associated with denitrification and phosphorus starvation regulation were significantly upregulated in the mixed forests; notably, the abundance of phosphorus starvation regulation genes in the HJSs was 18.84% higher than that in the CLSs. A co-occurrence network analysis demonstrated that the proportion of positive correlation edges in the HJP nitrogen cycling network reached as high as 75.0%, and the average degree of the HJS phosphorus cycling network (2.691) surpassed that of the CLSs. The structural equation modeling further revealed that the association strength between the fungi and phosphorus cycling genes in the mixed forests increased to R[2] = 0.915 (p < 0.01) from R[2] = 0.213 in the pure forests. This mixed planting practice transforms nutrient cycling from a resource-competitive mode to a microbially synergized mode, thereby forming an efficient endogenous nutrient cycling system. This synergistic rhizosphere microbial effect is a key internal mechanism for overcoming nutrient bottlenecks and should serve as a diagnostic indicator of soil recovery in the ecological restoration of degraded pine forests.}, }
@article {pmid42198637, year = {2026}, author = {Malleret, B and Kwak, ML and Chavatte, JM}, title = {Accelerating Progress on Ticks and Tick-Borne Diseases in Southeast Asia: Regional Challenges, Evidence Gaps, and Priorities (2023-2025).}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42198637}, issn = {2076-0817}, support = {NUHSRO/2025/017/T1/Seed-Sep24/Adhoc/01//Ministry of Education/ ; }, mesh = {Animals ; Humans ; Asia, Southeastern/epidemiology ; Evidence Gaps ; *Tick-Borne Diseases/epidemiology/prevention &amp; control ; *Ticks/microbiology ; Congresses as Topic ; }, abstract = {Southeast Asia (SEA) faces persistent gaps in regional understanding and control of ticks and tick-borne diseases (TBDs) despite recent advances (2023-2025). The second international symposium on ticks and TBDs in SEA (Singapore, August 2025), following the inaugural 2023 meeting in Cambodia, served as a catalyst for regional exchange that informed this perspective. SEA's ecological and host diversity supports complex tick-host-pathogen networks, yet evidence remains fragmented due to uneven sampling that has largely focused on livestock and peri-urban environments. Key constraints include limited taxonomic resolution driven by outdated or incomplete identification keys, under-sampling of soft ticks (Argasidae), and the absence of harmonized, open-access regional reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). While MALDI-TOF MS, proteomics, AI-assisted identification, and next-generation sequencing/metagenomics are increasingly applied, their broader regional uptake is limited by the absence of harmonized, open-access reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). Broad ecological surveys and integrated animal and human surveillance remain limited, and vector competence studies are constrained by the scarcity of SEA-derived tick colonies and cell lines. Regional data and recent findings (2024-2026) confirm circulation of multiple TBPs (including Anaplasma, Babesia, Borrelia, Coxiella, Ehrlichia, Rickettsia, and Theileria) and highlight emerging viral findings, including southward reports of Bandavirus dabieense. Human infestations and non-communicable tick bite outcomes (e.g., tick paralysis and alpha-gal syndrome) are recognized but remain under-reported due to low clinical awareness and limited diagnostics. Importantly, the diagnostic chain is further disrupted by missed/insufficient specimen collection at the point of care, and by constrained capacity to identify (especially immature) ticks to species level-limitations compounded by the absence of harmonized, open-access regional reference resources. The symposium identified six priorities: (1) full completion and regional validation of tick identification keys for adults (in progress) and immatures (to be initiated), plus an open-access DNA barcode library anchored by curated, voucher-based collections from all SEA countries; (2) harmonization of molecular and proteomic diagnostic platforms, including expansion of regional MALDI-TOF MS and NGS protocols and reference databases; (3) development of tick colonies and cell lines from locally prevalent species to support vector competence, vaccine, and acaricide testing; (4) expansion of One Health surveillance with enhanced ecological sampling at wildlife-livestock-human interfaces; (5) establishment of open-access, region-wide data platforms for integrated tick, TBP, and ecological metadata sharing; and (6) sustained investment in human resources, training, and policy advocacy to raise research and public health visibility of ticks and TBDs.}, }
@article {pmid42198700, year = {2026}, author = {Mansour, O and Fadeev, AV and Perederiy, AA and Ksenafontov, AD and Boyarintseva, AY and Danilenko, DM and Lioznov, DA and Komissarov, AB}, title = {Whole-Genome Phylogenetic Characterization of Human Parainfluenza Virus Type 4 Circulating in St. Petersburg, Russia.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198700}, issn = {1999-4915}, support = {TVKQ-2024-0003, registration number 124020500002-4//Ministry of Health of the Russian Federation (Project #TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing")/ ; }, mesh = {Humans ; *Phylogeny ; Russia/epidemiology ; *Genome, Viral ; Genetic Variation ; Whole Genome Sequencing ; *Parainfluenza Virus 4, Human/genetics/classification/isolation &amp; purification ; *Rubulavirus Infections/virology/epidemiology ; }, abstract = {Human parainfluenza virus type 4 (hPIV4) remains poorly characterized compared with other hPIV serotypes and information on its genomic diversity is particularly limited for Russia and Eastern Europe. In this study, we report the first complete genome sequences of hPIV4 isolates from Russia and place them in the context of global hPIV4 genetic diversity. Eight hPIV4 viruses were isolated in cell culture from respiratory samples collected from hospitalized children in Saint Petersburg between 2017/2018 and 2023/2024. Complete viral genomes were recovered using a metagenomic whole-genome amplification approach based on SMART-9N technology. Phylogenetic analysis of 178 complete hPIV4 genomes showed clear separation into hPIV4a (n = 132) and hPIV4b (n = 46) subtypes. Based on genetic distance approach, hPIV4a formed two major clusters, with the dominant cluster B subdivided into four subclusters (B1-B4); and subcluster B4 further resolved into four genetic lineages. All Russian isolates belonged to the subcluster B4 and were distributed among multiple co-circulating lineages. In contrast, hPIV4b genomes segregated into three distinct clusters, reflecting structured genetic diversity within the subtype. Collectively, this study provides, to the best of our knowledge, the first p-distance-based framework for hPIV4 whole-genome classification and contributes new complete genome sequences for an underrepresented region.}, }
@article {pmid42198703, year = {2026}, author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S}, title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198703}, issn = {1999-4915}, support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; }, mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Tropical Climate ; Phylogeny ; *Virome ; }, abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.}, }
@article {pmid42198741, year = {2026}, author = {Jia, L and De, R and Li, Z and Han, Z and Liu, L and Dong, H and Feng, S and Liu, R and Zhao, L}, title = {A Prolonged Norovirus Infection and the Molecular Evolution of Human Norovirus Within-Host in a Child with Burkitt Lymphoma.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198741}, issn = {1999-4915}, support = {Discipline Leader -02-20//Beijing Municipal Health Commission/ ; }, mesh = {Humans ; *Burkitt Lymphoma/virology/complications ; *Evolution, Molecular ; *Norovirus/genetics/classification/isolation &amp; purification ; Phylogeny ; *Caliciviridae Infections/virology/complications ; Genome, Viral ; Child ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Mutation ; }, abstract = {It has been reported that chronic infection of human norovirus (HuNoV) may potentially serve as a reservoir for viral variants with the possibility to evade population immunity or alter the binding sites of HBGA receptors. In this study, a child diagnosed with Burkitt lymphoma and positive for HuNoV determined by real-time PCR (qPCR) firstly in 15 August 2016, was followed up until 20 March 2018, and 26 fecal specimens and one vomitus were collected to trace the evolutionary characteristics of HuNoV by phylogenetic analysis, meta-genomics next-generation sequencing (mNGS), and temporal evolutionary analysis of VP1 among 23 specimens positive for HuNoV. There were 15 specimens with partial RdRp gene sequences forming an independent cluster with sequences of GII.P31, 14 with the region C sequences and 11 with P domain sequences of VP1 gene clustered together with HuNoV GII.4 Sydney_2012. All these sequences showed that mutations accumulated nearly in a time order, and more mutations were shown in the key epitopes A-E or near the binding sites for HBGA in subdomain P2 with higher evolutionary rates. Analysis of NGS data identified intra-host viral quasi-species, and two genome sequences of the same length from mNGS were assembled from N705, with mutations located in the region of subdomain P2 (1171 nt-1202 nt) which led to five amino acid mutations. In conclusion, the accumulated mutations of HuNoV, especially in subdomain P2, were explored in a child with Burkitt lymphoma, and the sequencing of HuNoV from immunocompromised individuals was proven critical for monitoring intra-host quasi-species evolution and potential variant emergence, providing basic data for clinical infection control.}, }
@article {pmid42198763, year = {2026}, author = {Kim, MJ and Kim, YJ and Ha, HJ and Park, JS and Rini, IA and Lee, S and Lee, TK}, title = {Biological Trajectory of Virophage Research and the Emergence of Marine Virophages: A Scoping Review.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198763}, issn = {1999-4915}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology Promotion/ ; }, mesh = {*Virophages/genetics/physiology ; Genome, Viral ; Giant Viruses/genetics ; *Aquatic Organisms/virology ; Seawater/virology ; Metagenome ; Virus Replication ; }, abstract = {Virophages are satellite viruses that depend on the replication machinery of giant double-stranded DNA viruses and influence the structure and dynamics of viral communities through multilayered interactions among giant viruses, their hosts, and virophages. Since the discovery of the Sputnik virophage in 2008, virophages have been increasingly recognized for their roles in regulating giant virus replication, contributing to host defense mechanisms, and shaping the evolution of mobile genetic elements. However, quantitative syntheses examining how virophage research has developed over time, particularly in marine environments, remain limited. Here, we conducted a bibliometric analysis of virophage research published between 2008 and 2025 using the Web of Science Core Collection. By comparing an overall virophage research corpus with a marine virophage sub-corpus, we assessed publication and citation trends, collaboration structures, and keyword-based intellectual and thematic evolution. Our results show that virophage research has gradually transitioned from an early phase dominated by landmark discoveries and experimental model systems to a data-intensive stage driven by genome- and metagenome-based analyses and computational approaches. Although marine virophage studies represent a relatively small proportion of the total literature, they exhibit sustained citation impact and form a distinct research axis within the field. In particular, marine-focused studies emphasize metagenomic discovery, genome sequence alignment, and the analysis of mobile genetic elements such as polinton-like viruses, highlighting the role of marine environments in accelerating the intellectual transition of virophage research. Collectively, these findings demonstrate that virophage research has moved beyond a "discovery and definition" phase toward data-driven integrative interpretation, with marine virophage research emerging as a key domain for understanding the structure and evolutionary dynamics of marine viral ecosystems.}, }
@article {pmid42199008, year = {2026}, author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S}, title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2677951}, pmid = {42199008}, issn = {1949-0984}, mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration &amp; dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.}, }
@article {pmid42199353, year = {2026}, author = {Bergot, M and Lefevre, CT and Grouzdev, DS and Menguy, N and Ortet, P and Denis, Y and Viollier, E and Jézéquel, D and Monteil, CL}, title = {Magnetotactic Bdellovibrionota from a ferruginous spring.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag116}, pmid = {42199353}, issn = {2730-6151}, abstract = {Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.}, }
@article {pmid42199424, year = {2026}, author = {Zhao, L and Wang, Q and Chen, J and Wang, J}, title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1767902}, pmid = {42199424}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; }, abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.<br><br>METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.<br><br>RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.<br><br>CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.}, }
@article {pmid42199698, year = {2026}, author = {Li, Q and Wang, X and Zhang, S and Wang, H and Li, X and Zhao, F}, title = {mNGS-Supported Interpretation of Staphylococcus pettenkoferi Bloodstream Infection After Intracerebral Hemorrhage: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {611927}, pmid = {42199698}, issn = {1178-6973}, abstract = {PURPOSE: Staphylococcus pettenkoferi is an uncommon coagulase-negative staphylococcus whose recovery from blood may be difficult to interpret because of the frequent contamination associated with this bacterial group. We report a case in which peripheral-blood metagenomic next-generation sequencing (mNGS) and repeated blood cultures supported clinically significant bloodstream infection after intracerebral hemorrhage.<br><br>PATIENTS AND METHODS: We described the clinical course, imaging findings, microbiological results, and antimicrobial management of an 85-year-old man admitted to the intensive care unit after intracerebral hemorrhage with intraventricular extension. Peripheral-blood mNGS and two sets of peripheral blood cultures were obtained during early fever evaluation.<br><br>RESULTS: Peripheral-blood mNGS, performed on samples obtained immediately after ICU admission and before neurosurgical intervention or intracranial device placement, detected S. pettenkoferi within 24&#xa0;h. At 72&#xa0;h, both peripheral blood culture sets yielded the same organism. Concordant results from mNGS and repeated peripheral blood cultures, together with the clinical context, supported clinically significant bloodstream infection rather than simple contamination. The respiratory tract was considered a presumed source in the setting of clinically suspected aspiration-related pulmonary infection, although it was not microbiologically confirmed.<br><br>CONCLUSION: This case highlights the need for cautious interpretation of uncommon coagulase-negative staphylococci recovered from blood. Peripheral-blood mNGS may provide early etiologic support, but conventional blood culture remains essential for confirmation and antimicrobial susceptibility testing.}, }
@article {pmid42200417, year = {2026}, author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X}, title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70046}, pmid = {42200417}, issn = {1365-2583}, support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; }, abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.}, }
@article {pmid42200512, year = {2026}, author = {Vergara, E and Khaleque, HN and Neira, G and Watkin, ELJ and Valdés, JH and Holmes, DS}, title = {Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001732}, pmid = {42200512}, issn = {2057-5858}, mesh = {Phylogeny ; *Sulfur/metabolism ; *Adaptation, Physiological/genetics ; *Rhodobacteraceae/genetics/metabolism/classification ; Genome, Bacterial ; Evolution, Molecular ; Hydrothermal Vents/microbiology ; Australia ; Oxidation-Reduction ; Italy ; Metagenome ; Pacific Ocean ; Bacterial Proteins/genetics/metabolism ; }, abstract = {This study compares predicted sulphur metabolism genes across four Acidihalobacter type strains and two metagenome-assembled genomes (MAGs), revealing genomic differences that appear to correspond to ecological specialization. Phylogenomic analysis separates the species into two clades: clade I includes Acidihalobacter ferrooxydans from a geothermal region in Italy and the two MAGs derived from deep-sea hydrothermal vents in the Pacific Ocean, while clade II comprises Acidihalobacter aeolianus and Acidihalobacter prosperus from a geothermal region in Italy and Acidihalobacter yilgarnensis from a saline and acidic drainage in Australia. Variations in sulphide/quinone oxidoreductases (SQRs) across the species, in particular in Ah. ferrooxydans and Ah. yilgarnensis, likely relate to the availability and speciation of sulphur substrates, which are strictly governed by local redox potential (Eh) and metal redox cycling in their respective habitats. Notably, only Ah. ferrooxydans (clade I) lacks the canonical sulphur/thiosulphate oxidation (Sox) system for thiosulphate oxidation found in clade II and instead encodes components of an alternative S4I pathway. We hypothesize that this difference reflects an adaptation to dynamic microniches going from highly reduced (sulphide-rich) to oxidized metastable sulphur intermediates. In contrast, the retention of the Sox system in clade II suggests a distinct strategy permitting greater metabolic versatility under fluctuating Eh-pH conditions.Differences in clade I terminal oxidases (cbb3-type cytochrome, bc1 complex) and regulatory elements appear to support further adaptation to environments with elevated H2S, setting this clade apart from clade II members. These adaptations, mainly evidenced by gene redundancy, gene loss and horizontal gene transfer, seem to reflect a unique ecological microniche and evolutionary trajectory for Ah. ferrooxydans distinct from other members of the genus, particularly from a sulphur-based energy metabolism perspective.}, }
@article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, }
@article {pmid42200658, year = {2026}, author = {Blanchard, JL}, title = {Learning R with generative AI in a metagenomic data science course.}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0034325}, doi = {10.1128/jmbe.00343-25}, pmid = {42200658}, issn = {1935-7877}, abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.}, }
@article {pmid42200756, year = {2026}, author = {Harrison, LB and Sohani, ZN and Lasry, D and Cheng, MP and Lee, TC and Babiker, A and Kadri, SS and Lawandi, A}, title = {Rapid Microbiological Diagnostics for Sepsis: Narrative Review of Current and Prospective Approaches.}, journal = {Critical care explorations}, volume = {8}, number = {6}, pages = {e1415}, pmid = {42200756}, issn = {2639-8028}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture/methods ; Molecular Diagnostic Techniques/methods ; *Microbiological Techniques/methods ; Rapid Diagnostic Tests ; }, abstract = {OBJECTIVES: In this review, we aim to provide critical care clinicians with a concise introduction to the current and prospective tools that exist for rapid diagnostics in sepsis employed in the microbiology laboratory. Our objective is to provide a primer for clinicians to engage with their colleagues in the microbiology laboratory for the selection and implementation of new and emerging tools.<br><br>DATA SOURCES: The primary literature, restricted to peer-reviewed sources, was queried using relevant search terms (e.g., sepsis, rapid diagnostics, microbiology, etc) using PubMed and Google Scholar (until February 2025), as well as review of citations of relevant articles.<br><br>STUDY SELECTION: After initial searches, literature was screened by each author responsible for the sections of this review: blood culture-based methods (L.B.H.), nonblood culture-based molecular diagnostics (D.L.), and antigen-based methods (Z.N.S.). Titles and abstracts of individual articles were reviewed by the respective section authors and articles describing microbiological diagnostic techniques that decrease the turnaround time for the identification of microorganisms and/or antimicrobial susceptibility testing with relevance to the diagnosis of sepsis were retained.<br><br>DATA EXTRACTION: Data from individual studies was extracted by each respective section author using Zotero reference management software and synthesized narratively.<br><br>DATA SYNTHESIS: Rapid diagnostics for sepsis can be broadly divided into three categories: those applied to incubated positive blood culture specimens, and culture-independent approaches applied directly to clinical specimens, which can be further divided into those based on the direct detection of the nucleic acids of microorganisms, and those based on the detection of antigens. Blood culture-based approaches rely on biological amplification of microorganisms present but aim to measure this amplified signal directly to speed identification of microorganisms or antimicrobial resistance relative to traditional plate-culture-based workflows. Nucleic acid and antigen detection methods can be performed directly on clinical specimens, and so promise more rapid diagnostics in sepsis, but with method-specific tradeoffs in sensitivity, specificity, and interpretation.<br><br>CONCLUSIONS: Evolutionary refinements of blood culture-based diagnostic approaches have decreased time to actionable information significantly while emerging and established culture-independent approaches can reduce time to actionable information to a few hours. In aggregate these interventions may have important clinical benefits, yet significant heterogeneity exists in the applicability and availability of technologies.}, }
@article {pmid42201023, year = {2026}, author = {Rehman, A and Awais, M and Baloch, HNUA and Leghari, MO and Ahmad, A and Javed, H}, title = {Sputum Liquid Biopsy for Lung Cancer Screening, Diagnosis, Subtyping, Surveillance, Response Prediction, and Prognostication: A Scoping Review.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {42201023}, issn = {2076-3271}, mesh = {Humans ; *Lung Neoplasms/diagnosis/pathology/metabolism ; *Sputum/metabolism ; Liquid Biopsy/methods ; Biomarkers, Tumor ; Prognosis ; *Early Detection of Cancer/methods ; }, abstract = {Background/Objectives: Liquid biopsy (LB) is transforming cancer care by enabling minimally invasive tumor profiling. While current research and clinical pathways mostly focus on blood LB, sputum represents a non-invasive, readily available respiratory specimen that may offer unique advantages for lung cancer (LC) care. Despite its potential, the maturity, breadth, and clinical applicability of sputum-based LB remain elusive. Methods: We conducted a scoping review to systematically map the existing literature on sputum LB in LC. Electronic databases were searched for studies evaluating sputum-derived biomarkers-cytologic, genomic, epigenetic, transcriptomic, proteomic, metabolomic, metagenomic, and extracellular vesicle-derived products-across the LC care continuum. Study designs, technologies, clinical contexts, and reported outcomes were extracted and synthesized qualitatively. Results: The literature demonstrated substantial heterogeneity in sputum collection, processing, and analytical platforms. Early work focused on cytometry and genetic alterations, while recent studies increasingly explore DNA methylomics, microRNAs, extracellular vesicle-derived products, and multi-omics approaches. The evidence suggests potential utility of sputum biomarkers for early detection and risk stratification, particularly in high-risk populations, with emerging data supporting roles in molecular subtyping, response monitoring, prognostication, and surveillance. However, few studies report prospective validation, direct comparison with blood-based LB, or impact on actual patient outcomes. Conclusions: Sputum LB is a promising yet underdeveloped modality in LC care. This scoping review highlights technological innovations alongside significant methodological heterogeneity and translational gaps. Future research should focus on standardization, prospective validation, impact on patient outcomes, and integration with blood- and other body fluid-based LB, as well as imaging biomarkers. This will enable incorporation of sputum-based LB into actual clinical pathways of LC care.}, }
@article {pmid42201143, year = {2026}, author = {Zhang, W and Eleftherianos, I and Mohamed, A and Smagghe, G and Chakkalakkal, G and Al-Akeel, R and Toprak, U and Tettamanti, G and Keyhani, N and Renault, D}, title = {Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag137}, pmid = {42201143}, issn = {1751-7370}, abstract = {Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.}, }
@article {pmid42201824, year = {2026}, author = {Lin, X and Asif, M and Li, W and Zhang, B and Li, Y and Yu, Y and Jiang, X}, title = {Long-Term Straw Return Reverses Antibiotic Resistance Accumulation in Maize Rhizosphere through Integrated Soil-Microbial Mechanisms.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {22}, pages = {15544-15556}, doi = {10.1021/acs.est.5c11371}, pmid = {42201824}, issn = {1520-5851}, mesh = {*Zea mays ; *Rhizosphere ; *Soil Microbiology ; Fertilizers ; Soil/chemistry ; *Drug Resistance, Microbial ; Agriculture ; Pseudomonas ; }, abstract = {The impact of long-term agricultural cultivation on antibiotic resistance has emerged as a critical environmental concern. However, previous studies have primarily examined organic fertilizers, and the effects of sustained chemical fertilizer use combined with straw incorporation over extended periods remain poorly understood. Here, we employed a 25-year field trial combined with metagenomic analysis to investigate the differential effects of chemical fertilization and straw incorporation on soil antibiotic resistance gene (ARG) dynamics in the maize rhizosphere. Results showed that long-term cultivation progressively increased ARG and virulence factor gene (VFG) abundance. Metagenomic analyses suggested that shifts in Pseudomonas populations and microbial metabolic pathways were associated with elevated levels of ARGs in the rhizosphere. Field inoculation with a synthetic Pseudomonas community further increased the ARG abundance, accompanied by reduced genomic GC content and enrichment of specific metabolic pathways. In contrast, straw amendment treatments reduced Pseudomonas abundance and soil acidification while increasing the soil total carbon and lignin degradation functional capacity. Our findings indicate that long-term straw incorporation represents a promising strategy for controlling antibiotic resistance dissemination in agricultural systems, offering valuable insights into sustainable crop management practices.}, }
@article {pmid42201863, year = {2026}, author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI}, title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0340244}, pmid = {42201863}, issn = {1932-6203}, mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; }, abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.}, }
@article {pmid42201897, year = {2026}, author = {, }, title = {Editorial Note: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0350242}, pmid = {42201897}, issn = {1932-6203}, }
@article {pmid42202516, year = {2026}, author = {Sun, X and Lin, Z and Ni, SQ}, title = {Multidrug-resistant bacteria contribute to core bacterial community and ARGs persistence during full-scale pharmaceutical wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142513}, doi = {10.1016/j.jhazmat.2026.142513}, pmid = {42202516}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; Waste Disposal, Fluid ; Drug Industry ; Water Pollutants, Chemical ; }, abstract = {Pharmaceutical wastewater treatment plants (WWTPs) are confronted with a wide range of contaminants, resulting in the accumulation of antibiotic resistance genes (ARGs) and the evolution of multidrug-resistant (MDR) bacteria. However, the ecological roles of these MDR residents during full-scale wastewater treatment remain unclear. In this study, the core bacterial communities as well as potential MDR bacteria for industrial WWTPs were firstly categorized out. Taxa belonging to MDR bacteria were frequently detected to persist with low relative abundance across different treatment units, even in the effluent. Then, the occurrence and health risk of ARGs were evaluated. Certain abundant and prevalent ARGs, such as fabG, macB, and adeF, were found to exhibit high prevalence. Some pivotal mobile genetic elements, acting as key network hubs, can link MDR bacteria with a broad range of ARGs. Finally, the result showed that several metagenome-assembled genomes recovered from the effluents were not only classified as MDR bacteria harboring ARGs with high risk, but also served as important members of the core bacterial community. These findings provide critical insights into the ecological roles of MDR bacteria during the full-scale pharmaceutical wastewater treatment, and emphasize the urgent need for real-time monitoring of wastewater-borne MDR bacteria for ecological health.}, }
@article {pmid42202519, year = {2026}, author = {Li, X and Wang, Y and Dang, X and Zhang, Y and Zhao, C and Hou, S and Li, B and Ma, F and Hao, L and Zhu, T}, title = {Molecular mechanism by which high temperature and RecBCD synergistically lower strand-separation barriers and promote destabilization of representative efflux-pump ARG fragments (macB/tetA) during hyperthermophilic composting.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142445}, doi = {10.1016/j.jhazmat.2026.142445}, pmid = {42202519}, issn = {1873-3336}, mesh = {*Hot Temperature ; *Composting ; *Bacterial Proteins/genetics ; Molecular Dynamics Simulation ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; Metagenomics ; Antiporters ; }, abstract = {Hyperthermophilic composting (HC) effectively mitigates antibiotic residues and antibiotic resistance genes (ARGs), yet the molecular basis of ARG-derived DNA destabilization under extreme heat remains unclear. Here, we established an HC system reaching 87.3 ℃ (∼360 K) and combined metagenomics, AlphaFold prediction, molecular dynamics (MD), and free-energy calculations to investigate representative efflux-pump ARG fragments (macB/tetA). HC removed oxytetracycline, enrofloxacin, and sulfamethoxazole by 98.44%, 92.34%, and 99.63%, respectively, while overall ARG abundance declined markedly. Metagenomics identified 796 ARGs, dominated by efflux mechanisms, and qPCR confirmed multi-order decreases in macB and tetA. Nucleic acid processing/degradation genes, including recD/RecBCD-related homologs, were enriched during the high-temperature phase and negatively associated with ARG abundance. Based on these data, we constructed a candidate RecBCD model from metagenomic recB/recC/recD homologs. MD showed that this model maintained overall structural integrity at 360 K. AlphaFold predicted end-loaded candidate RecBCD-DNA complexes (ipTM/pTM ≈ 0.89-0.90) with local duplex opening. Subsequent MD revealed that RecBCD-bound DNA became more flexible, displayed weakened/reorganized hydrogen-bond networks, and sampled more multistate free-energy basins. Umbrella sampling further showed that strand-separation PMFs at 360 K were ∼25-30 kJ·mol[-1] lower than at 330 K, with tetA exhibiting a lower barrier and greater thermal sensitivity than macB. Together, these results support a working model in which high temperature lowers DNA stability and strand-separation barriers, thereby facilitating candidate RecBCD-mediated loading and local processing of representative efflux-pump ARG-derived DNA fragments during HC.}, }
@article {pmid42202778, year = {2026}, author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M}, title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {6}, pages = {1135-1150.e6}, doi = {10.1016/j.chom.2026.05.001}, pmid = {42202778}, issn = {1934-6069}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/surgery/metabolism ; Female ; *Feces/microbiology/chemistry ; *Adenoma/microbiology/surgery ; *Metabolome ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Aged ; Metagenomics ; Metagenome ; }, abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.}, }
@article {pmid42202790, year = {2026}, author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R}, title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.}, journal = {Cell reports. Medicine}, volume = {7}, number = {6}, pages = {102835}, doi = {10.1016/j.xcrm.2026.102835}, pmid = {42202790}, issn = {2666-3791}, mesh = {*Diabetes Mellitus, Type 2/microbiology/epidemiology ; Humans ; Female ; Sweden/epidemiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Prospective Studies ; Male ; Incidence ; Eubacteriales ; }, abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.}, }
@article {pmid42203111, year = {2026}, author = {Wang, L and Bai, L and Li, H and Zhang, P and He, F}, title = {A case of imported infection in China: Initially treatment-unresponsive schistosomiasis coinfection with bladder tuberculosis.}, journal = {Indian journal of medical microbiology}, volume = {62}, number = {}, pages = {101157}, doi = {10.1016/j.ijmmb.2026.101157}, pmid = {42203111}, issn = {1998-3646}, abstract = {Schistosoma haematobium, endemic to sub-Saharan Africa, causes urogenital disease, differing from Schistosoma japonicum, which affects the hepatointestinal system and is the only endemic schistosome in China. A Chinese male with persistent hematuria after prolonged occupational exposure in Angola was initially attributed to S. japonicum. Following failed treatment, metagenomic sequencing confirmed S. haematobium infection, and subsequent urethral resection detected Mycobacterium tuberculosis DNA, establishing concurrent bladder tuberculosis. This case highlights the need for molecular diagnostics in patients with hematuria after sub-Saharan exposure and the immunomodulatory risks posed by helminth infections.}, }
@article {pmid42203372, year = {2026}, author = {McCann, P and Megaw, J and Gobert, GN}, title = {Parasite-associated microbiomes: An unseen microenvironment.}, journal = {Advances in parasitology}, volume = {131}, number = {}, pages = {31-70}, doi = {10.1016/bs.apar.2026.03.001}, pmid = {42203372}, issn = {2163-6079}, mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; }, abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.}, }
@article {pmid42203690, year = {2026}, author = {Fullam, A and Prasoodanan, PKV and Kuhn, M and Bork, P and Schmidt, TSB}, title = {microntology: a lightweight, data-driven controlled vocabulary to describe earth's microbial habitats.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {6}, pages = {}, pmid = {42203690}, issn = {1367-4811}, support = {12/RC/2273-P2//Research Ireland/ ; }, mesh = {*Ecosystem ; *Vocabulary, Controlled ; *Metagenomics/methods ; *Earth, Planet ; *Software ; }, abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.<br><br>RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.<br><br>AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305 626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.}, }
@article {pmid42203770, year = {2026}, author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M}, title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73297-5}, pmid = {42203770}, issn = {2041-1723}, support = {1026-00386B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; }, abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.}, }
@article {pmid42203854, year = {2026}, author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I}, title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42203854}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.}, }
@article {pmid42204574, year = {2026}, author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N}, title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.78243}, pmid = {42204574}, issn = {1531-8249}, support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; }, abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026.}, }
@article {pmid42204631, year = {2026}, author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH}, title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07471-5}, pmid = {42204631}, issn = {1756-3305}, support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.<br><br>METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples&#xa0;(n&#x2009;=&#x2009;46) was investigated by metagenomic shotgun sequencing&#xa0;and comparatively analysed at the&#xa0;phylum,&#xa0;genus, and&#xa0;species levels. In addition, the prevalence of potential pathogen DNA in head lice samples&#xa0;(n&#x2009;=&#x2009;204) was assessed&#xa0;using real-time PCR with stringent negative controls.<br><br>RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722&#xa0;genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level,&#xa0;DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial&#xa0;DNA&#xa0;from these taxa.<br><br>CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB&#xa0;microbiome in head lice. The high proportion of unannotated genes (>95%)&#xa0;underscores the limited representation of louse-associated microbial genomes in public databases and suggests &#xa0;substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may&#xa0;suggest prior&#xa0;exposure, mechanical carriage, or residual DNA from&#xa0;blood meals. These exploratory findings contribute new&#xa0;insights into the microbiota associated with human lice.}, }
@article {pmid42204733, year = {2026}, author = {Fang, Q and Liu, J and Xuan, C and Li, C and Jiang, X and Zhang, S and Li, Q and Liu, X and Liu, Q and Zhang, L and Wang, Y and Cui, J and Qu, Y and Zhang, J and Li, P and Chen, X}, title = {Targeting the gut‒kidney axis for lupus nephritis treatment: multimechanism regulatory strategies and evidence from Traditional Chinese medicine.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42204733}, issn = {1749-8546}, support = {2022YFC3602000//the National Key Research and Development Program of China/ ; 82274327//the National Natural Science Foundation of China/ ; 32141005//the National Natural Science Foundation of China/ ; }, abstract = {Lupus nephritis (LN) treatment remains challenging because of the limited efficacy and substantial side effects of conventional immunosuppressive therapies. Traditional Chinese medicine (TCM), with its holistic and multitarget approach, offers unique therapeutic potential. The emerging gut-kidney axis theory provides a new framework for understanding LN pathogenesis by linking gut dysbiosis and intestinal barrier injury to renal inflammation. This review systematically examines the role of gut-kidney axis dysregulation in LN progression and establishes connections between the TCM spleen-kidney correlation theory and this modern concept. Accumulating evidence suggests that TCM compounds and active ingredients alleviate renal injury and improve LN through multiple mechanisms. TCM compounds modulate the gut microbiota composition, enhance intestinal barrier integrity, reduce endotoxin translocation, and suppress systemic inflammation. These findings position the gut-kidney axis as a critical target for TCM intervention. Through multicomponent synergy, TCM restores gut homeostasis and inhibits aberrant immune responses. Future studies should integrate multiomics approaches, including metagenomics and metabolomics, and prospective clinical trials should dynamically track the gut microbiota and metabolite profiles in LN patients. Such investigations will clarify the precise mechanisms by which TCM modulates the gut-kidney axis and facilitate the development of personalized TCM-based therapeutic strategies.}, }
@article {pmid42204882, year = {2026}, author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H}, title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70339}, doi = {10.1111/1462-2920.70339}, pmid = {42204882}, issn = {1462-2920}, support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; }, abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH}}_4^{+} $$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.}, }
@article {pmid42205184, year = {2026}, author = {Wang, X and Wang, H and Liu, J and Zhang, H and Zhou, XJ}, title = {Gut Virome Characteristics and Network Alterations in IgA Nephropathy.}, journal = {Kidney international reports}, volume = {11}, number = {7}, pages = {106550}, pmid = {42205184}, issn = {2468-0249}, abstract = {INTRODUCTION: Emerging evidence implicates gut microbiota dysbiosis in the pathogenesis of IgA nephropathy (IgAN), yet the contribution of the gut virome remains unexplored. This study aimed to characterize virome signatures and virus-microbiota interactions in IgAN.<br><br>METHODS: We performed a rigorously matched case-control study including 32 patients with biopsy-proven IgAN and 32 healthy controls. Fecal viral-like particles and bacterial communities were profiled using metagenomic sequencing and full-length 16S ribosomal RNA (rRNA) sequencing. Statistical analysis included diversity, differential abundance, network analysis, and correlation with clinical indices.<br><br>RESULTS: IgAN subjects displayed significant reductions in gut virome richness (severe IgAN vs. healthy controls, P = 0.03), with a lower relative abundance of Caudoviricetes in severe IgAN (P = 0.045) and enrichment of Tectiliviricetes in mild disease (P = 0.03). We identified 113 differentially abundant bacteriophage contigs (82 up, 31 down; false discovery rate < 0.05); key predicted hosts shifted toward Bacteroides, Clostridium, and Roseburia in IgAN, whereas Faecalibacterium and Alistipes prevailed in controls. Viral and bacterial alpha diversity correlated in healthy controls but not in IgAN (r = 0.38, P = 0.03 vs. r = 0.04, P = 0.81). IgAN virome encoded more glyco-modifying enzymes (P < 0.05), with strong correlations to estimated glomerular filtration rate (eGFR) (r = 0.65, P = 0.001). Viral and bacterial alpha diversity were significantly correlated with proteinuria and gross hematuria (r = 0.18-0.25, - < 0.05).<br><br>CONCLUSION: This study describes potential alterations in gut virome diversity, bacteriophage composition, bacteriome-virome relationships, and predicted functional profiles in IgAN, suggesting potential relevance of the gut virome to intestinal ecological alterations.}, }
@article {pmid42205574, year = {2026}, author = {Liao, G and Xiao, J and Zhang, B and Wang, S and Wan, X and Zhang, C and Lyu, C and Yan, B and Zhao, Y and Kang, C and Zhang, Y and Yuan, F and Zhao, Z and Chen, Y and Guo, L and Zhang, Y}, title = {Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758116}, pmid = {42205574}, issn = {1664-302X}, abstract = {BACKGROUND: Excessive chemical fertilizer application has become a core bottleneck restricting the green and sustainable cultivation of Glycyrrhiza uralensis (licorice). Partial organic fertilizer substitution can improve soil microecology and licorice growth traits, yet its regulatory effects on microbial functional genes mediating soil carbon (C) and nitrogen (N) cycling remain unclear.<br><br>RESULTS: Using metagenomic sequencing, we investigated the effects of six fertilization regimes [100% organic fertilizer (OF100), 100% chemical fertilizer (OF0), and organic-inorganic combinations (OF25, OF50, OF75)] on the genetic potential of soil C and N cycling, as well as soil properties and licorice growth traits in bulk and rhizosphere soils of licorice. Organic substitution significantly altered the abundance of C and N cycling-related functional genes: OF100 significantly increased the abundance of genes associated with methane oxidation (pmoA/amoA), carbon degradation (pel, cbh) and nitrification (pmoB/amoB), while OF0 significantly upregulated the methanogenesis-related gene mttA and downregulated nitrogen degradation genes; optimized fertilization (OF50) significantly reduced the abundance of genes linked to excessive carbon degradation (malZ) and nitrogen loss genetic potential (nirK), and markedly increased the abundance of genes for carbon fixation (pccA) and nitrogen mineralization (GDH). PERMANOVA revealed that soil compartment (bulk vs. rhizosphere) explained 62.87% of the total variation in functional gene profiles, which was 5.67 times higher than the contribution of fertilization regime (11.10%).<br><br>CONCLUSION: Rational organic-inorganic fertilization effectively regulates soil microbial functional genes related to C and N cycling, optimizes soil nutrient cycling potential, reduces nutrient loss risk, and enhances nutrient supply efficiency for licorice growth. These findings provide a scientific basis for fertilizer management optimization and sustainable cultivation of licorice.}, }
@article {pmid42205899, year = {2026}, author = {Patil, BL and Shanmugaraj, C and Madhusudan, M}, title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {222}, pmid = {42205899}, issn = {2190-572X}, abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.}, }
@article {pmid42205903, year = {2026}, author = {Hameed, A and Ghate, SD and Shastry, RP}, title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {230}, pmid = {42205903}, issn = {2190-572X}, abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.}, }
@article {pmid42206066, year = {2026}, author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R}, title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.}, journal = {Infectious medicine}, volume = {5}, number = {2}, pages = {100260}, pmid = {42206066}, issn = {2772-431X}, abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.<br><br>METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.<br><br>RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 &#xd7; 10&#x207b;&#x2075; and 1.2 &#xd7; 10&#x207b;&#x2075;, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 &#xd7; 10&#x207b;&#x2075; and 1.1 &#xd7; 10&#x207b;&#x2074; in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid&#x2011;mediated ARGs and Cr, and between transposon&#x2011;mediated ARGs and Cr/V. The MP of transposon&#x2011;mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid&#x2011;mediated ARGs but positively with insertion sequence&#x2011;mediated ARGs. Ni concentration was positively associated with the MP of IS&#x2011;mediated VFGs.<br><br>CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.}, }
@article {pmid42206150, year = {2026}, author = {Sun, K and Wang, F and Niu, T and Wang, H and Liu, Y and Guo, L and Wang, X and Hou, X}, title = {Metagenomic and metabolomic insights into the rhizosphere of Paeonia suffruticosa 'Luoyang Hong' across a continuous cropping chronosequence.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1754999}, pmid = {42206150}, issn = {1664-462X}, abstract = {The cultivation of Paeonia suffruticosa 'Luoyang Hong', a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa 'Luoyang Hong'. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa 'Luoyang Hong', offering deeper insights into replanting issues and supporting future mitigation strategies.}, }
@article {pmid42206286, year = {2026}, author = {Oladejo, OA and Ibiwoye, DO and Faniyi, AA and Ayoola, MO and Oguntunji, AO and Ayansina, AD and Dahunsi, SO}, title = {Dynamics of enzyme and metabolic profile of broilers fed black soldier fly (Hermetiailucens) larvae-based diets.}, journal = {Biochemistry and biophysics reports}, volume = {46}, number = {}, pages = {102618}, pmid = {42206286}, issn = {2405-5808}, abstract = {This study investigated the impact of replacing fishmeal with black soldier fly larvae meal (BSFLM) on growth performance, microbial enzyme activity, and metabolic functions in broiler chickens. A total of fifty Arbor Acre Plus chicks were distributed across five dietary groups, including a control (100% fishmeal) and four diets containing increasing levels of BSFLM (25%, 50%, 75%, and 100%) in a completely randomized design. Broilers were reared over eight weeks, and cecal samples were subjected to 16S rRNA metagenomic sequencing to profile gut microbial enzyme activities and metabolic functions. Results revealed a progressive increase in microbial enzyme abundance and functional metabolic pathways with higher BSFLM inclusion, particularly in the 50% (T3) and 100% (T5) groups. Key enzymes, including ABC-2-type ATP-binding proteins, RNA polymerase sigma factors, and carbohydrate-active enzymes, were significantly upregulated, supporting enhanced carbohydrate fermentation, amino acid biosynthesis, and central carbon metabolism. Metabolic pathway analysis indicated a dietary shift from carbohydrate-driven fermentation in the control group to a more protein- and lipid-centered metabolism in BSFL-fed birds, with T3 showing a balanced metabolic profile and T5 exhibiting hyper-metabolic activity. These findings demonstrate that BSFLM can replace fishmeal without compromising gut health and may even enhance microbial functionality, with a 50% replacement emerging as an optimal inclusion level to sustain balanced microbial metabolism.}, }
@article {pmid42206340, year = {2026}, author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF}, title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0124}, pmid = {42206340}, issn = {1471-2970}, support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; }, abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206370, year = {2026}, author = {Chen, L and Lin, L and Wang, Z and Yu, L and Ren, B and Zhou, S and Wang, P and Li, Y and Lu, E and Dong, Z}, title = {Fusobacterium nucleatum-Derived Isoleucine Exacerbates Aneurysm by Inducing Ferroptosis in Vascular Smooth Muscle Cells.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.126.324050}, pmid = {42206370}, issn = {1524-4636}, abstract = {BACKGROUND: Bacterial communities and their metabolites are increasingly recognized as key contributors to cardiovascular disease, yet their role and mechanistic involvement in abdominal aortic aneurysm (AAA) pathogenesis remain insufficiently defined.<br><br>METHODS: Dental plaques from patients with AAA and matched healthy controls were subjected to metagenomic sequencing, and corresponding plasma samples underwent untargeted metabolomic profiling. In vivo, mice were topically exposed in the oral cavity to Fusobacterium nucleatum (Fn) followed by AngII (angiotensin II) infusion to evaluate its impact on AAA progression. A homologous recombination-based ilvE deletion strategy was used to confirm the role of Fn in isoleucine biosynthesis. Molecular assays were performed to assess ferroptosis-related signatures and histone acetylation in smooth muscle cells, while chromatin immunoprecipitation-quantitative polymerase chain reaction verified the specific acetylation target. In addition, dietary restriction of isoleucine was introduced in the AAA murine model to explore therapeutic relevance.<br><br>RESULTS: Patients with AAA showed a marked enrichment of Fn in dental plaque, and topical application of Fn aggravated AngII-induced AAA in mice. Elevated plasma isoleucine concentrations were observed in both human AAA and experimental models. Genetic deletion of ilvE in Fn diminished bacterial isoleucine release and mitigated AAA development in mice. Mechanistic analyses revealed that Fn-derived isoleucine promoted ferroptosis in smooth muscle cells through H3K9ac (histone H3 lysine 9 acetylation)-dependent transcriptional activation of ACSL4 (acyl-CoA [coenzyme A] synthetase long-chain family member 4), a core regulator of ferroptosis. Dietary isoleucine restriction in the AngII-induced model reduced H3K9ac, suppressed ferroptosis, and alleviated aneurysmal progression.<br><br>CONCLUSIONS: Fn-derived isoleucine drives ferroptosis in smooth muscle cells via H3K9ac-mediated activation of ACSL4, delineating a microbiota-metabolite-epigenetic axis in AAA pathogenesis and nominating dental plaque Fn abundance and circulating isoleucine as exploratory biomarker candidates requiring larger, independent validation.}, }
@article {pmid42206586, year = {2026}, author = {Yeo, S and Park, H}, title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681840}, pmid = {42206586}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation &amp; purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation &amp; purification/classification/genetics ; }, abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.}, }
@article {pmid42206864, year = {2026}, author = {Zhao, R and Biddle, JF}, title = {Community structure and methylation of microbes in an artificially forced sediment core.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0353325}, doi = {10.1128/spectrum.03533-25}, pmid = {42206864}, issn = {2165-0497}, abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.}, }
@article {pmid42207030, year = {2026}, author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S}, title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.}, journal = {Food &amp; function}, volume = {17}, number = {12}, pages = {5410-5424}, doi = {10.1039/d6fo01620k}, pmid = {42207030}, issn = {2042-650X}, mesh = {Animals ; Mice ; Liver/metabolism/drug effects ; *Plant Extracts/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Dexamethasone/adverse effects ; *Fatty Liver/chemically induced/drug therapy/metabolism ; *Tea/chemistry ; Mice, Inbred C57BL ; Multiomics ; Camellia sinensis/chemistry ; }, abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.}, }
@article {pmid42207032, year = {2026}, author = {Giani, N and John, J and Campbell, B}, title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0030926}, doi = {10.1128/mra.00309-26}, pmid = {42207032}, issn = {2576-098X}, abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.}, }
@article {pmid42207051, year = {2026}, author = {Sutanto, TPW and Pratama, A and Ishii, E and Iida, T and Matsuda, S}, title = {TsrA modulates type III secretion system 2 expression as a co-regulator of H-NS in Vibrio parahaemolyticus.}, journal = {Journal of bacteriology}, volume = {208}, number = {6}, pages = {e0055625}, pmid = {42207051}, issn = {1098-5530}, support = {20K07428, 23K06529//Japan Society for the Promotion of Science/ ; 23K14521, 25K18800//Japan Society for the Promotion of Science/ ; 23K05637//Japan Society for the Promotion of Science/ ; 2024N068//Shionogi Infectious Disease Research Promotion Foundation/ ; //BIKEN Foundation/ ; }, mesh = {*Vibrio parahaemolyticus/genetics/pathogenicity/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *DNA-Binding Proteins/genetics/metabolism ; *Type III Secretion Systems/genetics/metabolism ; Virulence/genetics ; Transcription Factors/genetics/metabolism ; Virulence Factors/genetics ; }, abstract = {Vibrio parahaemolyticus, a gram-negative marine bacterium, is a major cause of seafood-borne gastroenteritis worldwide. This pathogen relies on type III secretion system 2 (T3SS2), which is encoded on a pathogenicity island, for its enteropathogenicity. Expression of T3SS2 is activated by a regulatory pathway centered on the transcriptional activator VtrB, which is antagonized by the xenogeneic silencer, histone-like nucleoid-structuring protein (H-NS). However, the complete transcriptional network is not yet fully understood. In this study, we identified TsrA as a negative regulator of T3SS2 gene expression. TsrA is a small protein conserved among Vibrio species that lacks a putative DNA-binding motif but has been implicated in the regulation of virulence genes in Vibrio cholerae. In V. parahaemolyticus, deletion of tsrA increased VtrB production and T3SS2 secretion, thereby enhancing T3SS2-dependent pathogenicity. Transcription of vtrB occurs via a two-step activation process, in which TsrA affects the primary activation step, thereby modulating VtrB production. We further provide experimental evidence that TsrA physically interacts with H-NS via its C-terminal region, which correlates with its regulatory activity on vtrB expression. A systematic mutational analysis of the C-terminal 26 residues revealed several residues critical for TsrA regulatory activity. Moreover, the regulatory effect of TsrA on T3SS2 gene expression was dependent on H-NS, demonstrating that TsrA functions in concert with H-NS. Thus, our findings provide new insights into the regulatory mechanisms of virulence gene expression in V. parahaemolyticus by defining the role of TsrA in this network, while also placing TsrA among H-NS co-regulators.IMPORTANCENucleoid-associated proteins (NAPs) play key roles in virulence gene regulation in bacteria. The best-studied NAP is H-NS, which often functions with co-regulators to fine-tune gene expression. TsrA, a small protein lacking a DNA-binding motif conserved among Vibrio species, has been suggested to be functionally related to H-NS in Vibrio cholerae, although its mechanism remains unknown. Here, we demonstrate that TsrA negatively regulates the expression of type III secretion system 2 (T3SS2), a major virulence determinant of Vibrio parahaemolyticus, an important seafood-borne pathogen. TsrA modulates the transcription of vtrB, which encodes the essential activator for T3SS2 expression, through direct physical interaction with H-NS. Our findings reveal a molecular link between TsrA and H-NS, providing mechanistic insights into NAP- and TsrA-mediated regulation of virulence in Vibrio.}, }
@article {pmid42207344, year = {2026}, author = {Cagirgan, OY and Korkmaz, S and Diker, KS}, title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.}, journal = {Tropical animal health and production}, volume = {58}, number = {5}, pages = {}, pmid = {42207344}, issn = {1573-7438}, support = {VTF-190002//Bilimsel Ara&#x15f;t&#x131;rma Projeleri Birimi, Ayd&#x131;n Adnan Menderes &#xdc;niversitesi/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration &amp; dosage ; Amoxicillin/therapeutic use/administration &amp; dosage ; Necrosis/veterinary/microbiology ; Male ; }, abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.}, }
@article {pmid42207373, year = {2026}, author = {Shao, C and Li, J and Huang, C and Tang, M and Zeng, J and Zhou, W and Zhang, D and Zeng, G and Wang, J and Hua, T and Zhong, C and Hu, J and Xu, X}, title = {Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42207373}, issn = {1435-4373}, support = {20170522160421261//Bao'an District Science and Technology Program/ ; 2023B110008//Guangdong Provincial Clinical Research Center for Laboratory Medicine/ ; }, abstract = {RESEARCH BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a culture-independent pathogen identification method, which can directly sequence all nucleic acids present in clinical samples, and has shown transformative potential in the diagnostic field of complex, critical and emerging infectious diseases, but its clinical application value has not been fully evaluated. This study aims to compare the diagnostic efficacy of mNGS and traditional microbiological testing (TMT), and evaluate its impact on clinical decision-making.<br><br>RESEARCH METHODS: This retrospective study analyzed the data of the laboratory information system (LIS) of patients who received both mNGS and TMT testing.<br><br>RESEARCH RESULTS: In samples of bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF), the positive rates of mNGS were 86.70%, 77.17% and 53.57% respectively, which were significantly higher than the corresponding positive rates of TMT (41.38%, 14.13%, 17.86%). Clinical correlation analysis showed that 77.84%, 66.20% and 73.33% of the positive mNGS results of the three types of samples were of clinical significance respectively. 15.34%~29.58% of the cases adjusted their treatment regimens according to the positive mNGS results, and 33.33%~61.54% of the cases adjusted their treatment regimens according to the negative mNGS results. Most patients who had their treatment adjusted showed improvement or relief of symptoms. Overall, various pathogenic microorganisms were detected in more than 60% of the samples.<br><br>RESEARCH CONCLUSION: This study confirms the significant advantages of mNGS in the precise diagnosis of infectious diseases, as well as its value in guiding individualized treatment strategies.}, }
@article {pmid42208188, year = {2026}, author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S}, title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.}, journal = {Water research}, volume = {302}, number = {}, pages = {126138}, doi = {10.1016/j.watres.2026.126138}, pmid = {42208188}, issn = {1879-2448}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Wastewater/microbiology/chemistry ; Anaerobiosis ; Caffeine/metabolism ; Carbon Isotopes ; Bacteria/metabolism/genetics ; Naproxen/metabolism ; Demethylation ; Methane/metabolism ; Archaea/metabolism/genetics ; *Seawater/microbiology ; Oceans and Seas ; }, abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.}, }
@article {pmid42208292, year = {2026}, author = {Majumdar, A and Bagchi, D and Kotta-Loizou, I and Buck, M}, title = {The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142431}, doi = {10.1016/j.jhazmat.2026.142431}, pmid = {42208292}, issn = {1873-3336}, mesh = {Humans ; Risk Assessment ; *Drug Resistance, Microbial/genetics ; *One Health ; *Environmental Monitoring/methods ; *Drug Resistance, Bacterial/genetics ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.}, }
@article {pmid42208296, year = {2026}, author = {Wang, Q and Ma, Y and Niu, J and Liu, Y and Chao, C and Zhao, Y}, title = {Enhanced anti-toxicity memory of Cr(VI)-4-CP stressed denitrification by bio-promoter: Microbial cooperation and multi-path electron transfer drive toxics transformation-migration.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142497}, doi = {10.1016/j.jhazmat.2026.142497}, pmid = {42208296}, issn = {1873-3336}, mesh = {*Chromium/toxicity/chemistry/metabolism ; *Chlorophenols/toxicity/metabolism/chemistry ; *Water Pollutants, Chemical/toxicity/metabolism/chemistry ; *Denitrification/drug effects ; Electron Transport ; Molybdenum/chemistry ; Extracellular Polymeric Substance Matrix/metabolism ; Adenosine Triphosphate/metabolism ; Bacteria/metabolism ; Bioreactors ; }, abstract = {Coexisting heavy metals and organic pollutants in industrial wastewaters posed synergistic inhibition to denitrification by activating dissimilatory nitrate reduction and disrupting electron supply-consumption balance. Taking Cr(VI) and 4-chlorophenol (4-CP) as representative pollutants, this study proposed a combined bio-promoter composed of growth factors and phosphomolybdic acid (PMo12) to accelerate recovery and establish anti-toxicity memory under compound stress. The promoter restored over 90% nitrogen removal within 9 T and maintained 63.6% nitrogen removal under Cr(VI)-4-CP re-stress. Compared to first-stress, the recovered system reduced 37.44 mg/L more Cr(VI) and kept 4-CP below 5 mg/L, thus rapidly relieving Cr(VI)-4-CP toxicity and increasing the supply of direct electron donor nicotinamide adenine dinucleotide (NADH, 65.5%) and energy source adenosine triphosphate (ATP, 27.8%). Meanwhile, the enhanced extracellular polymeric substance (EPS) ensured 11.15 mg/g mixed liquid suspended solids (MLSS) more chromium immobilization with 97.9% distributed intercellularly, preventing Cr(VI) from invading cells and minimizing intracellular oxidative damage. The biofilm-fixed Mo (4.28 mg/g MLSS) shortened electron transfer distance to NO3[-]-N, which, combined with a 17.3% increase in cytochrome (cyt.c), formed a new mode of multi-path electron transfer. Microbacterium with glucose-4-CP co-metabolism and denitrification functions contributed 13.0% of the recovered community, transforming glucose and 4-CP competitive metabolism into collaborative metabolism, further enhancing the anti-toxicity memory, and ensuring efficient denitrification performance.}, }
@article {pmid42208547, year = {2026}, author = {Goldberg, H and Dyhrman, ST and DeMers, MA and Braakman, R and Hennon, GMM}, title = {Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70315}, doi = {10.1111/1462-2920.70315}, pmid = {42208547}, issn = {1462-2920}, support = {OCE-1937715//National Science Foundation/ ; OCE-2019589//National Science Foundation/ ; }, mesh = {*Hydrogen Peroxide/metabolism ; *Seawater/microbiology ; *Catalase/genetics/metabolism ; Ecosystem ; Oceans and Seas ; *Bacteria/genetics/metabolism/classification ; Bacterial Proteins/genetics/metabolism ; Metagenome ; *Microbiota ; Genome, Bacterial ; }, abstract = {Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying 'helper' microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes-including within the known 'helper' genus Alteromonas-and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on 'helpers'. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.}, }
@article {pmid42208809, year = {2026}, author = {Korva, M and Bogovič, P and Knap, N and Kogoj, R and Slunečko, J and Zakotnik, S and Suljič, A and Resman Rus, K and Pozvek, P and Strle, F and Avšič-Županc, T and Petrovec, M}, title = {Emerging human pathogen: Identifying Spiroplasma ixodetis as a frequent cause of unlocalised febrile illness.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106776}, doi = {10.1016/j.jinf.2026.106776}, pmid = {42208809}, issn = {1532-2742}, mesh = {Humans ; Female ; *Spiroplasma/isolation &amp; purification/genetics/classification ; Male ; Adult ; Aged ; Middle Aged ; *Communicable Diseases, Emerging/microbiology/epidemiology/diagnosis ; Prevalence ; *Gram-Negative Bacterial Infections/epidemiology/microbiology/diagnosis ; RNA, Ribosomal, 23S/genetics ; Young Adult ; Sequence Analysis, DNA ; Real-Time Polymerase Chain Reaction ; Cohort Studies ; DNA, Bacterial/genetics/chemistry ; RNA, Ribosomal, 16S/genetics ; Aged, 80 and over ; *Fever/microbiology ; Adolescent ; }, abstract = {OBJECTIVES: Febrile illness without clear localisation presents a significant diagnostic challenge due to non-specific symptoms and diverse aetiologies. Spiroplasma ixodetis, an emerging tick-associated pathogen previously linked mainly to congenital cataracts, has not been well characterised in adults. We investigated the prevalence and clinical features of S. ixodetis infection in adults with acute febrile illness without localisation.<br><br>METHODS: Shotgun metagenomic sequencing identified S. ixodetis in the initial 209 patient cohort and the sequences were used to developed a novel real-time PCR assay targeting the 23S rRNA gene. Initial cohort screening was followed by testing 128 patients from an additionally selected targeted cohort. Positive results were confirmed by sequencing of 16S and 23S rRNA genes.<br><br>RESULTS: S. ixodetis DNA was confirmed in 7.2% patients from the initial and in 35.2% patients from the additional cohort (60 in total). All were identified in the period from April to October and 57% reported a recent tick-bite. Clinical presentation was homogenous, characterised by fever, headache, bicytopenia and liver enzyme abnormalities. Outcomes were favourable, with 15% requiring hospitalisation.<br><br>CONCLUSION: This study identifies S. ixodetis as a previously unrecognised cause of adult febrile illness without localisation, bridging the gap between previously published data between tick studies and isolated human case reports.}, }
@article {pmid42208810, year = {2026}, author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB}, title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106774}, doi = {10.1016/j.jinf.2026.106774}, pmid = {42208810}, issn = {1532-2742}, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Female ; Male ; *Carrier State/microbiology/epidemiology ; Aged, 80 and over ; *Bacteria, Anaerobic/drug effects ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Aged ; Nursing Home Residents ; Prevalence ; }, abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.<br><br>METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.<br><br>RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (&#x3b2;=1.36, P=0.010) and higher overall pathobiont relative abundance (&#x3b2;=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (&#x3b2;=1.60, P=0.007) and relative abundance (&#x3b2;=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.<br><br>CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.}, }
@article {pmid42208932, year = {2026}, author = {Lv, H and Jin, S and Li, L and Ma, S and Wang, Y and Zhang, Y and Guo, K}, title = {Diagnostic accuracy of metagenomic next-generation sequencing for invasive pulmonary aspergillosis: A systematic review and meta-analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {170}, number = {}, pages = {108827}, doi = {10.1016/j.ijid.2026.108827}, pmid = {42208932}, issn = {1878-3511}, abstract = {OBJECTIVES: To systematically evaluate the diagnostic accuracy of metagenomic next‑generation sequencing (mNGS) for invasive pulmonary aspergillosis (IPA), and to compare its sensitivity and specificity with conventional methods.<br><br>METHODS: Meta&#x2011;analysis was performed to pool sensitivity, specificity, and diagnostic odds ratio (DOR). The comparison test between mNGS and conventional diagnostic methods was conducted through pairwise comparisons, and effect size was expressed using the risk difference (RD) and 95% confidence interval.<br><br>RESULTS: Twelve studies were included, the pooled sensitivity of mNGS was 0.75 (95% CI: 0.65-0.84), specificity 0.93 (95% CI: 0.84-0.97), DOR 35.69 (95% CI: 13.70-92.97). The comparative analysis showed mNGS had higher sensitivity compared with galactomannan (RD = 0.22, 95% CI: 0.16-0.29), culture (RD = 0.40, 95% CI: 0.26-0.55), and (1&#x2192;3)-&#x3b2;-d-glucan (BDG) (RD = 0.23, 95% CI: 0.09-0.37). For BDG assay, mNGS also demonstrated superior specificity (RD = 0.12, 95% CI: 0.04-0.20).<br><br>CONCLUSION: mNGS demonstrates promising diagnostic accuracy for IPA, with favorable sensitivity and specificity, and shows higher sensitivity than several conventional methods. BALF is the preferred specimen, and combined testing with multiple sample types improves diagnostic yield.}, }
@article {pmid42208954, year = {2026}, author = {Baker, B and Baz Lomba, JA and Bitilinyu-Bangoh, J and Berglöf, A and Bombaywala, S and Calvert-Joshua, T and Kaboré, B and Kingpriest, P and Lang, T and Levy, JI and Lompo, P and Lyimo, E and Martens, L and Mavoko, HM and Mesuere, B and Moremi, N and Mulder, N and Ndure, SL and Rameto, MA and Rinke de Wit, TF and Sebukoto, H and Smith, E and Tahita, MC and Tevuzula, VM and Tippett Barr, BA and Tiwari, A and Tran, T and Ubomba-Jaswa, E and Van Den Bossche, T and Wolday, D and Krolicka, A and Baraka, V and Pitkänen, T and Lood, R}, title = {Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101426}, doi = {10.1016/j.lanmic.2026.101426}, pmid = {42208954}, issn = {2666-5247}, abstract = {Persistent SARS-CoV-2 transmission, ongoing mpox outbreaks, and the continued spread of endemic diseases such as typhoid fever and cholera underscore the urgent need for global, multiomics surveillance. In this Personal View, we present Project ODIN, a consortium of European and African partners launched in 2023 that aims to meet this challenge by deploying innovative systems for near real-time pathogen detection and actionable public health insights. The project is a collaboration between high-income and low-income countries in northern Europe and sub-Saharan Africa. Focusing on low-income and middle-income countries, ODIN integrates metagenomics with mobile laboratory systems for comprehensive pathogen monitoring across diverse environments. ODIN emphasises standardised sampling, bioinformatics pipelines, and data-sharing protocols to ensure reliable, interoperable results while addressing infrastructure and resource limitations. By bridging gaps in genomic surveillance, these initiatives seek to strengthen outbreak preparedness, improve pathogen detection, monitor antimicrobial resistance, and provide a holistic approach to One Health challenges. Together, these innovations could advance global surveillance capacity-particularly in under-resourced regions-paving the way for effective disease control and evidence-based policy making.}, }
@article {pmid42209028, year = {2026}, author = {Hoeter, K and Marriott, L and Neuberger, EWI and Dagwadordsch, U and Kumar, RS and Simon, P and Bodenstein, M and Kersaudy-Kerhoas, M}, title = {Plasma metagenomic cfDNA sequencing identifies pathogens in culture-negative sepsis following urinary pouch rupture.}, journal = {BMJ case reports}, volume = {19}, number = {5}, pages = {}, pmid = {42209028}, issn = {1757-790X}, mesh = {Humans ; Female ; *Sepsis/microbiology/diagnosis/drug therapy/blood ; Anti-Bacterial Agents/therapeutic use ; *Cell-Free Nucleic Acids/blood ; *Pseudomonas Infections/diagnosis/drug therapy/blood ; Metagenomics/methods ; *Klebsiella Infections/diagnosis/drug therapy/blood ; Rupture, Spontaneous ; Klebsiella/isolation &amp; purification/genetics ; }, abstract = {A patient with a complex urological history presented with abdominal pain and respiratory distress after catheter dysfunction. She underwent emergency surgery for a ruptured urinary pouch. Sepsis was later diagnosed based on clinical deterioration, including tachycardia, fever, an elevated respiratory rate and raised inflammatory markers, but blood cultures remained negative. A metagenomic microbial cell-free DNA (cfDNA) assay (iSEP-SEQ), performed early from plasma as part of a research protocol, identified Klebsiella and Pseudomonas at the genus level. Results were obtained retrospectively and were not available in real time; therefore, they did not alter immediate management. These findings were confirmed by cultures from drainage fluid and urine. Broad-spectrum antibiotic treatment led to clinical improvement. This case highlights the limitations of conventional microbiological methods in culture-negative sepsis and illustrates the role of cfDNA-based metagenomic testing as an adjunctive and complementary diagnostic tool for early, accurate pathogen detection. Early use of such tools may support timely and targeted management in complex infectious disease presentations.}, }
@article {pmid42209192, year = {2026}, author = {Leggio, M and Schramm, S and Dietz, L and Ocón, B and Wirtz, S and Puertolas Balint, F and Yilmaz, B and Petzold, J and Liu, LJ and Dedden, M and Ekici, A and ,  and Meng, X and Bingham, D and Ullrich, KA and Heltmann-Meyer, S and Günther, C and Hildner, K and Atreya, R and Atreya, I and Müller, TM and Gerlach, RG and Schroeder, BO and Macpherson, A and Butcher, EC and Neurath, MF and Zundler, S and , }, title = {The endogenous peptide GPR15L shapes the intestinal microbiota to counteract colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337619}, pmid = {42209192}, issn = {1468-3288}, abstract = {BACKGROUND: The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far.<br><br>OBJECTIVE: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD.<br><br>DESIGN: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival.<br><br>RESULTS: GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival.<br><br>CONCLUSIONS: GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.}, }
@article {pmid42209465, year = {2026}, author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L}, title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73084-2}, pmid = {42209465}, issn = {2041-1723}, abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.}, }
@article {pmid42209510, year = {2026}, author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH}, title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01018-3}, pmid = {42209510}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; }, abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.}, }
@article {pmid42209552, year = {2026}, author = {Olszyński, RM and Mann, DG and Zakrzewski, PK and Peszek, &#x141; and Ács, &#xc9; and Shemesh, S and Trobajo, R}, title = {Nitzschia excavata sp. nov. (Bacillariaceae), a new diatom species from a post-mining reservoir revealed by morphology, molecular phylogeny, and metabarcoding-based biogeography.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42209552}, issn = {2045-2322}, support = {RRF 2.3.1 21 2022 00008//Sz&#xe9;chenyi Plan Plus programme/ ; RRF 2.3.1 21 2022 00008//Sz&#xe9;chenyi Plan Plus programme/ ; }, mesh = {*Diatoms/genetics/classification/ultrastructure ; *Phylogeny ; *DNA Barcoding, Taxonomic ; Phylogeography ; Mining ; DNA, Ribosomal/genetics ; Poland ; }, abstract = {The Bogdałów post-mining reservoir (Poland) represents a slightly alkaline, moderately mineralised ecosystem formed by flooding a former lignite pit. Its anthropogenic origin and stable physicochemical conditions have enabled the development of species-rich diatom assemblages, particularly numerous Nitzschia (Bacillariaceae) species. To explore this diversity, an integrative approach combining microscopy and DNA-based analyses was employed. Morphological examinations were performed using light and scanning electron microscopy, as well as confocal laser scanning microscopy. Molecular phylogenetic analyses were based on the sequencing of the nuclear SSU rDNA and the chloroplast rbcL and psbC gene markers. This comprehensive study led to the discovery and formal description of Nitzschia excavata sp. nov., distinguishable by unique morphological features and a phylogenetically distinct lineage. Furthermore, environmental DNA metabarcoding and metagenomic database searches revealed sequences identical or closely related to the N. excavata sp. nov. lineage in freshwater habitats across Europe and China, indicating that this taxon has an unexpectedly broad distribution. These findings underscore the value of integrating classical morphological analysis with multi-marker molecular data in diatom taxonomy and demonstrate that anthropogenic habitats may support taxa with broader distributions than previously recognized. The study highlights the important role of metabarcoding and metagenomics in revealing cryptic diversity and clarifying the biogeographic patterns of newly described species.}, }
@article {pmid42209868, year = {2026}, author = {Ajeh, IJ and Ikukpla'si, OSI}, title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42209868}, issn = {2589-0409}, mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; }, abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.}, }
@article {pmid42210135, year = {2026}, author = {Feng, W and Xiao, H and Hu, B and Chen, T and Hu, H and Guo, L and Guo, X and Zhu, L and Liu, G}, title = {Clinical characteristics, diagnosis, and management of central nervous system aspergillosis in children: a single-center experience.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13675-y}, pmid = {42210135}, issn = {1471-2334}, support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; PX2024042//Beijing Municipal Administration of Hospitals Incubating Program/ ; }, abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a severe and frequently misdiagnosed infection in pediatric patients. Systematic pediatric data on its clinical, radiological, diagnostic, and therapeutic features remain limited.<br><br>METHODS: We retrospectively identified children aged 0-18 years with proven or probable CNS aspergillosis admitted to Beijing Children's Hospital between January 2010 and December 2024. Demographic, clinical, laboratory, and imaging data were collected. Treatment regimens and clinical outcomes were systematically evaluated.<br><br>RESULTS: Sixteen patients were included (12 males), with a median age of 5 years. Hematological malignancies were the most common predisposing factor. Notably, 25% (4/16) of patients lacked identifiable predisposing conditions. Clinical presentations were nonspecific, with fever, seizures, and impaired consciousness being the most common features, and an initial misdiagnosis occurred in 56.3% (9/16) of cases. In contrast to the low yield of cerebrospinal fluid (CSF) cultures, CSF metagenomic next-generation sequencing (mNGS) detected Aspergillus nucleic acids in all tested patients (7/7). Magnetic resonance imaging (MRI) most commonly revealed irregular cerebral abscesses (14/16), frequently accompanied by meningeal enhancement (14/16) and obstructive hydrocephalus (10/16). Among evaluable patients receiving initial voriconazole monotherapy, a partial response was observed in 22.2% (2/9). Conversely, higher response rates were observed with regimens containing liposomal amphotericin B (L-AmB), including initial combination therapy (75.0%) and salvage treatment (80.0%). The all-cause mortality rate was 37.5% (6/16), and moderate-to-severe disability was present in 30.0% (3/10) of survivors.<br><br>CONCLUSIONS: Pediatric CNS aspergillosis can occur across a broad risk spectrum, often with nonspecific symptoms, leading to frequent misdiagnosis. Our findings support the early incorporation of CSF mNGS and comprehensive neuroimaging (including whole-neuraxis MRI when clinically indicated) to facilitate timely diagnosis and assess dissemination. The observed high rate of progression with initial voriconazole monotherapy and the relatively favorable responses associated with regimens containing L-AmB highlight the need for prospective pediatric studies to refine initial treatment strategies in severe disease.<br><br>CLINICAL TRIAL REGISTRATION: Not applicable.}, }
@article {pmid42210369, year = {2026}, author = {Pangestu, HS and Yang, I and Natasha, A and Rajoriya, S and Hennisa, H and Park, J and Park, K and Kim, J and Kim, SG and Klein, TA and Kim, HC and Oh, Y and Song, JW and Kim, WK}, title = {Molecular prevalence, genomic characterization, and zoonotic potential of novel paramyxovirus and hepacivirus in Alexandromys fortis, Republic of Korea.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42210369}, issn = {1297-9716}, support = {ProMIS ID C0039-09-ME//Global Emerging Infections Surveillance Branch (GEIS)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion/ ; RS-2023-KH140418//Government-wide R&amp;D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; 2024-ER2502-00//Korea National Institute of Health Research Project/ ; RS-202300249142//Basic Science Research Program through the NRF by the Ministry of Education/ ; NF22SA0082041//Novo Nordisk Foundation PAD award to CBL/ ; U01 AI151810/AI/NIAID NIH HHS/United States ; 2023R1A2C2006105//Basic Research Program through the NRF grant funded by the Korean government (MSIT)/ ; RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through High-Risk Animal Infectious Disease Control Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Animals ; Republic of Korea/epidemiology ; *Genome, Viral ; Phylogeny ; *Arvicolinae/virology ; *Paramyxoviridae Infections/veterinary/epidemiology/virology ; *Rodent Diseases/virology/epidemiology ; *Zoonoses/virology/epidemiology ; Prevalence ; *Paramyxoviridae/genetics/isolation &amp; purification ; *Hepatitis C/virology/epidemiology/veterinary ; }, abstract = {Rodents are substantial reservoirs of zoonotic viruses with regular human exposure restricted to a limited number of species. Numerous rodent species have been shown to harbor emerging viruses, including paramyxoviruses and hepaciviruses. Reed voles (Alexandromys fortis), a rodent species that inhabits grasslands and riparian environments throughout East Asia, remain poorly characterized in terms of their viral diversity. In this study, 258 A. fortis specimens collected from rural areas in Gyeonggi Province, Republic of Korea (ROK) were screened for paramyxoviruses and subjected to metagenomic next-generation sequencing. Genome characterization, phylogenetic and cophylogenetic assessments, and prediction of signal peptidase cleavage sites were performed to analyze the molecular features of the identified viruses. Zoonotic potential was evaluated using a genome-based machine-learning model. A nearly complete genome of a novel paramyxovirus, designated as Pyeongtaek Alexandromys paramyxovirus (PyAPV), was identified in six A. fortis specimens, with all sequences clustering within the genus Jeilongvirus. A nearly complete genome of a rodent-associated hepacivirus was also obtained from four specimens and classified as a distinct lineage within the species Hepacivirus J. These findings demonstrate the role of A. fortis as a natural reservoir of emerging viruses and expand current knowledge of rodent-associated viral diversity in the ROK.}, }
@article {pmid42210378, year = {2026}, author = {Han, J and Liu, J and Wang, T and Dong, B and Zhang, F and Li, S and Zou, Q and Li, D}, title = {Temporal variations in the gut microbiota of François' langur (Trachypithecus francoisi): implications for adaptation to seasonal dietary change and conservation.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00580-7}, pmid = {42210378}, issn = {2524-4671}, abstract = {Despite growing research on gut microbiota in wild primates, seasonal functional dynamics of the gut microbiota in this endangered folivorous species remain poorly understood. This study investigates the seasonal variations in the gut microbiota of François' langur (Trachypithecus francoisi) and their implications for dietary adaptation and conservation. Using shotgun metagenomic sequencing, fecal samples were collected across four seasons within the Mayanghe National Nature Reserve in China (n = 24). The study identified significant seasonal shifts in microbial diversity and composition. While alpha diversity metrics reflecting community evenness (Shannon and Simpson equivalents) remained stable (Padj > 0.05), species richness (Hill number, q = 0) was significantly lower in Fall compared to Spring and Winter (Padj = 0.013). Results revealed that dominant phyla included Bacillota and Bacteroidota, with a significant enrichment of Faecalibacterium during Fall. Functional analysis showed a predominance of carbohydrate metabolism, which remained stable at broad metabolic levels; however, fine-scale functional units (KOs and CAZy families) exhibited distinct seasonal signatures. A moderate correlation between taxonomic and functional profiles (Mantel r = 0.43, P = 0.001) suggests a partial decoupling. These findings highlight the ecological plasticity of the gut microbiota and underscore how taxonomic flexibility enables functional homeostasis, aiding the physiological resilience of endangered primates in fluctuating environments.}, }
@article {pmid42210496, year = {2026}, author = {Gourabi, MJR and Kargar, M and Kamali, A and Sharahi, JY}, title = {Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70320}, pmid = {42210496}, issn = {2045-8827}, mesh = {Humans ; *Coinfection/microbiology/drug therapy ; Biofilms/growth &amp; development ; *Microbial Interactions ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Candida albicans/physiology ; *Bacteria/drug effects ; *Fungi/physiology/drug effects ; *Mycoses/microbiology ; *Bacterial Infections/microbiology ; }, abstract = {Polymicrobial infections involving fungi and bacteria represent a major and increasingly recognized clinical challenge, in which interkingdom interactions significantly amplify disease severity, antimicrobial resistance, and treatment failure. Rather than passive co-existence, fungal-bacterial communities form highly coordinated systems driven by physical adhesion, quorum sensing, metabolic interdependence, and biofilm-mediated structural reinforcement. These cooperative interactions, exemplified by pairs such as Candida albicans-Staphylococcus aureus and Pseudomonas aeruginosa-Aspergillus fumigatus, promote the development of treatment-recalcitrant biofilms with enhanced immune evasion and multidrug tolerance. The global rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has further intensified this burden, with polymicrobial biofilms now representing a post-antibiotic clinical scenario in which therapeutic failure is driven not by individual resistant organisms but by emergent, cooperative resistance architectures. Conventional diagnostic approaches remain insufficient, as culture-based methods frequently fail to capture the complexity of mixed microbial communities. Emerging technologies such as MALDI-TOF mass spectrometry, metagenomic sequencing, and fluorescence in situ hybridization offer improved resolution but are not yet fully integrated into routine clinical practice. Therapeutically, increasing evidence indicates that monotherapy is inherently inadequate in polymicrobial infections due to the emergent nature of microbial cooperation. Effective management therefore requires combination strategies that simultaneously target multiple pathogens and their shared biofilm infrastructure. These include antibiotic-antifungal combinations, phage therapy, enzymatic and nanoparticle-mediated biofilm disruption, metabolic interference, and host-directed immunomodulation. Importantly, recent advances also highlight the role of biophysical properties such as biofilm viscoelasticity and matrix stiffness as critical and previously underappreciated therapeutic targets. This review uniquely integrates biochemical, biophysical, and therapeutic dimensions of polymicrobial infections into a unified systems-level framework in which microbial cooperation is the central driver of pathogenesis, resistance, and treatment failure. Fungal-bacterial interactions are thereby positioned along a dynamic continuum from commensalism to pathogenesis, shaped by host susceptibility and environmental perturbations. Future progress will depend on interdisciplinary strategies combining multi-omics technologies, precision diagnostics, and microbiome-informed therapeutic design to effectively disrupt these complex microbial networks.}, }
@article {pmid42210528, year = {2026}, author = {Zhou, X and Zhang, M and Zhou, J and Han, J}, title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70749}, pmid = {42210528}, issn = {1097-0010}, support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; }, abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.<br><br>RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-&#x3ba;B signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).<br><br>CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42210827, year = {2026}, author = {Syatrawati,  and Kuswinanti, T and Nasruddin, A and Rosmana, A and Hikmahwati, }, title = {Metagenomic Insights into Rhizosphere Fungal Communities Across Different Rice Cultivation Systems.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {29}, number = {3}, pages = {147-159}, doi = {10.3923/pjbs.2026.147.159}, pmid = {42210827}, issn = {1812-5735}, mesh = {*Oryza/microbiology/growth &amp; development ; *Rhizosphere ; *Metagenomics/methods ; *Fungi/genetics/classification ; Soil Microbiology ; Agriculture/methods ; }, abstract = {Background and Objective: Rhizosphere fungi play a crucial role in nutrient cycling and plant protection, yet most are difficult to cultivate using conventional methods. Consequently, their ecological functions remain largely unknown. Therefore, metagenomic approaches allow for comprehensive and accurate mapping of fungal taxonomic profiles without the need for cultivation and this study investigated the variation of rhizosphere fungi across different rice cultivation systems to elucidate their diverse potentials. Materials and Methods: A metagenomic approach was employed to identify fungi originating from the rhizosphere of rice cultivated in various field conditions, including irrigated, rainfed and organic rice fields. The diversity of fungi from rhizosphere samples was assessed to comprehend the relationships and metrics within the rice cropping systems utilized by farmers. Results: The findings indicated that the rhizosphere fungal index from organic rice fields exhibited the highest Shannon and Simpson index values compared to those from irrigated and rainfed rice fields. Conclusion: Metagenomic analysis revealed that the most dominant fungal diversity at the family level was Trichocomaceae, at the genus level was Talaromyces and at the species level was Talaromyces wortmannii.}, }
@article {pmid42211404, year = {2026}, author = {Su, L and Zhang, Y and Xie, Y and Wu, J and Yang, Y and Li, Y and Huang, Y and Liu, X and Wei, X and Chen, Q}, title = {Integrated metabolomics and gut microbiota analyses reveal the protective effects of matrine in ulcerative colitis.}, journal = {Frontiers in chemistry}, volume = {14}, number = {}, pages = {1826894}, pmid = {42211404}, issn = {2296-2646}, abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by gut microbial dysbiosis and metabolic dysfunction. Matrine, a natural alkaloid with anti-inflammatory properties, shows therapeutic potential; however, its mechanisms involving the coordinated modulation of bacteria, fungi, and host intestinal luminal metabolism remain unclear.<br><br>METHODS: We evaluated the therapeutic efficacy of matrine using a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis. Disease severity was assessed via the disease activity index, colon length, and histopathology. Integrated multi-omics approaches, including metagenomics, ITS fungal sequencing, and untargeted metabolomics of intestinal luminal contents, were employed to systematically characterize the regulatory effects of matrine on gut bacteria, fungi, and metabolic profiles.<br><br>RESULTS: Here, we demonstrated that oral matrine significantly alleviated disease severity in a DSS-induced UC mouse model, as evidenced by improved disease activity index, colon length, histopathology, and restoration of tight junction proteins. Integrated multiomics revealed that matrine restored bacterial homeostasis-suppressing Escherichia while enriching SCFAs-producing taxa (Muribaculum, Paramuribaculum, Clostridium). Metagenomic predictions revealed that matrine treatment reversed the model-induced suppression of carbohydrate metabolism and bile acid biosynthesis while upregulating depleted CAZy enzyme families, thereby correcting dysregulated metabolic functions in colitis. Furthermore, matrine rebalanced the mycobiota by normalizing the Ascomycota/Basidiomycota ratio. Intestinal luminal contents untargeted metabolomics identified 43 matrine-responsive metabolites, implicating correction of bile acid metabolism, attenuation of leukotriene-mediated inflammation, and reversal of acylcarnitine-driven epithelial energy disruption. Critically, pro-inflammatory metabolites correlated positively with Escherichia and negatively with beneficial symbionts.<br><br>CONCLUSION: Our findings established that matrine exerted protective effects in UC through a unified "microbiota-metabolism" axis, highlighting its promise as a multi-target therapeutic agent for UC.}, }
@article {pmid42211783, year = {2026}, author = {Ding, F and Li, Y and He, T and Wang, Y and Li, Y and Huang, Y and Yin, G and Yang, J and Liu, Y and Li, Y and Li, T and Hou, L and Liu, M}, title = {Deciphering the drivers of antibiotic resistance gene transmission in the megacity: Co-occurring contaminants and bacterial community.}, journal = {Eco-Environment &amp; Health}, volume = {5}, number = {2}, pages = {100242}, pmid = {42211783}, issn = {2772-9850}, abstract = {Urban waters are widely contaminated with co-occurring microplastics and antibiotics. Human-land interactions (e.g., wastewater discharge, stormwater runoff, and land use) drive contaminant distribution and antimicrobial resistance. Nevertheless, there is a lack of systematic research evaluating the role of co-occurring contaminants in shaping the spread of antibiotic resistance genes (ARGs). In this study, a metagenomic approach was used to characterize the diversity and distribution of ARGs based on contaminant co-occurring patterns. The random forests and partial least squares path model (PLS-PM) were used to identify and prioritize the factors impacting ARGs, leading to a thorough environmental health ecological risk evaluation. Industrial waters, especially pharmaceutical factories, were significant reservoirs and hotspots for the development of ARGs. Urban estuaries further gathered and amplified the effects of co-occurring contaminants, thereby enhancing the prevalence of ARGs. The potential spread of ARGs was dominated by contaminant co-occurring patterns in urban waters, whereas microbial communities dominated in sediments. Urban zoning comprehensively affected environmental health risks, indicating that environmental management strategies, such as controlling pollution sources and implementing remediation, should prioritize water bodies in agricultural areas and sediments in commercial/residential areas.}, }
@article {pmid42211787, year = {2026}, author = {Zhang, R and Chen, YK and Zhu, QY and Feng, RY and Liu, H and Ma, MM and Wang, XJ}, title = {Metagenomic profiling of ocular surface microbiome alterations in patients with progressive supranuclear palsy-Richardson's syndrome.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100605}, pmid = {42211787}, issn = {2666-5174}, abstract = {This study employed shotgun metagenomic sequencing to characterize the ocular surface microbiome in 20 progressive supranuclear palsy-Richardson's syndrome (PSP-RS) patients, 17 Parkinson's disease (PD) patients, and 30 healthy controls (HC). Comparative analysis revealed that PSP-RS patients exhibited significantly altered microbial β-diversity compared to HC, while PD patients showed no such significant changes. Both patient groups demonstrated decreased abundance of g_Vibrio, with PSP-RS patients additionally showing marked increases in g_Acinetobacter and g_Anaerococcus. Importantly, correlation analyses identified that increased g_Acinetobacter abundance was positively associated with ocular motor impairment severity, while elevated g_Anaerococcus levels correlated with both freezing of gait severity and longer disease duration in PSP-RS patients. This is the first shotgun metagenomic investigation of the ocular surface microbiome in PSP-RS and these findings provide evidence that specific alterations in the ocular surface microbiome may contribute to PSP-RS pathogenesis and disease progression.}, }
@article {pmid42211840, year = {2026}, author = {Pesantes, N and Barberá, A and Pérez-Rocher, B and Artacho, A and Vargas, SL and Moya, A and Ruiz-Ruiz, S}, title = {Correction: Influence of mental health medication on microbiota in the elderly population in the Valencian region.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861757}, doi = {10.3389/fmicb.2026.1861757}, pmid = {42211840}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1094071.].}, }
@article {pmid42211849, year = {2026}, author = {Du, R and Xu, C and Zhao, D and Zeng, H and Cheng, Y and Tang, K and Cai, P and Zhang, Y}, title = {Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824768}, pmid = {42211849}, issn = {1664-302X}, abstract = {Estuarine sediments are pivotal zones for iron (Fe) cycling, mediated by microbial communities and coupled to carbon, nitrogen, sulfur and phosphorus transformations. However, the microbial iron metabolic processes in estuarine sediments remain poorly characterized, particularly under hypoxia. This study compared metagenomes from the Oujiang River Estuary, an oxic estuary, and the Yangtze River Estuary, a seasonally hypoxic estuary, complemented by sediment core incubations to assess geochemical responses to deoxygenation. The taxonomic affiliations of iron metabolism-related genes in the oxic estuary were homogeneous with depth, dominated by Proteobacteria and Thermodesulfobacteriota. In contrast, the hypoxic estuary exhibited strong stratification, with the surface enriched in Proteobacteria and deeper horizons dominated by Chloroflexota and Candidatus Bathyarchaeota. The surface sediments of the hypoxic estuary at 0-8 centimeters below the seafloor showed a hotspot with co-enrichment of dissimilatory iron reduction (e.g., mtrABC) and iron oxidation genes (e.g., mtoA) relative to both deeper layers in the same estuary and the oxic estuary, consistent with elevated genetic potential for Fe redox turnover. This hotspot also harbored high-affinity Fe acquisition systems (siderophores, inorganic Fe transporters, and heme uptake), suggesting the potential for microbial competition for iron. Co-occurrence networks connecting Fe metabolism with carbon, nitrogen, sulfur and phosphorus cycling were more complex in the hypoxic estuary than in the oxic estuary, revealing strong associations between Fe acquisition/redox cycling and organic matter turnover. A 16-day incubation of sediment cores from the oxic estuary showed that short-term deoxygenation enhanced dissolved Fe, phosphate, and ammonium release. Overall, our results suggest that bottom-water hypoxia is associated with major shifts in microbial iron metabolism potential, with implications for iron-organic matter interactions and nutrient regeneration under coastal deoxygenation.}, }
@article {pmid42211850, year = {2026}, author = {Li, L and Liu, R and Yang, H and Zhao, Y}, title = {Metagenomic sequencing reveals structural and functional differentiation of rhizosphere bacterial communities driven by nitrogen and potassium deficiency associated with root rot of Schisandra chinensis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827096}, pmid = {42211850}, issn = {1664-302X}, abstract = {BACKGROUND: Frequent incidence of root rot in Schisandra chinensis impairs its yield and quality, yet the rhizosphere microecological mechanism driving this incidence remains unclear.<br><br>METHODS: To clarify this mechanism, healthy and root rot-infected S. chinensis plants were analyzed in this study. The plant growth, rhizosphere soil physicochemical properties, and the structural and functional differences in rhizosphere bacterial communities under both conditions were analyzed.<br><br>RESULTS: Our results showed that root rot significantly inhibited S. chinensis growth and pathogen colonization-induced rhizosphere acidification, with reduced hydrolyzable nitrogen (HN) and available potassium (AK). Analysis of the intergroup differences in bacterial species revealed that the healthy rhizosphere was enriched with Acidobacteriota, Luteitalea, Pseudomonadota, Pseudolabrys, and Methylomirabilota, whereas infected rhizosphere was dominated by Gaiella (Actinomycetota), Gemmatimonas (Gemmatimonadota), Bradyrhizobium, and Sphingomicrobium (Pseudomonadota). Functional annotation based on COG, KEGG, and CAZy databases revealed that the bacteria of the healthy rhizosphere were enriched in defensive-cooperative functions (synergistic metabolism, secondary metabolite synthesis, complex carbon metabolism), while those of the infected rhizosphere exhibited simplified survival functions (individual metabolism, ABC transport, simple carbohydrate metabolism). Redundancy analysis identified HN and AK as key nutrients driving community differentiation in the rhizosphere.<br><br>CONCLUSION: This study revealed that root rot in S. chinensis is closely associated with an imbalance in the rhizosphere environment-bacterial community-function system, with healthy plants exhibiting specific core bacterial biomarkers and more complex synergistic metabolic networks, while HN and AK are key nutrients influencing rhizosphere bacterial communities. This study clarifies the rhizosphere microecological mechanism associated with S. chinensis root rot, providing a theoretical basis for its control.}, }
@article {pmid42212564, year = {2026}, author = {Kim, Y and Kim, JK and Her, M and Kong, HS and Moon, JS and Yun, CS}, title = {Shotgun Metagenomic Diagnosis of Unidentified Pathogens in Hepatic Necrosis Samples from Samgye Chickens.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-235}, doi = {10.1080/03079457.2026.2674233}, pmid = {42212564}, issn = {1465-3338}, abstract = {Chicken infectious anemia virus (CIAV), infectious bursal disease virus (IBDV), and Eimeria spp. are major immunosuppressive pathogens in chickens that predispose host to secondary infections, including Clostridium septicum-associated hepatic necrosis. In this case, shotgun metagenomic sequencing was applied to identify C. septicum that could not be isolated by traditional bacterial culture in Samgye chickens. Six 35-day-old Samgye chicken carcasses were submitted for disease diagnosis, histopathological examination, and bacterial and viral isolation/identification were performed. Pooled liver samples were subjected to shotgun metagenomic sequencing to identify microbial composition, virulence factors, and antimicrobial resistance genes. Samgye chickens exhibited dorsal dermatitis, hepatic necrosis, and splenomegaly. Histopathology revealed hepatic necrosis with bacterial colonies and lymphoid depletion. PCR detected CIAV, antigenic variant IBDV, chicken astrovirus, and Eimeria, whereas bacterial culture yielded no growth. Shotgun metagenomic analysis identified C. septicum as predominant bacterium, and CIAV as dominant viral pathogen. The α-toxin and the antimicrobial resistance tetA(P) genes were detected from liver samples. This is the first report of concurrent CIAV, avIBDV, Eimeria spp., and C. septicum infection from Samgye chickens in South Korea, suggesting that immunosuppressive infections may predispose chickens to C. septicum-associated hepatic necrosis and highlight the diagnostic utility of shotgun metagenomic sequencing.}, }
@article {pmid42212611, year = {2026}, author = {Sauer, P}, title = {[Current trends in sepsis diagnosis - from classic culture to advanced molecular identification].}, journal = {Klinicka mikrobiologie a infekcni lekarstvi}, volume = {32}, number = {1}, pages = {24-29}, pmid = {42212611}, issn = {1211-264X}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture ; *Molecular Diagnostic Techniques/trends ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Sepsis is a critical condition characterized by life-threatening organ dysfunction caused by a dysregulated host response to infection, where each hour of delay in initiating adequate therapy increases mortality by 7-10%. This paper summarizes current trends in microbiological diagnostics, moving from the gold standard of blood culture toward advanced molecular identification. The traditional culture-based process is limited by a time lag of 12-48 hours. Modern approaches include accelerating identification from positive blood cultures using MALDI-TOF MS and RAST methods, which reduce the time to targeted treatment. Significant innovation is represented by culture-independent technologies such as T2MR, SepsiTest-UMD, Cube Dx, and InfectID-BSI, enabling pathogen detection directly from whole blood within a few hours. The future of sepsis diagnosis is further enhanced by digital PCR for absolute quantification of bacterial load, metagenomic sequencing (mNGS) for identifying unexpected pathogens, and transcriptomics for assessing the host immune response. Integrating these technologies with artificial intelligence (AI) predictive models paves the way for precision medicine and personalized care for septic patients. Keywords: sepsis, blood culture, molecular diagnostics, PCR, mNGS, MALDI-TOF MS, artificial intelligence.}, }
@article {pmid42212684, year = {2026}, author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X}, title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672791}, pmid = {42212684}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Artificial Intelligence ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome ; Multiomics/methods/trends ; *Precision Medicine/methods ; *Tumor Microenvironment ; }, abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.}, }
@article {pmid42212786, year = {2026}, author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E}, title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0171425}, doi = {10.1128/msystems.01714-25}, pmid = {42212786}, issn = {2379-5077}, abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.<br><br>IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.}, }
@article {pmid42212790, year = {2026}, author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T}, title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014426}, doi = {10.1128/msystems.00144-26}, pmid = {42212790}, issn = {2379-5077}, abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.}, }
@article {pmid42212800, year = {2026}, author = {Yabe, S and Zheng, Y and Takahashi, S and Yang, C and Nose, Y and Yamazaki, S and Okuma, N and Rachmania, MK and Ningsih, F and Sjamsuridzal, W and Sato, M and Toyooka, K and Ichihashi, Y}, title = {Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019726}, doi = {10.1128/msystems.00197-26}, pmid = {42212800}, issn = {2379-5077}, abstract = {UNLABELLED: Soils harbor immense biosynthetic gene cluster (BGC) diversity that mediates microbial interactions, yet this potential remains unevenly mapped and poorly characterized across diverse bacterial lineages. Ktedonobacteria (phylum Chloroflexota) are an actinomycete-like lineage widely distributed in terrestrial soils, including oligotrophic volcanic deposits; however, their secondary metabolism and genome architecture remain poorly characterized. Here, we integrate targeted cultivation from volcanic soils at Mount Zao (Japan) with genome-resolved metagenomics and comparative analysis of public genomes to examine biosynthetic potential across 183 ktedonobacterial genomes. We identified 1,546 BGCs and grouped them into 1,162 non-redundant gene-cluster families (GCFs) using antiSMASH and BiG-SLiCE. Nearly one quarter of genomes encoded ≥10 distinct GCFs, and several family-level clades exhibited high GCF richness that approached that of Streptomyces within our data set, highlighting a putatively biosynthetically rich yet underexplored soil bacterial lineage. Most ktedonobacterial BGCs were highly divergent from current reference collections and exhibited unusually low intra-genomic redundancy, suggesting broad putative chemical diversity. Long-read assemblies from 10 cultured strains revealed recurrent 1.6-3.5 Mb ECE-like contigs with chromid-like features, but distinct maintenance features. These replicons were consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the phylogenetic landscape of soil biosynthetic diversity and highlight ECE-like contigs as major genomic reservoirs for secondary metabolism in Ktedonobacteria.<br><br>IMPORTANCE: Soil bacteria produce many of the small molecules that become medicines and help microbes interact with each other. Yet most of this chemical diversity remains unexplored because many soil lineages are difficult to cultivate and remain genomically underrepresented. Much of what we know comes from well-studied groups such as actinomycetes, leaving many soil lineages largely unexplored. We analyzed 183 genomes from Ktedonobacteria, an actinomycete-like group within the phylum Chloroflexota that is widespread in terrestrial soils, including nutrient-poor volcanic deposits. We uncovered a large and diverse set of gene clusters predicted to produce secondary metabolites, many of which lack close counterparts in current reference collections. We also show that these clusters are concentrated on large ECE-like contigs with chromid-like features, pointing to a dedicated genomic reservoir that can accumulate and reshuffle biosynthetic traits. Our results expand the known sources of soil biosynthetic diversity and provide a foundation for future cultivation and functional characterization of Ktedonobacteria metabolites.}, }
@article {pmid42213267, year = {2026}, author = {Gulnihol, S and Abdukhamid, N and Rustam, T and Firdavs, U and Gholami, AA}, title = {Methodological concerns in the association between gut microbiota and sarcopenia: from cross‑sectional associations to statistical fragility.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {}, pmid = {42213267}, issn = {1720-8319}, mesh = {Humans ; *Sarcopenia/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aged ; Iran ; }, abstract = {This commentary critically appraises the cross‑sectional study by Nasrollahizadeh et al. on gut microbiota and sarcopenia in Iranian older adults. Key limitations include; after FDR correction for twelve bacterial genera, no significant differences remained between groups; Akkermansia lost significance in sensitivity analyses; Lactobacillus showed a confidence interval including 1.00; four primer pairs lacked validation with no MIQE‑compliant efficiency data; the cross‑sectional design precludes causal inference; and no sample size justification was reported. The study offers valuable hypothesis‑generating data, but evidence remains preliminary. Future longitudinal studies with metagenomic approaches are essential.}, }
@article {pmid42213269, year = {2026}, author = {Song, X and Cai, D and Yu, X and Zhang, X and Zhu, W}, title = {Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42213269}, issn = {1678-4405}, support = {Z2021067//Tianjin Municipal Transportation Commission Science and Technology Development Plan Project/ ; Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)//Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)/ ; }, mesh = {*Lactuca/microbiology/growth &amp; development ; Soil Microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Hydroponics/methods ; *Microbiota ; Metagenome ; Biodiversity ; }, abstract = {BACKGROUND: Lettuce cultivation primarily involves two methods: traditional soil-based cultivation and modern hydroponic systems. However, research on the microbial community structure of lettuce under these distinct cultivation approache is still limited.<br><br>METHOD: This study employed whole-genome shotgun metagenomic sequencing (metagenomic sequencing) to analyze the impact of soil-based and hydroponic cultivation systems on the microbial community structure and functional profiles of lettuce.<br><br>RESULTS: The microbial diversity index of soil samples was significantly higher than that of hydroponic samples, indicating a more diverse and complex microbial community in the soil environment. Key functional phylum, including Acidobacteriota and Actinomycetota, were more abundant in soil samples, supporting nutrient cycling and plant-microbe interactions through pathways involved in carbon metabolism, organic matter decomposition, and antibiotic biosynthesis. In contrast, hydroponic samples were dominated by Cyanobacteriota and Verrucomicrobiota, with enrichment of pathways associated with stress response, including quorum sensing, ABC transporters, and oxidative phosphorylation. Although &#x3b1;-diversity did not differ significantly between cultivation systems, their microbial community composition and functional profiles were markedly distinct: soil-grown lettuce exhibited enrichment in sugar catabolism and synergistic prokaryotic metabolic functions, whereas hydroponic lettuce showed a predominance of energy metabolism and enrichment of viral-related pathways. Furthermore, differential distribution of antibiotic resistance genes underscores the role of environmental selective pressures in shaping microbial functional adaptations.<br><br>CONCLUSION: This study demonstrates that different cultivation methods significantly influence the microbial community structure and function in lettuce. These findings provide a theoretical foundation for optimizing cultivation systems and offer scientific guidance for precisely modulating microbial functions to promote lettuce growth and health.}, }
@article {pmid42213733, year = {2026}, author = {Wheelahan, JW and Vaz, PK and Legione, AR and Hartley, CA and Rourke, NL and Lynch, M and McMeekin, B and Dobson, EC and Devlin, JM}, title = {Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus).}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0345964}, pmid = {42213733}, issn = {1932-6203}, mesh = {Animals ; Australia ; *Elephants/virology ; *Genome, Viral ; Genomics ; *Herpesviridae/genetics ; *Herpesviridae Infections/veterinary/virology ; Phylogeny ; Viral Load ; Fatal Outcome ; }, abstract = {Elephant endotheliotropic herpesviruses (EEHV) pose a significant threat to the conservation of Asian elephants (Elephas maximus) worldwide, with a high mortality rate in young elephants. However, several components of EEHV virology remain underexplored, particularly for EEHV1B. This study describes a fatal case of EEHV1B infection in a nine-year-old Asian elephant from an ex situ conservation herd, examining herd viral dynamics, tissue viral loads and comparative genomics. This elephant succumbed to haemorrhagic disease within three days of developing clinical signs, despite therapeutic intervention. Quantitative PCR (qPCR) was performed on serial trunk washes and whole-blood surveillance samples collected before and after the clinical event, as well as on post-mortem tissues preserved in different storage media (DNA/RNA Shield, RNALater, and viral transport medium). Metagenomic next-generation sequencing of infected tissues was performed to characterise the complete viral genome, analyse variation from other published EEHV genomes and assess for evidence of viral recombination between EEHV subspecies. The affected elephant demonstrated a marked viraemia at onset of clinical disease, with viral load peaking at 5.47 x 106 viral genome equivalents per mL of blood, one day after the onset of clinical signs. Samples stored in viral transport medium yielded the greatest viral and host DNA recovery by qPCR, although tissues stored at -80 °C without media were still suitable for molecular detection. Whole genome sequencing demonstrated 96.0% pairwise nucleotide identity between the assembled genome (EEHV1B_AUP_01_2023, GenBank accession: PX651398) and the previously reported EEHV1B sequence (KC462164), and a maximum of 90.9% identity to published EEHV1A genomes, with evidence of recombination between the viral subspecies at several genomic regions. Viral recombination between EEHV subspecies may have significant implications for the pathogenesis of EEHV disease, the reliability of molecular diagnostics and the efficacy of vaccinations and anti-viral therapy.}, }
@article {pmid42213849, year = {2026}, author = {Meijer, J and Skiadas, P and Rainey, PB and Hogeweg, P and Dutilh, BE}, title = {Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.}, journal = {Science advances}, volume = {12}, number = {22}, pages = {eaeb8246}, pmid = {42213849}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics/physiology ; *Soil Microbiology ; *Evolution, Molecular ; Ecosystem ; *Composting ; Metagenomics ; Phylogeny ; Genome, Viral ; }, abstract = {Bacteriophages play critical roles in microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. Here, we tracked viral dynamics in 20 compost-derived microbial communities over 1 year. Communities formed two alternative stable types, each dominated by distinct cellulose degraders and comprising hundreds of genera. In one community type, we observed massive, parallel outbreaks of Theomophage, a previously uncharacterized member of the Schitoviridae, reaching up to 74% of metagenomic reads-the largest bacteriophage outbreak documented to date. Despite extensive replication, Theomophage displayed notable genetic stability during outbreaks and over time. In contrast, the experimental migration of viral communities triggered rapid evolution driven by recombination and the accumulation of newly arising mutations, particularly after colonization of communities of the alternative type in which the phage was initially absent. These results reveal the spatial and temporal scales at which bacteriophage microdiversity evolves in complex ecosystems and show that viral mixing, likely common in nature, can rapidly accelerate phage evolution.}, }
@article {pmid42214271, year = {2026}, author = {Lin, Y and Roy, S and Hagedoorn, PL}, title = {Microbial melanin-like material: A factor beyond influencing the brown color of activated sludge.}, journal = {Water research}, volume = {303}, number = {}, pages = {126195}, doi = {10.1016/j.watres.2026.126195}, pmid = {42214271}, issn = {1879-2448}, abstract = {Melanin is a group of phenolic-quinone pigments. Natural melanin is nearly ubiquitous; found in all types of living organisms, ranging from mammals to bacteria. However, its presence and biosynthesis genomic potential in activated sludge have not been investigated. To explore this potential, melanin-like material was extracted from activated sludge collected from a municipal wastewater treatment plant. The extracted melanin-like material was characterized through biochemical analyses in comparison to synthetic melanin and humic acids that are commercially available. Metagenomic analysis of microbial community members in activated sludge and detection of tyrosine-derived melanin synthesis genes was performed. Additionally, the potential application of the extracted melanin-like material as a natural pigment was evaluated by testing its ability to color wool yarn. It was found that melanin-like material extracted from activated sludge accounted for around 11% of sludge dry mass. The isolated material displayed intrinsic autofluorescence, strong UV absorption, high oxidative stability, and free radical-rich EPR signal. FTIR analysis indicated a mixed polymer dominated by pyomelanin-like structures with eumelanin features, distinguishing it from synthetic melanin and humic acid. Metagenomic screening of the sludge community revealed widespread genomic potential for pyomelanin monomeric precursors biosynthesis across key functional genera (e.g. genera Zoogloea, Nitrotoga, Nitrosomonas, Ca. Accumulibacter, Azonexus, Ca. Competibacter, Propionivibrio, and Rhodoferax). These results suggest that microbial melanin-like material is an overlooked contributor to sludge coloration. Furthermore, the extracted pigment exhibited high affinity and wash fastness on wool fibers, demonstrating its potential for valorization as a sustainable biobased colorant.}, }
@article {pmid42214309, year = {2026}, author = {Guo, N and Chen, J and Lei, Z and Qu, L and Xie, W and Yin, K and Yang, Y}, title = {Evidence for the connectivity of antibiotic resistance genes between seamount and coastal environments.}, journal = {Ecotoxicology and environmental safety}, volume = {319}, number = {}, pages = {120325}, doi = {10.1016/j.ecoenv.2026.120325}, pmid = {42214309}, issn = {1090-2414}, mesh = {*Geologic Sediments/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Seawater/microbiology ; *Bacteria/genetics ; China ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; }, abstract = {Antibiotic resistance genes (ARGs) have drawn global attention and are ubiquitously detected in marine environments. Seamounts, prominent seafloor features with high biodiversity, may be hotspots for ARG proliferation and transfer. However, little is known about the existence, microbial associations, or connectivity with terrestrial sources of ARGs in seamounts. In this study, high-throughput sequencing approaches were employed to investigate the distribution, hosts, mobility, and coastal connectivity of ARGs in sediments from the Zhongnan Seamount, South China Sea. The most abundant ARG types were elfamycin, aminoglycoside, and tetracycline. ARG abundance was significantly higher in abyssopelagic zone sediments, suggesting the seamount acts as a sink and deep-sea regions are a major ARG reservoir. Results indicated high horizontal gene transfer potential, with key genes EF-Tu, rpsJ, parC, and parE as predominant mediators. Metagenome-assembled genomes identified 36 bacterial genera as ARG hosts, dominated by Methylomirabilota and Pseudomonadota. The source tracking and genetic connectivity analysis revealed a clear input of coastal ARGs to the seamount, emphasizing the need to investigate global ARG dissemination and its potential ecological effects. Overall, these findings identify the seamount environment as a deep-sea ARG hotspot, providing valuable insights into the prevalence, hosts, and sources of ARGs in the marine ecosystem.}, }
@article {pmid42214347, year = {2026}, author = {Peredo, EL and Kulp, R and Rodriguez, F and Weintraub, MN and Anand, M and Bixler, S and Koller, J and Lee, C and Mathai, D and Tuytschaevers, S and Kumar, G}, title = {Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0038026}, doi = {10.1128/mra.00380-26}, pmid = {42214347}, issn = {2576-098X}, abstract = {Biological soil crusts (BSCs) are complex structures composed of prokaryotes, green microalgae, fungi, and small mosses that bind soil particles together. To further understand the microbial composition and interactions among members of these consortia, we investigated the microbial diversity of BSCs found in a xeric patch in northwestern Ohio.}, }
@article {pmid42214368, year = {2026}, author = {Karmarkar, B and Dhotre, D}, title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0321425}, doi = {10.1128/spectrum.03214-25}, pmid = {42214368}, issn = {2165-0497}, abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.<br><br>IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.}, }
@article {pmid42214386, year = {2026}, author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG}, title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.}, journal = {mBio}, volume = {}, number = {}, pages = {e0071126}, doi = {10.1128/mbio.00711-26}, pmid = {42214386}, issn = {2150-7511}, abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.<br><br>IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.<br><br>CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.}, }
@article {pmid42214591, year = {2026}, author = {Zhu, Y and Li, D and Ma, B and Zhang, T and Zeng, H and Zhang, J and Li, S and Ding, F}, title = {Effluent-released sludge in granular anammox systems: nitrogen transformation potential and potential biosafety concerns.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124887}, doi = {10.1016/j.envres.2026.124887}, pmid = {42214591}, issn = {1096-0953}, abstract = {Granular anaerobic ammonium oxidation (anammox) sludge enables effective biomass retention and supports the stable operation of anammox reactors. During long-term operation, however, effluent-released sludge (ERS) is continuously washed out with the effluent, exhibiting physicochemical and microbial characteristics that differ markedly from those of retained sludge (RS). The functional role and biosafety implications of ERS remain poorly understood. In this study, RS and ERS from the same granular anammox reactor were systematically compared in terms of nitrogen removal performance, microbial community composition, functional gene profiles, and biosafety-related features. RS maintained high anammox activity, whereas ERS showed reduced anammox performance but was characterized by a pronounced enrichment of comammox Nitrospira, supporting more diverse nitrogen transformation pathways. Metagenomic and 16S rRNA analyses further indicated the co-occurrence of comammox Nitrospira and heterotrophic denitrifiers in ERS, suggesting a potential metabolic linkage involving nitrate production and partial reduction to nitrite that may complement anammox activity. Functional pathway analysis revealed diminished autotrophic carbon fixation in ERS, alongside enhanced heterotrophic metabolism and cobalamin biosynthesis. In parallel, ERS exhibited elevated abundances of antibiotic resistance genes and pathogenic taxa. Collectively, these results demonstrate that ERS represents a functionally distinct biomass fraction with unique microbial and metabolic characteristics, as well as potential biosafety implications, warranting further consideration in the evaluation and management of granular anammox systems.}, }
@article {pmid42214592, year = {2026}, author = {Zhu, Y and Liu, H and Yi, Y and Li, Z and Ye, J}, title = {Agricultural allochthonous dissolved organic matter is associated with microbial functional differentiation in methane- and nitrogen-related gene profiles in rural rivers.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124865}, doi = {10.1016/j.envres.2026.124865}, pmid = {42214592}, issn = {1096-0953}, abstract = {Agricultural non-point source (ANPS) pollution introduces chemically complex dissolved organic matter (DOM) into rural rivers, yet how different agricultural practices structure DOM-microbial differentiation at the molecular scale remains unclear. Here, we compared rivers polluted by three dominant ANPS subtypes-aquaculture (AQ), livestock and poultry farming (LP), and crop farming (CF)-across winter and summer in Shanghai, China, by integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) with 16S rRNA gene sequencing and metagenomics. Distinct DOM-microbial differentiation patterns were identified among ANPS subtypes. AQ was characterized by higher proportions of heteroatom-rich compounds (30.6%) and higher-molecular-weight compounds, LP by more aromatic and lignin-/tannin-associated molecular features (AI_mod = 0.261), and CF by CHOS-enriched (26.8%) but overall lower DOM chemodiversity. These molecular fingerprints co-occurred with differences in microbial diversity, community assembly (βNTI), and co-occurrence network topology, indicating relatively stable DOM-microbial templates shaped by long-term agricultural inputs. Seasonal variability further modified DOM composition and microbial differentiation, but responses differed among ANPS subtypes. Event-driven systems (AQ and LP) exhibited pronounced winter-summer shifts, whereas the background-dominated system (CF) showed weaker temporal variability but more persistent DOM-microbial coupling patterns. Low-to medium-molecular-weight (m/z 100-550) DOM fractions showed the strongest co-variation with nitrogen- and methane-related functional gene potentials, suggesting molecular-weight-dependent associations between DOM composition and microbial functional gene profiles. Overall, these findings suggest that ANPS pollution comprises source- and season-specific DOM-microbial templates that can be distinguished using molecular and functional indicators, providing a basis for source-oriented monitoring and targeted management of agriculturally impacted rural river systems.}, }
@article {pmid42214594, year = {2026}, author = {Zhang, Y and Zhang, L and Zhang, S and Yang, C and Wang, Z and Si, G and Peng, Y}, title = {Synergistic antibiotic-laden wastewater treatment doubles denitrification rate in a pilot mineral-based autotrophic biofilter by breaking microbial spatial-metabolic constraints.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124860}, doi = {10.1016/j.envres.2026.124860}, pmid = {42214594}, issn = {1096-0953}, mesh = {*Denitrification ; *Wastewater/chemistry/microbiology ; *Anti-Bacterial Agents ; Autotrophic Processes ; Sulfides ; *Waste Disposal, Fluid/methods ; Bacteria/metabolism ; *Water Pollutants, Chemical/metabolism ; Pilot Projects ; Iron ; Filtration ; *Bioreactors/microbiology ; }, abstract = {The practical application of pyrite-based autotrophic denitrification biofilters (PADB) is limited by their low nitrogen removal rate (NRR). This study demonstrates that in a pilot-scale PADB (750 L) treating NO3[-]-N wastewater, heterotrophic bacterial consortia (HBs) severely impair the denitrification activity of autotrophic denitrifying bacteria (ADB) through network encapsulation and metabolic shunting. However, after switching to treating composite wastewater containing antibiotics, the system achieved an antibiotic removal rate of 95.12%. And it's NRR from 32.37 to 63.15 mg N/(L·d), representing a 0.95-fold enhancement. Integrated co-occurrence network and metagenomic analyses revealed a three-stage cascade reaction underlying this improvement: (i) The antibiotic stress halted carbon-feeding from ADB and hydrolytic-acidifying bacteria to HBs (fermentation gene abundance decreased by 1.89-58.45%), depriving HBs of energetic and substrate support and resulting in their selective elimination (0.63-fold decrease in relative abundance). This relieved ADB's metabolic burden and shortened their physical distance to pyrite; (ii) Elevated electron and energy demand in ADB activated dormant genes for electron shuttle synthesis (menC/E: 0 to 342/402 TPM) and upregulated sulfur metabolism genes (∼3.9-fold), enhancing pyrite dissolution and electron harvesting; (iii) This augmented electron flow stimulated ADB's carbon fixation pathway (Calvin-Benson-Bassham cycle genes upregulated 14.89-fold) and amplified energy metabolism (1.33-1.55-fold enhancement in glycolysis and Tricarboxylic Acid cycle), supplying ample material and energy for ADB proliferation and denitrification. Consequently, ADB enrichment accelerated 509-fold, while the abundance of key denitrification genes (napA/B, nosZ) increased by 2.1-11.04-fold. These molecular and population-level changes doubled the system's NRR compared to its original level.}, }
@article {pmid42214595, year = {2026}, author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X}, title = {Nanoplastics reshape nitrogen cycling in submerged macrophyte systems: A metagenomic perspective.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124885}, doi = {10.1016/j.envres.2026.124885}, pmid = {42214595}, issn = {1096-0953}, mesh = {*Nitrogen Cycle/drug effects ; Metagenomics ; Rhizosphere ; *Water Pollutants, Chemical/toxicity ; Nitrogen/metabolism ; *Magnoliopsida/metabolism/drug effects ; Bacteria/metabolism/genetics ; Microbiota/drug effects ; }, abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.}, }
@article {pmid42214685, year = {2026}, author = {Jiang, TA and Prioult, G and Quann, E}, title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101621}, doi = {10.1016/j.tjnut.2026.101621}, pmid = {42214685}, issn = {1541-6100}, abstract = {Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health, but are constrained by poor bioavailability. Only 5%‒10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract; the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits, owing to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways. Production of these metabolites varies markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes-termed metabotypes-that strongly influence clinical and nutritional responsiveness. This review synthesizes recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and examines how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes. We further evaluate emerging evidence supporting synergistic synbiotics-targeted combinations of probiotics with specific polyphenol or bioactive precursors-as a strategy to standardize and enhance the generation of beneficial microbial metabolites. These synbiotic strategies demonstrate the capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging. Together, these findings position metabolite-guided synbiotics as a promising paradigm for precision nutrition. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate translation of microbiota-targeted interventions.}, }
@article {pmid42214867, year = {2026}, author = {Lu, J and Zhang, S and Guo, Y and Wu, H and Hu, Z and Kong, Q and Zhang, J}, title = {Magnetite-facilitated AHL-mediated quorum sensing enhances nitrate removal and mitigates nitrous oxide emissions in constructed wetlands under polycyclic aromatic hydrocarbons stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142523}, doi = {10.1016/j.jhazmat.2026.142523}, pmid = {42214867}, issn = {1873-3336}, mesh = {*Quorum Sensing/drug effects ; *Nitrates/metabolism ; *Wetlands ; *Polycyclic Aromatic Hydrocarbons/toxicity ; *Nitrous Oxide/metabolism/analysis ; *Acyl-Butyrolactones/metabolism ; *Water Pollutants, Chemical ; *Ferrosoferric Oxide/chemistry ; }, abstract = {The performance of constructed wetlands (CWs) in removing nitrate (NO3[-]-N) and mitigating nitrous oxide (N2O) emissions can be impaired by trace organic pollutants like polycyclic aromatic hydrocarbons (PAHs). Magnetite has been widely applied as a substrate to regulate nitrogen transformation in CWs; however, its potential role in mediating quorum sensing (QS) to alleviate PAH-induced inhibition remains unclear. In this study, conventional CWs (CW-A) and magnetite-amended CWs (CW-B) were established to evaluate NO3[-]-N removal and N2O emissions and the associated mechanisms under PAH-stress conditions. Results indicated that CW-B maintained a high NO3[-]-N removal efficiency (90.14%), whereas CW-A exhibited a marked decline from 65.06% to 47.32%. Magnetite amendment reduced N2O emissions by 68.97% compared with CW-A. Furthermore, the enhanced performance of CW‑B was closely linked to the strengthening of QS. CW-B sustained elevated levels of acyl-homoserine lactone (AHL) signaling molecules (e.g., C8-HSL) under PAH stress, while these signals were suppressed in CW-A. Metagenomic analysis revealed enrichment of key functional genera (e.g., Tessaracoccus and Pseudomonas) and genes associated with QS and nitrogen transformation (e.g., luxI, nirS, and nosZ) in CW-B, supporting enhanced NO3[-]-N removal and reduced N2O emissions. The reinforced QS further promoted interspecies electron transfer and enhanced microbial network robustness and resilience. Additionally, PAHs stimulated the DNRA process and enhanced the abundance of DNRA-related genes (i.e., nrfA and nrfH) in both CWs, leading to increased effluent total nitrogen. Overall, this study elucidates a magnetite-mediated QS mechanism that enhances nitrogen transformation and microbial metabolic stability in CWs under PAH stress.}, }
@article {pmid42215097, year = {2026}, author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L}, title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119428}, doi = {10.1016/j.foodres.2026.119428}, pmid = {42215097}, issn = {1873-7145}, mesh = {*Alcoholic Beverages/microbiology/analysis ; Bacteria/metabolism/classification ; China ; Fermentation ; *Flavoring Agents/metabolism ; *Food Microbiology ; Fungi/metabolism/classification/genetics ; Gas Chromatography-Mass Spectrometry ; Metabolomics/methods ; Metagenomics ; *Microbiota/physiology ; *Multiomics ; *Taste ; Temperature ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.}, }
@article {pmid42215200, year = {2026}, author = {Jones, RC and Visger, CJ and Lopez, CA}, title = {The microbiota of wild fermented cider from U.S. west coast apples.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105120}, doi = {10.1016/j.fm.2026.105120}, pmid = {42215200}, issn = {1095-9998}, mesh = {*Malus/microbiology ; Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Yeasts/isolation &amp; purification/classification/genetics/metabolism ; United States ; Food Microbiology ; Fruit/microbiology ; }, abstract = {Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.}, }
@article {pmid42215210, year = {2026}, author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L}, title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105130}, doi = {10.1016/j.fm.2026.105130}, pmid = {42215210}, issn = {1095-9998}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; }, abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.}, }
@article {pmid42215376, year = {2026}, author = {Kiguchi, Y and Suzuki, Y}, title = {Giants within: a new class of microbial mobile elements.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2026.05.004}, pmid = {42215376}, issn = {0168-9525}, abstract = {Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.}, }
@article {pmid42215825, year = {2026}, author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L}, title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42215825}, issn = {1618-1905}, support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; }, abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.}, }
@article {pmid42215894, year = {2026}, author = {Russell, T and Formiconi, E and Murphy, A and Hortion, J and McElroy, M and Casey, M and Cuartero, LG and Mee, JF and Jahns, H and Kelly, C and Byrne, J and Feeney, ER and Mallon, PW and Gautier, VW}, title = {One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05105-5}, pmid = {42215894}, issn = {1471-2180}, support = {101132970, EU4H-2022-DGA-MS-IBA3//European Commission/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for robust viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions.<br><br>RESULTS: The study evaluated two shotgun mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 18 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 88.9% of 18 DNA and RNA viruses previously detected by PCR were identified, including from samples with low nucleic acid concentrations (<&#x2009;1 ng/&#xb5;l) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available.<br><br>CONCLUSIONS: These results demonstrate the feasibility and robustness of the swab and tissue mNGS workflows for virus identification across a range of complex clinical specimens supporting their use in investigations of suspected viral diseases of unknown aetiology and is currently being evaluated for early detection of emerging viral threats at the animal-human interface.}, }
@article {pmid42216070, year = {2026}, author = {Liu, LM and Zhang, YL and Zhou, JT and Yu, QQ and Zhang, WY and Wang, WF and Pang, SD and Miao, H and Zhao, YY}, title = {Ureic clearance granule ameliorates chronic kidney disease by reshaping microbial dysbiosis via modulating bile acid metabolism.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42216070}, issn = {1749-8546}, support = {82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Shaanxi Key Science and Technology Plan Project/ ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a highly prevalent global public health problem that inevitably leads to renal failure. Although renin-angiotensin system blockers, as first-line therapy, can reduce proteinuria, they cannot prevent the progression to end-stage renal disease. Therefore, the development of new treatment strategies is urgently required. The uremic clearance granule (UCG) was widely used in patients with CKD. However, the underlying molecular mechanisms of UCG for CKD treatment remain unclear.<br><br>METHODS: Fecal gut microbiota and serum metabolites were analyzed using metagenomics and metabolomics, respectively. The expression of extracellular matrix components, Takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), and nuclear factor kappa B (NF-&#x3ba;B) p65 was examined by in adenine-induced CKD rats.<br><br>RESULTS: UCG improved renal function and alleviated kidney fibrosis in adenine-induced CKD rats. Mechanistically, significantly altered gut bacteria, including Helicobacter hepaticus, Gemella hemolysans, Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, Alistipes finegoldii, and Eubacterium limosum, showed strong linear correlations with serum creatinine levels in CKD rats. UCG treatment improved aberrant changes in these gut bacteria, indicating that UCG can reshape gut microbiota dysbiosis. Microbial-derived metabolites act as a bridge between gut microbiota and host. Further analysis showed that serum bile acids, including ursodeoxycholic acid (UDCA), taurodeoxycholic acid, and hyodeoxycholic acid (HDCA), were strongly correlated with serum creatinine levels in CKD rats, and these aberrant metabolites were reversed by UCG treatment. Notably, both UDCA and HDCA showed strong linear correlations with Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, and Eubacterium limosum, suggesting that UCG regulates microbial-derived metabolites. Moreover, UCG treatment upregulated protein expression of TGR5, GLP-1R, and downregulated NF-&#x3ba;B p65 protein expression in the kidney tissues of CKD rats, indicating that renoprotective effects of UCG are associated with modulation of microbial dysbiosis, regulation of bile acid metabolism and improvement of TGR5, GLP-1R, and NF-&#x3ba;B signaling.<br><br>CONCLUSIONS: This study is the first to demonstrate that UCG ameliorates CKD and renal fibrosis by reshaping microbial dysbiosis and microbial-derived bile acid metabolism. Altered gut microbiota and metabolites may serve as biomarkers to evaluate efficacy of UCG. UCG may exert its renoprotective effects by enhancing TGR5, GLP-1R, and NF-&#x3ba;B p65 expression through regulating microbial dysbiosis-mediated bile acid metabolism.}, }
@article {pmid42216221, year = {2026}, author = {Zhang, K and Duan, C and Chen, J and He, Q and Jin, Y and Liu, J and Lin, R and Han, C}, title = {Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00839-z}, pmid = {42216221}, issn = {1757-4749}, support = {2024M761069//Postdoctoral Research Foundation of China/ ; 82470679//National Natural Science Foundation of China/ ; 2023YFC2307001//National Natural Science Foundation of China/ ; 82170570//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.<br><br>METHODS: Based on the established Apc[Min/+] mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.<br><br>RESULTS: The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-&#x3ba;B pathway.<br><br>CONCLUSIONS: Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.}, }
@article {pmid42216275, year = {2026}, author = {Wong, ELY and Otte, J and Schmitt, I}, title = {Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.}, journal = {Genome biology and evolution}, volume = {18}, number = {6}, pages = {}, pmid = {42216275}, issn = {1759-6653}, support = {//Centre for Translational Biodiversity Genomics/ ; LOEWE/1/10/519/03/03.001(0014)/52//Hessian Ministry of Science and Research, Arts and Culture/ ; }, mesh = {*Phylogeny ; *Genome, Mitochondrial ; *Lichens/genetics ; Symbiosis ; *Genome, Chloroplast ; *Chlorophyta/genetics/classification ; *Evolution, Molecular ; Climate ; }, abstract = {The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) Trebouxia jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20) and T. barrenoae (S28); a newly designated OTU T. sp. (A57), and several Single-Occurrence Sequences (SOS) from clades A, I, and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial (32 genes) genes are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine, and valine content) mirror findings in mycobiont nuclear genomes from the same samples and highlight shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6, and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia and provides valuable resources for future ecological and evolutionary research.}, }
@article {pmid42216291, year = {2026}, author = {Zwartjes, MSZ and de Jonge, PA and van de Laar, AW and Bruin, SC and Meijnikman, AS and Groen, AK and Gerdes, VEA and Nieuwdorp, M}, title = {Adipose Tissue Inflammation, Oxidative Stress, and Altered Adipogenesis Are Associated With Dyslipidemia in Obesity: A Multiomics Profiling Study.}, journal = {Journal of the American Heart Association}, volume = {15}, number = {11}, pages = {e047397}, doi = {10.1161/JAHA.125.047397}, pmid = {42216291}, issn = {2047-9980}, mesh = {Humans ; *Oxidative Stress ; *Dyslipidemias/metabolism/genetics/etiology ; Male ; Female ; *Adipogenesis/genetics ; Multiomics ; Cross-Sectional Studies ; Middle Aged ; *Adipose Tissue/metabolism ; Adult ; Adipokines/blood ; *Obesity, Morbid/surgery/complications/metabolism ; Metabolomics ; *Inflammation/metabolism ; Bariatric Surgery ; Longitudinal Studies ; Gene Expression Profiling ; Obesity ; }, abstract = {BACKGROUND: Obesity is an important risk factor for cardiometabolic disease, including dyslipidemia and atherosclerotic cardiovascular disease. Although the role of the liver in dyslipidemia is established, the contribution of adipose tissue is less clear. This study aims to clarify the role of adipose tissue in lipid metabolism and dyslipidemia.<br><br>METHODS: We conducted a cross-sectional analysis of 125 patients from the BARIA (The Immune System and Microbial Tone in Relation to NAFLD/NASH Before and After Bariatric Surgery in the Morbidly Obese in Amsterdam) longitudinal cohort study undergoing bariatric surgery. Comprehensive phenotyping included fasting untargeted plasma metabolomics, lipid, lipoprotein, adipokine profiling, RNA sequencing, and fecal shotgun metagenomics. Tissue transcriptomic and plasma metabolites were compared between individuals with and without dyslipidemia.<br><br>RESULTS: Dyslipidemia was present in 43 of 125 individuals (34.4%), with higher triglycerides (1.62 versus 1.24&#x2009;mmol/L), apoB (apolipoprotein B; 93.15 versus 81.81&#x2009;mg/dL), and lower high-density lipoprotein (1.02 versus 1.35&#x2009;mmol/L) and apoAI (136.40 versus 161.35&#x2009;mg/dL). Plasma adipokines showed limited differences: leptin concentrations were lower in dyslipidemia in unadjusted analysis but reduced after adjustment for age, sex, and body weight (adjusted P=0.057). RNA sequencing identified altered gene expression of liver, jejunum, visceral and subcutaneous adipose tissue, most pronounced in subcutaneous adipose tissue. Dyslipidemia was associated with adipose tissue pathways related to inflammation, oxidative stress, and adipogenesis. Plasma metabolomics revealed associations with endocannabinoid-like, secondary bile acid, plasmalogen, butyrate, and sphingolipid metabolites. Gut metagenome analysis found modest differences.<br><br>CONCLUSIONS: Dyslipidemia in obesity is associated with transcriptomic alterations in adipose tissue, including subcutaneous adipose tissue, involving inflammation, oxidative stress, and adipogenesis. These findings support a role of adipose tissue in lipid regulation beyond hepatic pathways.}, }
@article {pmid42217053, year = {2026}, author = {Ortiz-Gasca, A and Aguirre-Noyola, JL and Ruiz-Rivas, M and de Los Santos-Villalobos, S and Trejo-Aguilar, D and Gómez-Godínez, LJ}, title = {Molecular markers for the study of arbuscular mycorrhizal fungi.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42217053}, issn = {1432-072X}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; Genetic Markers ; DNA, Fungal/genetics ; Metagenomics/methods ; DNA, Ribosomal/genetics ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are central components of terrestrial ecosystems and agroecosystems. However, their accurate identification remains methodologically challenging due to their complex biology and the limitations of traditional morphological approaches. Over the past three decades, molecular tools have profoundly reshaped AMF research, shifting from spore-based identification and Sanger sequencing of ribosomal markers toward high-throughput amplicon sequencing and, more recently, metagenomic frameworks that enable community-level and functional analyses. This review critically examines the conceptual and technical evolution of AMF identification strategies, comparing morphological characterization, ribosomal DNA markers (SSU, ITS, LSU), multilocus approaches, metabarcoding, and whole-genome metagenomics. We analyze their taxonomic coverage, resolution, and methodological biases, including primer specificity, intragenomic rDNA variation, database limitations, and bioinformatic pipeline effects. Attention is given to how marker selection influences ecological interpretation, cross-study comparability, and functional inference. Finally, we propose practical guidelines for aligning marker choice with study objectives and outline validation strategies-such as mock communities, curated reference databases, and multi-marker integration-to improve reproducibility and taxonomic robustness. By integrating historical perspective, methodological evaluation, and applied recommendations, this review provides a decision-oriented framework to support more accurate and comparable assessments of Glomeromycota diversity.}, }
@article {pmid42217383, year = {2026}, author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W}, title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.}, journal = {Water research}, volume = {303}, number = {}, pages = {126182}, doi = {10.1016/j.watres.2026.126182}, pmid = {42217383}, issn = {1879-2448}, abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.}, }
@article {pmid42217591, year = {2026}, author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H}, title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.}, journal = {Pharmacological research}, volume = {229}, number = {}, pages = {108273}, doi = {10.1016/j.phrs.2026.108273}, pmid = {42217591}, issn = {1096-1186}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy ; Animals ; Metabolomics ; Precision Medicine ; }, abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.}, }
@article {pmid42217781, year = {2026}, author = {Kim, S and Kang, MG and Oh, S and Jang, KB and Kim, Y}, title = {Genome-based characterization of flavor development via metabolic interactions between Lentilactobacillus kefiri and Kluyveromyces marxianus during milk kefir fermentation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28435}, pmid = {42217781}, issn = {1525-3198}, abstract = {Kefir, a fermented milk product comprising complex consortia of bacteria and yeasts, develops its characteristic flavor through coordinated microbial interactions. In this study, we investigated flavor compound biosynthesis and development by kefir-derived lactic acid bacteria and yeast during kefir fermentation, integrating genome-based predictions with metabolite validation. Metagenomic analysis identified Lactobacillus and Kluyveromyces as predominant genera in both kefir grains and fermented milk kefir. Lentilactobacillus kefiri SLAM023B and Kluyveromyces marxianus SLAM005Y were isolated and subjected to hybrid genome sequencing on Illumina and Nanopore platforms. Functional annotation via KEGG pathway mapping revealed featured pathways including amino acid and fatty acid metabolism, as well as interconversion of alcohol, aldehyde, and acid, contributing to the formation and generation of flavor compounds. Notably, K. marxianus SLAM005Y produced fruity fusel alcohols, whereas L. kefiri SLAM023B contributed fatty acid-derived precursors. The coculture of the 2 strains significantly enhanced ester synthesis, particularly ethyl acetate and isoamyl acetate, imparting fruity and creamy sensory notes to the fermentation profile. In addition, increases in ethyl octanoate and C6/C8 fatty acids introduced fruity and cheese-like characteristics, while levels of grassy aldehydes were reduced. Correlation analysis supported the complementary metabolic roles and potential cross-feeding mechanisms between the strains, which help explain the development of kefir flavor. Taken together, this study provides a genomic and functional framework to examine cooperative metabolism in kefir and identifies molecular targets for improving the sensory properties of fermented dairy products.}, }
@article {pmid42217859, year = {2026}, author = {Qin, W and Zhang, H and Wang, H and Zhou, J and Wang, F}, title = {Pharmaceutical-driven disinfection by-products formation and antibiotic resistance gene enrichment under intensified chlorination during pandemic.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {1-10}, doi = {10.1016/j.jes.2025.06.056}, pmid = {42217859}, issn = {1001-0742}, mesh = {Halogenation ; *Disinfection/methods ; *Drug Resistance, Microbial/genetics ; Pandemics ; *Disinfectants ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; *Chlorine ; Anti-Bacterial Agents ; Wastewater/chemistry ; }, abstract = {Intensified chlorine disinfection during pandemic is widely implemented in hospital and municipal wastewaters to inactivate pathogens. However, high concentrations of residual chlorine in treated wastewaters might bring secondary environmental risks. This study investigated the impacts of intensified chlorine disinfection on disinfection by-product (DBP) formation from six commonly used pandemic-related drugs and antibiotic resistance gene (ARG) enrichment in sewage. Results showed that high chlorine dosage of 2000 µmol/L led to DBP yields and estimated toxicity that were 1-2 orders of magnitude higher than those under normal chlorine dosage of 40-100 µmol/L. Intensified chlorine disinfection and drug overuse during the pandemic evidently increased the contribution of drugs as precursors to DBPs formation (29.2 %-78.8 %) in sewage. Two antibiotics emerged as major dichloroacetonitrile precursors, two bromine expectorants dominated haloacetic acids and Br-DBP formation, while two ICMs were critical precursors of iodinated acetamides. These DBPs were the main contributors to the estimated toxicity of the chlorinated drugs. Bromine expectorants produced DBPs with yields and estimated toxicity 1-2 orders of magnitude greater than other drugs. Metagenomic sequencing results showed that low chlorine up-regulated ARGs and related mobile genetic elements, driving ARGs enrichment and horizontal transfer. High chlorine in short term inhibited the total ARGs, but enriched the multidrug resistance gene subtypes related to the efflux/mutation pathway and transfer, thereby selected highly chlorine-resistant bacteria with strong antibiotic resistance. These findings reveal the environmental risks of intensified chlorine disinfection and suggest that optimizing chlorine dosage is crucial to mitigate these environmental risks and protect public health.}, }
@article {pmid42217876, year = {2026}, author = {Xiao, Y and Ouyang, Q and Wen, X and Tong, H}, title = {Coupling mechanisms between microbial arsenic metabolism and carbon cycling in arsenic-contaminated groundwater.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {269-276}, doi = {10.1016/j.jes.2025.10.032}, pmid = {42217876}, issn = {1001-0742}, mesh = {*Arsenic/metabolism/analysis ; *Groundwater/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; *Carbon Cycle ; China ; Bacteria/metabolism ; *Water Microbiology ; Carbon/metabolism ; }, abstract = {Microorganisms in groundwater play a critical role in global carbon (C) cycling. However, how arsenic (As) contamination influences microbially mediated As cycling and its coupling with C metabolism remains poorly understood. Herein, we investigated the associative coupling of microbial function genes between As and C cycling in groundwater from a typical As-contaminated industrial site in southern China. Metagenomic analyses revealed that As concentrations governed microbial community assembly, leading to distinct community structures and dominant taxa. Key microbial groups, including Pseudomonadota and Euryarchaeota, exhibited dual metabolic capabilities for both As and C transformation. Compared to the Safe group (As < 10 μg/L), the Toxic group (As > 10 μg/L) displayed greater dissimilarities in the distribution of As- and C-related functional genes. A strong correlation between As- and C-cycling genes suggests a potential trade-off mechanism between microbial As resistance and organic C utilization. Furthermore, microbial function gene-based co-occurrence networks demonstrated more complex and stable network structures in the Toxic group. The enhanced coupling between As-C functional genes likely increased microbial community resilience against environmental stressors. While observed As-C coupling mechanisms may extrapolate to chemically analogous groundwater systems, their quantitative contribution to global C budgets requires validation across diverse biogeographic contexts. This study offers novel insights into the complex coupling network between As and C metabolic pathways in groundwater microbial communities and underscores their broader implications for global biogeochemical C cycling.}, }
@article {pmid42217938, year = {2026}, author = {Dwivedi, S and Agnihotri, R and Kumar, V and Mishra, S and Tiwari, RK and Adhikari, D and Sharma, P and Kumar, S and Verma, T and Gupta, A and Sinam, G and Pandey, V}, title = {Scientific evidence validating spiritual beliefs for controlling pathogenic microbes in the Ganga river.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {93-106}, doi = {10.1016/j.jes.2026.01.083}, pmid = {42217938}, issn = {1001-0742}, mesh = {*Rivers/microbiology ; Archaea ; Bacteria ; *Water Microbiology ; Microbiota ; Bacteriophages ; Biodiversity ; }, abstract = {During the Kumbh, the Ganga at the Sangam in Prayagraj, where it meets the Yamuna, showed greater microbial diversity than either river before their confluence. Mass bathing altered the density and diversity of archaea, bacteria, phages and viruses, while fungi, protozoans, cyanobacteria, green algae and diatoms remained largely unaffected. Notably, this study was the first to report archaeal phages, cyanophages and mycophages in the river system. Archaea species richness was higher in the Yamuna (127 spp. during Pre Kumbh), whereas bacterial diversity was greater in the Ganga (2764 spp.). The Ganga exhibited a higher relative abundance of skin, oral and gut archaea and bacteria, except for gut bacteria, which were more prevalent in the Yamuna. Skin and gut archaea showed strong positive correlations with the number of devotees (r = 0.818 and r = 0.870, respectively), while oral archaea were less affected. Pathogenic microbes with high fatality rates were more common in the Yamuna. Variations in archaeal, bacterial, phage and viral communities were influenced by physico-chemical parameters, ion levels, nutrient content and devotee's load. The Ganga exhibited higher phage diversity and a greater phage-to-bacteria ratio than the Yamuna. Hence, phages regulate the pathogenic bacteria through predator-prey dynamics, consequently reducing infection risks. Despite mass bathing by over 100 million devotees, which sharply increased nutrient and pollution levels, no endemic or epidemic outbreaks were reported.}, }
@article {pmid42218119, year = {2026}, author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL}, title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73465-7}, pmid = {42218119}, issn = {2041-1723}, support = {R21CA290426//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.}, }
@article {pmid42218218, year = {2026}, author = {Zhu, G and Yang, G}, title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01030-7}, pmid = {42218218}, issn = {2055-5008}, support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; }, abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.}, }
@article {pmid42218514, year = {2026}, author = {Fabre, V and Robinson, ML and Martino, F and Monge, R and Forastiero, A and Corso, A and Pasteran, F and Karyakarte, R and Randive, B and Singh, S and Naik, M and Prasad, HB and Schwab, KJ and Simner, PJ and Berman, Y and Foy, WI and Salinas, AB and Gupta, A and Lu, J and Vasquez, AM and Noble-Wang, J and Moser, KA and Perry-Dow, KA and Patrick, M and Rock, C}, title = {Environmental reservoirs of carbapenem-resistant organisms in the intensive care unit: a multicenter longitudinal study in two middle-income country hospitals.}, journal = {Antimicrobial resistance and infection control}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13756-026-01768-x}, pmid = {42218514}, issn = {2047-2994}, support = {75D30121D12750/CC/CDC HHS/United States ; }, abstract = {BACKGROUND: There is limited data regarding environmental reservoirs of carbapenem-resistant organisms (CRO) during non-outbreak settings in resource-limited hospitals, or the role of these reservoirs in healthcare transmission.<br><br>METHODS: Prospective longitudinal study in which sinks and high-touch surfaces (HTS) were sampled prior to room cleaning in intensive care units (ICUs) in two hospitals (hospital A, Argentina, and hospital B, India), July 2023-February 2024. Selective media was used to recover CROs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) pairwise analysis were performed on environmental and clinical isolates to evaluate bacterial transmission dynamics. Metagenomic sequencing was performed to evaluate bacterial diversity of environmental samples.<br><br>RESULTS: Of 541 environmental samples collected, 47.9% in hospital A and 97.5% in hospital B grew at least one CRO. Most CROs tested for the presence of a carbapenemase were positive (63.9-91.0% for hospital A and B isolates, respectively). Carbapenemase producer (CP)-Acinetobacter baumannii and CP-Pseudomonas spp. predominated in HTS and sinks samples, respectively, in hospital A; while CP-Klebsiella pneumoniae predominated in hospital B samples. WGS of 113 CRO isolates and SNP analysis demonstrated certain lineages established enduring reservoirs in the ICUs environment (e.g., blaVIM-36 P. aeruginosa ST395 isolates with 2-9 SNP difference were detected in sinks over 7&#xa0;months). Several clusters involving environmental and clinical isolates that shared an epidemiological link and displayed&#x2009;&#x2264;&#x2009;10 SNP difference were identified (e.g., blaOXA-23 A. baumannii ST195 isolated from three unique patients who stayed in the same private room on sampling months 4, 5, 6 and 7, and from HTS of that room on sampling month 5 displayed 0-3 SNP difference). Metagenomic analysis identified additional AMR genes of clinical importance.<br><br>CONCLUSIONS: CROs were abundant and persisted in the ICU environment in countries with high prevalence of MDROs. Our data suggests movement of clones between the environment and patients.}, }
@article {pmid42218533, year = {2026}, author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY}, title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01680-4}, pmid = {42218533}, issn = {1756-994X}, support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; }, abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.<br><br>METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n&#x2009;=&#x2009;60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n&#x2009;=&#x2009;20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.<br><br>RESULTS: Durable disease control (PFS&#x2009;&#x2265;&#x2009;24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.<br><br>CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).}, }
@article {pmid42218921, year = {2026}, author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X}, title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.}, journal = {Molecular phylogenetics and evolution}, volume = {223}, number = {}, pages = {108650}, doi = {10.1016/j.ympev.2026.108650}, pmid = {42218921}, issn = {1095-9513}, abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.<br><br>METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.<br><br>PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.<br><br>CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.}, }
@article {pmid42219044, year = {2026}, author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A}, title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.}, journal = {Journal of microbiological methods}, volume = {246}, number = {}, pages = {107565}, doi = {10.1016/j.mimet.2026.107565}, pmid = {42219044}, issn = {1872-8359}, mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Pasteurellaceae/genetics/isolation &amp; purification/classification ; Chickens/microbiology ; DNA Primers/genetics ; Cecum/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Poultry Diseases/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Pasteurellaceae Infections/veterinary/microbiology/diagnosis ; }, abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.}, }
@article {pmid42219122, year = {2026}, author = {Wang, X and Huang, Y and Xu, J and Lin, B and Chen, X and Li, ZH}, title = {Exogenous floc-granule replacement regulates particle-size distribution and signaling-associated ecological responses in aerobic granular sludge.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135039}, doi = {10.1016/j.biortech.2026.135039}, pmid = {42219122}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Particle Size ; Bioreactors/microbiology ; Extracellular Polymeric Substance Matrix/metabolism ; Aerobiosis ; Flocculation ; *Signal Transduction ; Bacteria/metabolism/genetics ; Acyl-Butyrolactones/metabolism ; Biological Oxygen Demand Analysis ; }, abstract = {Aerobic granular sludge (AGS) operation remains constrained by excessive granule enlargement, particle-size redistribution, and structural instability. In this study, exogenous floc-granule replacement was evaluated as a chemical-free, in situ particle-size management strategy for AGS. A conventional granulation reactor (R1) and an exogenous floc-granule replacement reactor (R2) were operated in parallel to compare granulation dynamics, reactor performance, extracellular polymeric substances (EPS), extracellular acyl-homoserine lactones (AHLs), respiration, bacterial partitioning, metagenomic functional gene profiles, and microbial co-occurrence patterns. During the first replacement window, R2 maintained smaller and more uniform granules than R1, with mean particle size of 220 μm on Day 83 compared with 378 μm in R1. R2 also maintained comparable chemical oxygen demand and NH4[+]-N removal performance and showed lower nitrite accumulation during rapid granulation. Particle-size regulation was accompanied by lower extracellular AHL accumulation, altered EPS composition, and distinct respiratory allocation, reflecting higher autotrophic-to-heterotrophic respiration ratio in R2 than in R1 on Day 82 (0.10 vs. 0.07). Comparative characterization indicated that exogenous flocs represented a distinct biomass fraction with smaller particle size, lower protein-to-polysaccharide ratio, and lower extracellular AHL accumulation than endogenous flocs and mature granules. Metagenomic and co-occurrence network analyses showed higher abundance of quorum quenching (QQ)-related genes and greater representation of QQ- or combined quorum sensing /QQ-associated taxa in R2. Overall, exogenous floc-granule replacement represents a tunable structure-based strategy for regulating AGS particle-size distribution, but its effectiveness should be further evaluated according to application scenario.}, }
@article {pmid42219517, year = {2026}, author = {Velando, F and Molina, L and Hurtado, I and van Dillewijn, P and Segura, A}, title = {Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00914-7}, pmid = {42219517}, issn = {2524-6372}, abstract = {BACKGROUND: In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).<br><br>RESULTS: Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.<br><br>CONCLUSIONS: Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.}, }
@article {pmid42219665, year = {2026}, author = {Recio, MI and de la Torre, J and Rocha-Martin, J and de la Mata, I and Ramos, JL}, title = {A Biotechnological Approach to Enzyme-Based Fertilisers: Immobilisation of Acid Phosphatases.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70385}, pmid = {42219665}, issn = {1751-7915}, support = {PID2021-123469OB-IOO//Agencia Estatal de Investigaci&#xf3;n/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; PREDOC_01447//Consejer&#xed;a de Conocimiento, Investigaci&#xf3;n y Universidad, Junta de Andaluc&#xed;a/ ; }, mesh = {*Acid Phosphatase/metabolism/chemistry ; *Enzymes, Immobilized/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Clay ; *Fertilizers/analysis ; Aluminum Silicates/chemistry ; *Biotechnology/methods ; Temperature ; Soil/chemistry ; }, abstract = {We explore enzyme-based technologies as sustainable alternatives to conventional chemical fertilisers, addressing the challenges associated with using enzymes in free or immobilised form for agricultural applications. We use the metagenome-derived Class A acid phosphatase M2-32, selected for its high activity, broad pH tolerance and thermophilic properties, and evaluated its immobilisation on clay minerals to enhance stability and applicability in soils. Several clays were tested as immobilisation supports. Bentonite caused complete enzyme inactivation, while kaolin formed aggregates and was unsuitable. In contrast, palygorskite, sepiolite and agrozeolite adsorbed more than 99% of the added enzyme. However, only a fraction of the immobilised enzyme retained catalytic activity, with optimal performance observed at moderate protein loading (40-80 μg protein). Among the tested supports, palygorskite consistently provided the highest specific activity (22,000 ± 2200 U/mg), followed by sepiolite (11,000 ± 730 U/mg), whereas agrozeolite (2250 ± 40 U/mg) showed comparatively low activity. ATR-FTIR spectroscopy confirmed successful enzyme immobilisation without significant alteration of the clay structures. Immobilised M2-32 preserved a broad pH range (between 4 and 8.5) and thermophilic behaviour similar to the free enzyme, remaining active up to 50°C. Immobilisation increased substrate affinity while reducing Vmax relative to the free enzyme. To assess environmental compatibility, the effects of free and palygorskite-immobilised M2-32 on soil microbial communities were evaluated using corn rhizosphere microcosms with different organic matter contents. Metabarcoding high-throughput sequencing revealed that microbial diversity and community structure were primarily shaped by soil type, plant presence and incubation time. Enzyme application, whether free or immobilised, did not significantly alter microbial diversity or composition. Overall, these results support palygorskite-immobilised M2-32 as a promising, environmentally compatible candidate for enzyme-based fertiliser development.}, }
@article {pmid42219690, year = {2026}, author = {Zhu, P and Yuan, X and Wang, X and Shi, Y}, title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70343}, doi = {10.1111/1462-2920.70343}, pmid = {42219690}, issn = {1462-2920}, support = {SDAIT0107//Shandong Modern Agricultural Technology &amp; Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; }, mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention &amp; control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; }, abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.}, }
@article {pmid42219901, year = {2026}, author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B}, title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {6}, pages = {}, doi = {10.1093/jac/dkag190}, pmid = {42219901}, issn = {1460-2091}, support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ionophores/pharmacology/administration &amp; dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; }, abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.<br><br>OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.<br><br>METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.<br><br>RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.<br><br>CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.}, }
@article {pmid42221085, year = {2026}, author = {Liu, F and Yang, K and Wu, M and Li, P and Luo, L}, title = {Case Report: Basal ganglia brain abscess caused by Nocardia farcinica.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1798434}, pmid = {42221085}, issn = {2296-858X}, abstract = {We report a rare case of Nocardia farcinica brain abscess in the basal ganglia, detailing its diagnosis, management, and rehabilitation. Diagnosing brain abscess based solely on clinical and imaging findings remains extremely challenging. Fortunately, metagenomic next-generation sequencing (mNGS) proved valuable in this case by rapidly identifying the pathogen, thereby facilitating targeted antibiotic therapy. This case highlights the importance of differentiating brain abscess from ischemic stroke and intracranial tumors. After completing a full course of anti-infective therapy and comprehensive rehabilitation, the patient achieved significant recovery in activities of daily living (ADL).}, }
@article {pmid42221483, year = {2026}, author = {Yang, H and Liu, S and Chen, X and Yin, C and Xiao, L and Xu, W and Lv, S and Xie, L and Yin, C}, title = {Gut microbiota-associated immunomodulation contributes to the protective effects of fluvastatin against endometriosis in a mouse model, accompanied by increased Akkermansia muciniphila abundance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1762444}, pmid = {42221483}, issn = {1664-302X}, abstract = {BACKGROUND: Endometriosis (EMs) is a chronic inflammatory disease characterized by tumor-like growth behavior and limited therapeutic options. Increasing evidence suggests that gut microbiota may contribute to EMs progression by promoting chronic inflammation and immune dysregulation. Fluvastatin, a lipid-lowering agent, exhibits anti-inflammatory, anti-tumor, and immunomodulatory effects and has also been reported to influence microbial homeostasis. However, the relationship among fluvastatin treatment, gut microbiota, and EMs progression remains unclear. This study aimed to investigate this relationship.<br><br>MATERIALS AND METHODS: A mouse model of EMs was established by autologous uterine tissue transplantation, followed by oral fluvastatin administration for 3 weeks. Lesion growth, inflammatory responses, and immune characteristics were evaluated by histology, quantitative PCR, flow cytometry, immunofluorescence, and immunohistochemistry. Gut microbiota involvement was assessed using antibiotic-mediated microbiota depletion and fecal microbiota transplantation (FMT). Microbial composition was analyzed by metagenomic sequencing. The role of Akkermansia muciniphila was evaluated by direct oral supplementation.<br><br>RESULTS: Fluvastatin significantly reduced the volume and mass of ectopic lesions and decreased the mRNA expression of pro-inflammatory cytokines. It was also associated with changes in macrophage polarization-related markers and reduced abnormal activation of splenic immune cells. Antibiotic-induced gut microbiota depletion attenuated the protective effects associated with fluvastatin treatment, whereas FMT from fluvastatin-treated mice partially transferred similar protective changes. Metagenomic analysis revealed that fluvastatin reshaped gut microbiota composition and increased the abundance of Akkermansia muciniphila. Moreover, oral supplementation with Akkermansia muciniphila attenuated EMs progression and was associated with anti-inflammatory and immune-related changes similar to those observed after fluvastatin treatment.<br><br>CONCLUSION: These findings suggest that the protective effects associated with fluvastatin treatment are accompanied by changes in gut microbiota composition, including increased abundance of Akkermansia muciniphila. Gut microbiota may contribute to the beneficial effects of fluvastatin in EMs. These results support the potential value of microbiota-informed therapeutic strategies for EMs.}, }
@article {pmid42221497, year = {2026}, author = {Taussig, R and Peralta, R and Bustamante, JP}, title = {A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833002}, pmid = {42221497}, issn = {1664-302X}, abstract = {INTRODUCTION: Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.<br><br>METHODS: This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.<br><br>RESULTS: The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.<br><br>DISCUSSION: Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.}, }
@article {pmid42221499, year = {2026}, author = {Chang, N and Li, N and Li, W and Xue, J and Zheng, Y and Zhao, C and Zhang, S and Zhang, Y and Yin, G and Bao, M and Shen, W}, title = {Control efficacy and groundwater risk of antibiotic resistance genes in semi-arid landfill leachate treatment: seasonal insights and engineering implications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807935}, pmid = {42221499}, issn = {1664-302X}, abstract = {Landfill leachate is a critical reservoir of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), posing prominent risks to groundwater, especially in semi-arid regions. This study focused on the performance of landfill leachate treatment system in Hohhot (Inner Mongolia, semi-arid region), investigating the seasonal variation across three seasons (spring, summer, and autumn), migration characteristics, and control effect of ARGs/MGEs through process optimization-oriented monitoring. Metagenomic sequencing was employed to analyze four key matrices (raw leachate, ultrafiltration effluent, treated leachate, and adjacent groundwater) across three seasons. The treatment system achieved efficient removal of conventional pollutants but failed to eliminate ARGs, MGEs, and antibiotic-resistant bacteria. Instead, it enriched high-risk hosts (e.g., Pseudomonas_E) and transposases (e.g., tnpA), exacerbating horizontal gene transfer potential. ARGs abundance showed pronounced peaks in summer and autumn among the sampled seasons. Notably, the resistome profile of treated leachate was highly similar to that of groundwater, indicating incomplete ARG containment and hydrological connectivity between the treatment system and groundwater. A dual-track health-environmental risk framework was applied to the detected ARG subtypes, revealing that overall risk burden was concentrated in a small set of high-priority determinants. The top contributors were dominated by mobility- and co-selection-linked markers (intI1, tnpA, IS6100, IS26, and qacE△1) together with clinically relevant resistance genes (sul1, aacA, and aadA), underscoring the coupling between resistance functions and genetic mobility in the leachate-groundwater continuum. Collectively, these findings indicate that semi-arid landfill systems can act as both sinks and sources of high-risk resistance determinants, and they highlight the need to integrate ARGs/MGEs-targeted treatment upgrades, seasonally adaptive operational strategies, and risk-based dual-track monitoring into leachate management. This study therefore provides actionable engineering insights for optimizing leachate treatment performance and mitigating cross-media contamination in water-scarce environments.}, }
@article {pmid42221583, year = {2026}, author = {David Hanna, LB and Steinig, E and Bond, K and Lim, CK and Ramachandran, PS}, title = {Enrichment techniques for clinical metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1723747}, pmid = {42221583}, issn = {2235-2988}, mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; CRISPR-Cas Systems ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses a significant challenge, often overshadowing low-abundance pathogen sequences and increasing the cost of mNGS due to the high sequencing depth required. Enrichment techniques which selectively amplify pathogen-specific sequences can help to overcome this challenge, improving the sensitivity, specificity, and overall efficiency of mNGS - albeit while compromising the hypothesis-free nature and breadth of shotgun mNGS. As such, they can augment the use of mNGS in clinical scenarios where a more targeted approach is needed. This review provides a comprehensive analysis of the main enrichment techniques currently employed in the field, including PCR-based enrichment, CRISPR-Cas9 enrichment, molecular inversion probes (MIP), nanopore adaptive sequencing (AS), and hybridisation capture-based methods. We evaluate each method on a range of metrics including methodology, cost, sensitivity, specificity, and ease of integration into clinical workflows, as well as describing their application to date for purposes including pathogen detection, antimicrobial resistance profiling, and whole-genome sequencing across diverse clinical sample types. Current limitations and future directions for refinement and implementation of these techniques are also discussed. By summarising the current landscape and latest advancements in mNGS enrichment strategies, this review aims to guide the optimisation of mNGS workflows in clinical diagnostics and highlight key areas for future research.}, }
@article {pmid42221911, year = {2026}, author = {Gazulla, CR and Ferrera, I and Balagué, V and Marín-Vindas, C and González-Vega, A and Escánez-Pérez, J and Fraile-Nuez, E and Arrieta, JM and Gasol, JM and Sánchez, O}, title = {Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag076}, pmid = {42221911}, issn = {2730-6151}, abstract = {The surface ocean exhibits strong vertical gradients in light irradiance, nutrients, and temperature, shaping the phytoplankton distribution, which often defines a deep chlorophyll maximum (DCM). Aerobic anoxygenic phototrophic (AAP) bacteria inhabit the euphotic zone, with their abundances generally following the chlorophyll a variability. While AAP bacterial communities are known to differ across regions with contrasting environmental conditions, their vertical distribution remains poorly understood. We hypothesized that the diversity and community structure of AAP bacteria vary across the vertical gradient, in relation to changes in environmental variables and following the DCM profile. To test this hypothesis, we studied the composition of AAP communities at different depths along the DCM structure in the South and Central Atlantic Ocean, by means of amplicon sequencing of the pufM gene. The results show significant differences in richness, community structure, and taxonomic composition of samples from different layers of the DCM, highlighting the dependence of AAP bacteria on its structure. Remarkably, the use of primers with broad phylogenetic coverage enabled the recovery of several AAP phylogroups previously detected only through metagenomics. We show that they represent a significant fraction of marine AAP communities, provide clues about their ecological preferences, and confirm their association with the family Candidatus Luxescamonaceae.}, }
@article {pmid42222018, year = {2026}, author = {Ye, J and Ye, L and Sun, W and Xie, S and Lai, Z}, title = {A case of infective endocarditis caused by Streptococcus gordonii complicated with bacterial meningitis and cerebral infarction -- Application of metagenomic next-generation sequencing (mNGS).}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02608}, pmid = {42222018}, issn = {2214-2509}, abstract = {This study reports a case of infective endocarditis (IE) caused by Streptococcus gordonii. The patient presented with cerebral infarction as the initial manifestation, complicated by bacterial meningitis and mitral regurgitation. The diagnosis of Streptococcus gordonii-induced infective endocarditis was facilitated by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). Streptococcus gordonii was detected by CSF mNGS within 40 h after admission, which was 30 h earlier than the positive result of blood culture. During anti-infective therapy, the patient experienced recurrent thromboembolic events and underwent emergency mechanical thrombectomy due to occlusion of the left vertebral artery. Despite aggressive treatment, the patient eventually died of heart failure. This case indicates that Streptococcus gordonii is a rare pathogen of infective endocarditis, and its clinical presentation complicated by cerebral infarction and bacterial meningitis is distinctive; particularly, complex cases requiring mechanical thrombectomy are extremely rare in clinical practice. As an important complement to conventional bacterial culture, mNGS can shorten diagnostic delay, especially in patients with negative blood or CSF cultures. For patients with concurrent cerebral infarction and meningitis, the possibility of infective endocarditis should be highly suspected, and indications for valve replacement surgery should be evaluated as early as possible in high-risk cases.}, }
@article {pmid42222019, year = {2026}, author = {Wang, F and Xie, C and Zhao, M and Pan, Y and Xie, Y and Wang, X and Zhu, W and Xie, Y}, title = {VV-ECMO-supported management of severe ARDS secondary to melioidosis sepsis: A case report and concise review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02612}, pmid = {42222019}, issn = {2214-2509}, abstract = {Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), is a life-threatening tropical infection that is frequently underdiagnosed because of its heterogeneous and nonspecific clinical presentation. We report a critically ill patient from an endemic area who developed fulminant pneumonia that progressed to septic shock and severe acute respiratory distress syndrome. Despite empirical broad-spectrum antimicrobial therapy, respiratory failure worsened, prompting early etiologic investigation with metagenomic next-generation sequencing, which identified B. pseudomallei and was subsequently confirmed by culture. The patient required early venovenous extracorporeal membrane oxygenation (ECMO) for refractory hypoxemia. Management included a targeted antimicrobial therapy in accordance with current guidelines and CT-guided drainage of a pulmonary abscess as definitive source control. The patient achieved full recovery without recurrence at follow-up. Early identification of the causative pathogen and timely source control were central to the management of melioidosis-associated severe ARDS. Advanced supportive measures, including ECMO, may be considered in selected patients with refractory hypoxemia as part of management involving multiple specialties.}, }
@article {pmid42222035, year = {2026}, author = {Liu, YH and Fang, SR and Chen, W and Wu, YF and Liu, DK and Li, T}, title = {Comparative Study of Confirmed versus Suspected Cases of Vibrio vulnificus Infection in Chaoshan District, Guangdong, China.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {613123}, pmid = {42222035}, issn = {1178-6973}, abstract = {OBJECTIVE: To compare the epidemiological, clinical, and laboratory data of patients with confirmed and suspected Vibrio vulnificus infection in Chaoshan District, Guangdong.<br><br>METHODS: This retrospective study analyzed 25 confirmed cases and 23 suspected cases of V. vulnificus infection at the First Affiliated Hospital of Shantou University Medical College from January 2014 to December 2025. A confirmed case was defined by the presence of a positive result from culture and/or mNGS and a suspected case by the experience of a clear marine trauma followed by rapidly progressive soft tissue manifestations, but without etiological confirmation of V. vulnificus infection after exclusion of other infectious etiologies. The epidemiological history, early clinical manifestations, routine blood parameters, and in-hospital outcomes of the two groups were compared.<br><br>RESULTS: The confirmed group had a greater severity of soft tissue infection (84.0% vs 26.0%, P<0.01) and more involved sites (88.0% vs 47.8%, P<0.01). The laboratory data indicated the confirmed group had more abnormalities in markers of tissue injury (creatinine kinase, lactate dehydrogenase), coagulation function (platelets, prothrombin time, international normalized ratio), liver function (aspartate transaminase, total bilirubin), renal function (serum creatinine), and lipid and nutritional markers (all P<0.05). The confirmed group also had significantly higher rates of in-hospital mortality (32.0% vs 0%), multi-organ dysfunction syndrome (36.0% vs 0%), and surgical intervention (60.0% vs 30.4%), and a greater economic burden (all P<0.001).<br><br>CONCLUSION: There are significant differences in the early clinical manifestations, routine blood parameters, and in-hospital outcomes for patients with confirmed and suspected V. vulnificus infection.}, }
@article {pmid42222136, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC}, title = {Protist community sites and structure under two barn management systems at a commercial dairy.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1803341}, pmid = {42222136}, issn = {2813-4338}, abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.<br><br>METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.<br><br>RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.<br><br>DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.}, }
@article {pmid42222213, year = {2026}, author = {Zhou, Y and Lai, Y and Zhou, F and Wang, X and He, X and Jin, J and Zhang, R}, title = {Morphological analysis of bronchoalveolar lavage fluid in diagnosing pulmonary aspergilloma in a patient with rheumatoid arthritis: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {32}, number = {1}, pages = {191}, pmid = {42222213}, issn = {1792-1015}, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder that primarily affects the joints and may be associated with systemic complications. Patients with RA have an increased susceptibility to opportunistic infections, attributable to inherent immune dysregulation as well as immunosuppressive therapies, including tocilizumab, particularly among those with comorbidities or high disease activity. Notably, the use of tumor necrosis factor inhibitors, such as adalimumab and etanercept, has been associated with a higher incidence of invasive pulmonary aspergillosis and chronic pulmonary aspergillosis. The present study reports a rare case of pulmonary aspergilloma in a 75-year-old female RA patient with prior tuberculosis and long-term tocilizumab use. The patient was diagnosed via bronchoalveolar lavage fluid morphology, fungal culture, Aspergillus galactomannan assay, metagenomic next-generation sequencing and pathology, and the patient achieved symptom resolution and improved imaging after 6 months of treatment with voriconazole. These findings underscore the need for vigilant monitoring and individualized management strategies in this patient population.}, }
@article {pmid42222492, year = {2026}, author = {Tran, TTT and Nguyen, OTK and Hoang, PH and Nguyen, NP and To, HTM and Nguyen, HQ}, title = {Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21262}, pmid = {42222492}, issn = {2167-8359}, mesh = {*Feces/microbiology/chemistry ; Vietnam ; *Coffee/metabolism/microbiology ; *Metabolomics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Fermentation ; Humans ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism ; Animals ; }, abstract = {BACKGROUND: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets.<br><br>METHODS: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups.<br><br>RESULTS: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter, and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6-hydroxyangolensic acid methyl ester, 4-aminobenzoic acid and caffeine were more abundant in civets on a coffee-cherry diet, meanwhile the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs, and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.}, }
@article {pmid42222536, year = {2026}, author = {Yang, H and Zhao, L}, title = {Clinical characteristics and prognostic analysis of patients with herpesvirus meningitis/encephalitis based on cerebrospinal fluid mNGS positivity.}, journal = {Frontiers in neurology}, volume = {17}, number = {}, pages = {1808867}, pmid = {42222536}, issn = {1664-2295}, abstract = {BACKGROUND: Herpes viruses are a major cause of meningitis/encephalitis in adults. However, their individual clinical phenotypes and outcomes remain incompletely delineated. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) offers a powerful tool for precise pathogen identification, facilitating the comparison of distinct herpes virus infections.<br><br>METHODS: This retrospective cohort study analyzed 66 patients with CSF-mNGS confirmed herpes virus meningitis/encephalitis at a single center between October 2019 and August 2025. The cohort was stratified into five etiological groups: herpes simplex virus type 1 (HSV-1, n&#x202f;=&#x202f;10), herpes simplex virus type 2 (HSV-2, n&#x202f;=&#x202f;5), varicella-zoster virus (VZV, n&#x202f;=&#x202f;27), Epstein-Barr virus (EBV, n&#x202f;=&#x202f;15), and human herpesvirus 7 (HHV-7, n&#x202f;=&#x202f;9). Demographic, clinical, laboratory, and neuroimaging data were collected. Outcomes were assessed using the Glasgow Outcome Scale (GOS) at 3&#x202f;months post-discharge.<br><br>RESULTS: Distinct clinical phenotypes were observed. HSV-1 encephalitis typically presented with psychiatric symptoms, seizures, and temporal lobe involvement on MRI. HSV-2 infection manifested primarily as a febrile headache syndrome with minimal brain parenchymal involvement. VZV infection was associated with the most intense CSF inflammatory response (highest WBC and protein), a higher incidence of hypoglycorrhachia (25.9%) and hypochloridia (40.7%), and unique complications like cranial neuritis and vasculopathy. EBV infections occurred in older patients and showed features overlapping with HSV-1. HHV-7 infected a significantly younger population and was strikingly associated with elevated intracranial pressure (ICP&#x202f;&#x2265;&#x202f;330 mmH2O in 33.3%). Multivariate analysis identified a longer interval from symptom onset to hospitalization (OR: 1.118, p&#x202f;=&#x202f;0.025) and an abnormal EEG (OR: 0.066, p&#x202f;<&#x202f;0.001) as independent predictors of an unfavorable outcome (GOS&#x202f;<&#x202f;5). Antiviral or steroid therapy was not significantly associated with prognosis in this cohort.<br><br>CONCLUSION: CSF-mNGS reveals distinct and clinically significant phenotypic differences among various herpesvirus meningitis/encephalitis. VZV is characterized by a vigorous CSF inflammatory response and vascular complications, while HHV-7 predominantly affects younger adults and is significantly associated with intracranial hypertension. These findings underscore the value of mNGS in enabling pathogen-directed diagnosis and management, moving beyond syndromic approaches.}, }
@article {pmid42222738, year = {2026}, author = {Park, JH and Chung, J and Lee, HJ and Na, HS}, title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2679807}, pmid = {42222738}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.<br><br>OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.<br><br>METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.<br><br>RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.<br><br>CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.}, }
@article {pmid42222901, year = {2026}, author = {Dong, Y and Hu, D and Yang, R and Xin, T and Guan, Y and Zhu, X and Ding, Y and Cui, S and Wang, R and Wang, X and Niu, Y and Kong, X}, title = {Early-Life Obesity Leaves a Metabolic Memory That Accelerates Aging-Related Decline Through the Gut Microbiota-GABA Axis.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {11}, pages = {e70513}, doi = {10.1002/mnfr.70513}, pmid = {42222901}, issn = {1613-4133}, support = {2024YFF1106004//National Key Research and Development Program/ ; PL2025H095//Natural Science Foundation of Heilongjiang Province/ ; }, mesh = {Animals ; *gamma-Aminobutyric Acid/metabolism/pharmacology ; *Aging/metabolism/physiology ; *Obesity/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat/adverse effects ; Male ; Oxidative Stress ; Rats ; Lipid Metabolism ; }, abstract = {Childhood obesity is a critical public health concern. Whether diet-induced transient obesity during development negatively impacts later-life health remains unclear, and mechanisms are poorly understood. This study investigates whether these effects persist into aging and employs integrated omics to explore underlying mechanisms. Using a high-fat diet (HFD) to induce transient developmental obesity in post-weaning rats and larval Drosophila, we examined the long-term effects on aging metabolic health in both species. Transient developmental obesity in rats was linked to accelerated aging, weight loss, worsened metabolism, colonic inflammation, and oxidative stress. Metabolomics revealed persistent gamma aminobutyric acid (GABA) dysregulation associated with intestinal ammonia levels, and gut metagenomics showed a reduction in Lactobacillales, correlating with adverse health outcomes. In Drosophila, exogenous GABA extended HF-diet lifespan. It reduced trehalose, triglycerides (TG), and oxidative stress; concurrently, it restored intestinal Lactobacillus and activated the phosphotransferase system (PTS), thereby improving metabolic homeostasis and redox status. Transient developmental obesity is associated with reduced gut Lactobacillus abundance, which may contribute to decreased GABA levels and subsequent disruption of glucose (GLU) metabolism, potentially involving the PTS pathway. These interconnected alterations may ultimately lead to systemic dysregulation of GLU and lipid metabolism and redox homeostasis in later life, compromising overall health and longevity.}, }
@article {pmid42223080, year = {2026}, author = {An, SY and Kim, I and Hong, SH and Kim, EH and Suh, JY}, title = {AcrIIA8 is a putative phage structural protein of the HTJ2 family that does not inhibit Streptococcus pyogenes Cas9.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {7}, pages = {e70651}, pmid = {42223080}, issn = {1469-896X}, support = {RS-2025-23525174//National Research Foundation of Korea/ ; RS-2024-00440614//National Research Foundation of Korea/ ; BDB-2025-04-04230007//Korea Institute of Marine Science &amp; Technology Promotion/ ; }, mesh = {*Streptococcus pyogenes/enzymology/genetics/virology ; *CRISPR-Associated Protein 9/antagonists &amp; inhibitors/chemistry/metabolism ; *Viral Structural Proteins/chemistry/metabolism/genetics ; *Bacteriophages/chemistry ; }, abstract = {Anti-CRISPR (Acr) proteins are phage-encoded anti-defense factors that suppress CRISPR-Cas immunity in bacteria. AcrIIA8 was previously identified as an inhibitor of Streptococcus pyogenes Cas9 (SpyCas9) through functional assays of metagenomic libraries. Here, we report that AcrIIA8 does not inhibit SpyCas9 in biochemical assays under a range of buffer conditions and temperatures. The solution structure and dynamics of AcrIIA8 reveal a six-stranded β-barrel fold with flexible β1-β2 and β2-β3 loops, characteristic of phage virion-assembly proteins. In addition, genomic context analysis places AcrIIA8 and its homologs within conserved prophage morphogenetic regions at the position expected for type II head-tail joining (HTJ2) proteins. We further detected no interaction between AcrIIA8 and SpyCas9 in NMR titration experiments, suggesting that they do not specifically associate. Taken together, these findings argue against assigning AcrIIA8 as a SpyCas9 inhibitor and instead support its annotation as a putative phage structural protein of the HTJ2 family.}, }
@article {pmid42223254, year = {2026}, author = {Petricciuolo, M and Carnevali, A and Torboli, A and Postinghel, M and Guasticchi, A and Foladori, P and Cadonna, M and Federici, E}, title = {Wastewater-Based Assessment of Antimicrobial Resistance and Bacterial Communities in Urban and Rural Areas in the Province of Trento (Italy).}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70319}, pmid = {42223254}, issn = {2045-8827}, support = {//CINECA/ ; //Ministero dell'Universit&#xe0; e della Ricerca/ ; }, mesh = {Italy ; *Bacteria/drug effects/genetics/isolation &amp; purification/classification ; *Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Sewage/microbiology ; }, abstract = {Wastewater-based epidemiology (WBE) can supplement clinical surveillance for assessing the spread of antimicrobial resistance (AMR) across the population. We have analyzed sewage samples from seven wastewater treatment plants in the Province of Trento (Italy) using both culture-based and metagenomic DNA methods to investigate the prevalence of antimicrobial-resistant bacteria (ARBs) and resistance genes in urban and rural areas. ESBL-Escherichia coli prevalence was higher in urban areas than in rural ones. As determined by qPCR and dPCR, intI1 and genes associated with widespread resistances, namely, to tetracyclines (tetA), sulfonamides (sul1), and fluoroquinolones (qnrS), were abundant regardless of the area of origin. Among the genes coding for clinically relevant resistances, only that related to macrolides resistance (ermB) was abundant, while the others, namely, those to third-generation cephalosporins (blaCTX-M), carbapenems (blaKPC), vancomycin (vanA), and methicillin (mecA), were detected at much lower concentrations. Further, the abundances of ermB, blaKPC, and vanA were significantly higher in urban areas. 16S rRNA amplicon sequencing showed the occurrence of complex bacterial communities and the abundance of Acinetobacter, Pseudomonas, and Streptococcus, genera that may include ARBs reported in the WHO Bacterial Priority Pathogens List, with the latter showing higher prevalence in urban areas. Taken together, our data highlights the importance of implementing WBE studies across geographical areas with different characteristics in terms of vocation, number of municipalities, and population size, such as urban and rural ones. By providing a comprehensive understanding of AMR at the population level, this approach can inform and support more effective public health interventions.}, }
@article {pmid42223272, year = {2026}, author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC}, title = {Mapping the soil microbiome functions shaping wetland methane emissions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068025}, doi = {10.1128/msystems.00680-25}, pmid = {42223272}, issn = {2379-5077}, abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.}, }
@article {pmid42223530, year = {2026}, author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag140}, pmid = {42223530}, issn = {1751-7370}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid42224759, year = {2026}, author = {Xu, M and Qi, S and Yu, X and Han, S and Xiao, R and Guo, J and Wang, C and Zhu, N and Lu, H}, title = {Resistome risks of biological wastewater treatment communities: A global dataset of activated sludge, anaerobic digestion, and anammox.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142561}, doi = {10.1016/j.jhazmat.2026.142561}, pmid = {42224759}, issn = {1873-3336}, abstract = {Activated sludge (AS), anaerobic digestion (AD), and anammox (AMX) systems are widely used for wastewater treatment. Their microbial communities harbor resistomes, including but not limited to antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), which may pose potential risks to human and ecological health if they are mobilized or transferred to pathogenic hosts. However, cross-process comparisons of resistome risks are limited at a global scale. This study analyzed 225 metagenomic datasets (210 public: 70 each for AS, AD, AMX; plus 15 in-house AMX) to assess resistome risks and identified key influential factors. Overall, within the constraints of current data availability, North America, Europe and Asia systems exhibited comparable risk levels. AD systems exhibited more than 2-fold higher human health resistome risks (potentials for human pathogens of acute resistance concern to acquire ARGs) than AS and AMX systems. Mesophilic and co-digestion AD systems posed 30-90% higher risks than thermophilic and mono-digestion systems with higher abundance of pathogens, ARGs, and MRGs. AMX systems, otherwise, showed higher ecological resistome risks (overall mobility of ARGs/MRGs and potentials for pathogen acquisition) than AS and AD. The conservative AMX communities contained core taxa that harbor 19.8% more ARGs/MRGs per genome and exhibit 31.4% higher horizontal gene transfer potential than non-core taxa. Key operating factors influencing resistome risks included temperature for AD, and organic loading, influent antibiotics and heavy metals for AMX. These findings provide insights into future wastewater treatment towards improved efficacy and reduced resistome risks.}, }
@article {pmid42224761, year = {2026}, author = {Ma, S and Zhao, B and Jing, G and Han, M and Wang, M and Shan, X and Wang, Z and Lu, S and Liu, X and Wu, F}, title = {Vertical stratification and distribution patterns of the ARG resistome in Fuxian Lake: Insights from a global baseline.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142528}, doi = {10.1016/j.jhazmat.2026.142528}, pmid = {42224761}, issn = {1873-3336}, abstract = {Deep lakes are critical reservoirs for antibiotic resistance genes (ARGs), yet global ARG dynamics and vertical mechanisms remain poorly constrained. By combining metagenomics with a global comparative analysis across 17 plateau lakes and 83 Fuxian Lake samples, this study investigates ARG distribution from macro- to micro-scales. The macro-scale analysis identified Longitude, Latitude, and Temperature (all p-values < 0.05) as dominant constraints on ARG abundance. A distinct, synergistic mechanism drives vertical stratification: ARG enrichment occurs in the deep layer (50-150 m) at the lake center, but enrichment shifts to the shallow layer (0-40 m) in the tourism area. This complex pattern is governed by a biotic-abiotic synergy. Specifically, ARG dynamics in the deep layer are jointly regulated by biotic factors and physicochemical constraints such as pH and ORP. Differences observed at the local scale, including the increase in ARG abundance and rare-to-core conversion, contrast with broader patterns observed across plateau lakes. This study provides the first global distribution spectrum of ARGs in plateau lakes and reveals crucial interactive patterns. The persistent presence of high-risk ARGs and critical priority pathogens necessitates heightened vigilance. We propose controlling anthropogenic inputs and mitigating the risk of deep sediment pollutant release as crucial strategies for these vital freshwater resources.}, }
@article {pmid42224764, year = {2026}, author = {Sun, Y and Yu, Z and Wu, C and Wang, J and Feng, X}, title = {First insights into agricultural practice-driven mobilization and methylation of arsenic and mercury in soil with implications for groundwater risk mitigation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142530}, doi = {10.1016/j.jhazmat.2026.142530}, pmid = {42224764}, issn = {1873-3336}, abstract = {The migration of heavy metals from soils to groundwater via karst conduits (e.g., dolines) in karst terrains threatens the safety of anthropogenic water supplies. Despite widespread recognition of contamination risks, the underlying mechanisms governing the transformation and mobilization of heavy metals, particularly those mediated by agricultural activities, remain inadequately characterized. Here, we systematically studied the impact of rice straw return (RS) on the biogeochemical transformation processes of both arsenic (As) and mercury (Hg) from a co-polluted soil in karst regions using a combination of geochemical, microbial, and spectroscopic approaches. The results indicated that RS enhanced the desorption of As from Fe(III)oxyhydroxides and methylation of As(III). Metagenomic sequencing analyses revealed that RS increased the abundance of Fe-reducing bacteria (FeRB) and As-methylating microorganisms, which collectively drive As mobilization and transformation. Furthermore, RS promoted the release of Hg from Fe(III)oxyhydroxides and stimulated methylmercury (MeHg) formation, primarily due to the increased abundance of Hg-methylating microbes and hgcAB genes, as well as enhanced Hg availability through the transformation of HgS into organic matter bound Hg and nano-HgS. These findings are essential for predicting As and Hg leaching risks from soils to groundwater under the influence of agricultural practices in karst regions worldwide.}, }
@article {pmid42224874, year = {2026}, author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF}, title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.}, journal = {The Science of the total environment}, volume = {1042}, number = {}, pages = {181905}, doi = {10.1016/j.scitotenv.2026.181905}, pmid = {42224874}, issn = {1879-1026}, mesh = {*Climate Change ; *Soil Microbiology ; *Machine Learning ; Agriculture ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Predictive Learning Models ; Boosting Machine Learning Algorithms ; Random Forest ; *Environmental Monitoring/methods ; }, abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.}, }
@article {pmid42225156, year = {2026}, author = {Feng, S and Bao, Y and Zhu, X and Wu, J and Chen, W and Huang, D and Zhou, T and Meng, L and Lee, CH and Li, D and Huang, M}, title = {Biodegradable versus persistent nanoplastics reshape nitrogen metabolism and biofilm architecture in denitrifying biofilters.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135048}, doi = {10.1016/j.biortech.2026.135048}, pmid = {42225156}, issn = {1873-2976}, mesh = {*Microplastics/metabolism/toxicity ; Wastewater/chemistry/microbiology ; *Water Purification/methods ; Biodegradable Plastics/analysis/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Nitrogen Cycle ; *Nitrogen/analysis/metabolism ; Filtration/instrumentation/methods ; Extracellular Polymeric Substance Matrix/metabolism ; Polyesters/analysis/metabolism ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; Denitrification/physiology ; }, abstract = {The presence of nanoplastics (NPs) in biological wastewater treatment systems is an emerging concern. Nevertheless, their differential influence on critical biofilm-mediated processes has yet to be fully elucidated. In this study, denitrifying biofilters were exposed to biodegradable polylactic acid nanoplastics (PLA-NPs) and non-biodegradable polystyrene nanoplastics (PS-NPs) to simulate both typical and cumulative high-exposure scenarios. Results showed that long-term NP stress significantly reduced the denitrification performance, with a maximum inhibition of 35% in total nitrogen (TN) removal. Mechanistically, PLA and PS induced distinct biofilm remodeling strategies. PLA exposure enhanced nitrate assimilation pathways, promoting nitrogen sequestration into microbial biomass. In contrast, PS-NPs elicited concentration-dependent stress responses. Low PS exposure was associated with reduced extracellular polymeric substances (EPS) and enhanced carbohydrate degradation potential, whereas high PS concentrations were linked to altered EPS composition, decreased microbial diversity, and directional succession toward stress-tolerant genera. Metagenomic analysis revealed shifts in central carbon metabolic strategies, including enhanced gluconeogenesis and EPS precursor synthesis under NP exposure. Differences in substrate bioavailability between PLA and PS treatments further contributed to distinct carbon utilization patterns within the biofilms. Overall, this study demonstrates that NP biodegradability governs biofilm functional stability, nitrogen transformation, and denitrification performance, providing mechanistic insight into NP-biofilm interactions in engineered systems.}, }
@article {pmid42225158, year = {2026}, author = {Wang, M and Wang, H and Liang, X and Li, J and Wang, C and Cui, L and Yang, S and Lin, J and Yang, Q and Yang, Z}, title = {Enhanced phenanthrene degradation in microalgae-bacteria systems: Mechanistic roles of exogenous and indigenous degraders.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135034}, doi = {10.1016/j.biortech.2026.135034}, pmid = {42225158}, issn = {1873-2976}, mesh = {*Phenanthrenes/metabolism ; Biodegradation, Environmental ; *Microalgae/metabolism/growth &amp; development ; *Bacteria/metabolism ; Biomass ; *Chlorella vulgaris/metabolism/growth &amp; development ; Extracellular Polymeric Substance Matrix/metabolism ; Biofilms ; }, abstract = {This study investigates the synergistic mechanisms of phenanthrene (PHE) biodegradation using Chlorella vulgaris consortia with exogenous (EB) and indigenous (IB) bacteria. Results showed that both cooperative systems significantly enhanced algal growth and PHE removal, with biomass increasing by 17.2% (C.v-EB) and 75.0% (C.v-IB), and biodegradation rates reaching 75.3%-78.4%. Mechanistically, C.v-EB relied on enzymatic antioxidant responses (SOD and CAT) and a protein-rich extracellular polymeric substance (EPS) shield to mitigate oxidative stress. In contrast, C.v-IB exhibited superior resilience through non-enzymatic redox regulation (glutathione/thioredoxin systems) and the formation of a dense, biofilm-like EPS matrix supported by active transport genes (wzm/wzt). Metagenomic analysis revealed that C.v-IB possessed higher metabolic redundancy and energy production efficiency, organized into a coordinated "Degradation-Defense-Communication" genomic architecture via quorum sensing. Furthermore, both consortia expanded the metabolic landscape of PHE, effectively eliminating intermediate toxicity through divergent pathways. These findings provide a systematic framework for developing robust algal-bacterial biotechnologies for the remediation of polycyclic aromatic hydrocarbons in wastewater.}, }
@article {pmid42225249, year = {2026}, author = {Nie, X and Qin, J and Liu, M and Wang, H and Hou, K and Duan, Y}, title = {Process-level design of engineered microalgal-bacterial systems for carbon-efficient nitrogen removal from low C/N wastewater: carbon/electron redistribution revealed by metabolic network analysis.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124883}, doi = {10.1016/j.envres.2026.124883}, pmid = {42225249}, issn = {1096-0953}, abstract = {Carbon scarcity in low carbon-to-nitrogen (C/N) wastewater limits electron donor availability and constrains biological nitrogen removal. Although microalgal-bacterial symbiosis (MBS) is a promising low-input alternative, the mechanisms that sustain nitrogen removal under carbon-limited conditions remain unclear. Here, process-level characterization and metagenomic analysis were combined to investigate community assembly and carbon/electron redistribution in engineered MBS systems. Under the tested conditions, a balanced algae-to-bacteria ratio (1:1) created the most stable niche and achieved >97% NH4[+]-N removal with minimal nitrate accumulation, indicating effective coupling of nitrification, denitrification, and assimilation. Extracellular polymeric substances (EPS) dynamics showed a shift from accumulation to reutilization during prolonged carbon limitation: polysaccharides decreased in the later stage as external chemical oxygen demand (COD) was depleted, suggesting mobilization of EPS as an internal carbon source. Consistently, tricarboxylic acid (TCA) cycle genes (e.g., IDH, OGDH, mdh) were enriched whereas glycolysis-related genes (e.g., GAPDH, PGK) declined, indicating a shift in metabolic potential toward greater generation of reducing equivalents. Overall, the results suggest that EPS functions as a dynamic carbon reservoir and that algae-bacteria interactions promote carbon/electron redistribution under carbon-limited conditions. This study provides a process-level basis for designing carbon-efficient wastewater treatment systems.}, }
@article {pmid42226305, year = {2026}, author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R}, title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42226305}, issn = {1756-994X}, support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; }, mesh = {Humans ; Female ; *Fasting ; Adult ; Male ; Blood Pressure ; Weight Loss ; Metabolomics ; Middle Aged ; Biomarkers ; }, abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.<br><br>METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.<br><br>RESULTS: MFP participants (n&#x2009;=&#x2009;32) experienced weight loss compared to controls (-&#x2009;0.52&#x2009;&#xb1;&#x2009;0.03&#xa0;kg vs.&#x2009;-&#x2009;0.03&#x2009;&#xb1;&#x2009;0.02&#xa0;kg, p&#x2009;<&#x2009;0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56&#x2009;&#xb1;&#x2009;0.12 mmHg vs.&#x2009;-&#x2009;0.16&#x2009;&#xb1;&#x2009;0.12 mmHg, p&#x2009;<&#x2009;0.05 and diastolic: -0.36&#x2009;&#xb1;&#x2009;0.08 mmHg vs.&#x2009;-&#x2009;0.01&#x2009;&#xb1;&#x2009;0.08 mmHg, p&#x2009;<&#x2009;0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.<br><br>CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.<br><br>CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.}, }
@article {pmid42226423, year = {2026}, author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W}, title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.260317}, pmid = {42226423}, issn = {2765-0189}, abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.<br><br>METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.<br><br>RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.<br><br>CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.}, }
@article {pmid42227278, year = {2026}, author = {Li, W and Wang, Z and Fu, H and Ma, YR and Gu, Y and Zhuang, JL and Zhao, YX and Liu, YD and Yang, Q and Shapleigh, JP and Jin, RC and Guo, J and Kartal, B and Rittmann, BE}, title = {A Novel Freshwater Anammox Species of Candidatus Loosdrechtia Thriving Under Dual Salinity and Sulfate Stresses.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {23}, pages = {16629-16640}, doi = {10.1021/acs.est.6c03295}, pmid = {42227278}, issn = {1520-5851}, mesh = {Fresh Water ; Oxidation-Reduction ; Salinity ; Sulfates ; *Planctomycetes/classification/isolation &amp; purification ; }, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are key players in the global nitrogen cycle and are widely applied in energy-efficient nitrogen removal processes. However, their activity is often inhibited in saline and sulfate-rich environments. Here, we report the discovery and characterization of Candidatus Loostrechtia thiotolerans (HSAMX1), a novel nonmarine anammox species that became dominant under combined high salinity (3% by weight) and high sulfate concentrations (∼86 mM). Through integrated metagenomic and metatranscriptomic analyses, we reveal the physiological and molecular strategies enabling HSAMX1 to thrive under dual-stress conditions. In response to osmotic stress, HSAMX1 activated ion export systems and subsequently synthesized organic osmoprotectant solutes to maintain cellular homeostasis. It also encoded and strongly expressed the sulfide:quinone oxidoreductase (SQR) gene, which accounted for over 90% of the total community SQR transcription. Intriguingly, HSAMX1 did not emerge under either salinity or sulfate stress alone, suggesting a previously unrecognized niche shaped by the interactions of these two stressors. These findings expand our understanding of nonmarine anammox diversity and identify a promising candidate for nitrogen removal in sulfate-laden, saline wastewater.}, }
@article {pmid42227352, year = {2026}, author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT}, title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70190}, pmid = {42227352}, issn = {1365-2591}, support = {//European Society of Endodontology/ ; }, abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.<br><br>METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (<&#x2009;3&#x2009;mm) or large (>&#x2009;7&#x2009;mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p&#x2009;<&#x2009;0.05 was considered as significant.<br><br>RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p&#x2009;=&#x2009;0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.<br><br>CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.}, }
@article {pmid42227741, year = {2026}, author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD}, title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0018826}, doi = {10.1128/msystems.00188-26}, pmid = {42227741}, issn = {2379-5077}, abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.}, }
@article {pmid42227750, year = {2026}, author = {Becker, DJ and Dyer, KE and Olbrys, BL and Hightower, MG and Allira, M and Demory, B and Lock, LR and Taylor, KN and Bhata, NN and Hernandez, SM and Lawson, PA and Youssef, NH and Miller, SL and Elshahed, MS and Verrett, TB and Clark, KL}, title = {Molecular detection of relapsing fever Borrelia puertoricensis in migratory Mexican free-tailed bats.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0008526}, doi = {10.1128/msphere.00085-26}, pmid = {42227750}, issn = {2379-5042}, abstract = {UNLABELLED: Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America.<br><br>IMPORTANCE: Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.}, }
@article {pmid42227946, year = {2026}, author = {Wang, H and Wang, X and Xiu, Z and Wei, H and Cai, H and Chen, J and Zhang, T and Yang, Y}, title = {Substrate-driven microbial specialization and cooperative dechlorination of chlorinated pollutants in estuarine ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0023526}, doi = {10.1128/aem.00235-26}, pmid = {42227946}, issn = {1098-5336}, abstract = {Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 ± 0.9 µM d[-1]. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.}, }
@article {pmid42228562, year = {2026}, author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N}, title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117478}, doi = {10.1016/j.celrep.2026.117478}, pmid = {42228562}, issn = {2211-1247}, abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.}, }
@article {pmid42229136, year = {2026}, author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E}, title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142560}, doi = {10.1016/j.jhazmat.2026.142560}, pmid = {42229136}, issn = {1873-3336}, abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.}, }
@article {pmid42229568, year = {2026}, author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G}, title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124851}, doi = {10.1016/j.envres.2026.124851}, pmid = {42229568}, issn = {1096-0953}, abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (±40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.}, }
@article {pmid42229596, year = {2026}, author = {Lou, D and Duan, J and Zhou, B and Zhou, H and Wang, Y and Yang, J and Cui, J and Ma, X and Tan, J and Duan, H}, title = {Characterization and activity enhancement of a novel thermostable 3-quinuclidinone reductase through modulating the microenvironment of catalytic residues.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135058}, doi = {10.1016/j.biortech.2026.135058}, pmid = {42229596}, issn = {1873-2976}, mesh = {Molecular Dynamics Simulation ; Enzyme Stability ; *Oxidoreductases/metabolism/chemistry/genetics ; Catalytic Domain ; *Quinuclidines/metabolism ; *Temperature ; Biocatalysis ; Mutation ; Thermodynamics ; Kinetics ; }, abstract = {The biocatalytic synthesis of chiral alcohols offers a sustainable alternative to traditional chemical catalysis, yet the lack of robust, high-efficiency enzymes remains an industrial bottleneck. Here, a novel thermostable 3-quinuclidinone reductase (SdQR) was discovered via metagenomic mining of hot spring environments and biochemically characterized. Among the candidates, the H161Q variant, situated proximal to the conserved catalytic triad, emerged as a high-potential lead. Experimental validation revealed that the H161Q mutation yielded a 16-fold increase in catalytic efficiency (kcat/Km) over the wild-type enzyme while preserving its exceptional thermostability. Molecular dynamics (MD) simulations and MM-PBSA calculations elucidated the mechanistic basis for this enhancement: the mutation establishes a "structurally rigid yet physicochemically fluid" microenvironment. This subtle shift optimizes the hydrophobic landscape within the active pocket and modulates cofactor binding thermodynamics, lowering the desolvation energy barrier without compromising the robust structural scaffold. This study provides a highly potent biocatalyst for the asymmetric synthesis of (R)-3-quinuclidinol, and highlights a sophisticated engineering paradigm for the precise physicochemical fine-tuning of catalytic microenvironments in industrial enzymes.}, }
@article {pmid42229597, year = {2026}, author = {Besharati Fard, M and Kwon, S and De Vrieze, J and Wu, D}, title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135056}, doi = {10.1016/j.biortech.2026.135056}, pmid = {42229597}, issn = {1873-2976}, mesh = {*Caprylates/pharmacology ; *Fluorocarbons/pharmacology ; *Sewage/microbiology ; Anaerobiosis/drug effects ; *Microalgae/metabolism/drug effects ; *Bacteria/metabolism/drug effects/genetics ; Aerobiosis/drug effects ; *Metagenomics ; Methane/biosynthesis/metabolism ; Bioreactors/microbiology ; Fatty Acids, Volatile/metabolism ; Biofuels ; Biological Oxygen Demand Analysis ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.}, }
@article {pmid42229598, year = {2026}, author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135043}, doi = {10.1016/j.biortech.2026.135043}, pmid = {42229598}, issn = {1873-2976}, abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.}, }
@article {pmid42229914, year = {2026}, author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L}, title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.}, journal = {Pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1542/peds.2025-073077}, pmid = {42229914}, issn = {1098-4275}, abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.}, }
@article {pmid42230119, year = {2026}, author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G}, title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338252}, pmid = {42230119}, issn = {1468-3288}, abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.}, }
@article {pmid42230654, year = {2026}, author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F}, title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01029-0}, pmid = {42230654}, issn = {2055-5008}, abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.}, }
@article {pmid42230804, year = {2026}, author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP}, title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {42230804}, issn = {2731-8745}, support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; }, abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.}, }
@article {pmid42231385, year = {2026}, author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N}, title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01343-5}, pmid = {42231385}, issn = {1475-2891}, support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; }, abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.<br><br>METHODS: A total of 102 male Han participants was randomized to curcumin (812&#xa0;mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.<br><br>RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P&#x2009;=&#x2009;0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P&#x2009;<&#x2009;0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P&#x2009;<&#x2009;0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P&#x2009;<&#x2009;0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.<br><br>CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.<br><br>TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.}, }
@article {pmid42231497, year = {2026}, author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I}, title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02443-4}, pmid = {42231497}, issn = {2049-2618}, abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.<br><br>RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.<br><br>CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.}, }
@article {pmid42231509, year = {2026}, author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F}, title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42231509}, issn = {2049-2618}, support = {FESR1078-MummyLabs//European Regional Development Fund/ ; }, mesh = {*Mummies/microbiology ; *Microbiota/genetics ; Humans ; Metagenomics/methods ; DNA, Ancient/analysis ; *Ice Cover/microbiology ; Sequence Analysis, DNA ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Phylogeny ; Biodiversity ; }, abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.<br><br>RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.<br><br>CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.}, }
@article {pmid42231528, year = {2026}, author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA}, title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679516}, pmid = {42231528}, issn = {1949-0984}, mesh = {Animals ; *Prebiotics/administration &amp; dosage ; *Obesity/metabolism/microbiology/physiopathology/complications ; *Osteoarthritis, Knee/metabolism/microbiology/physiopathology ; Rats ; Multiomics ; Humans ; *Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; }, abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.}, }
@article {pmid42232316, year = {2026}, author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist &amp; Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {211}, pmid = {42232316}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).}, }
@article {pmid42232360, year = {2026}, author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L}, title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.}, journal = {Open medicine (Warsaw, Poland)}, volume = {21}, number = {1}, pages = {20261445}, pmid = {42232360}, issn = {2391-5463}, abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.<br><br>METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain&#xa0;BALF.<br><br>RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58&#x202f;%).<br><br>CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.}, }
@article {pmid42232489, year = {2026}, author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N}, title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103997}, pmid = {42232489}, issn = {2590-1575}, abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.}, }
@article {pmid42232626, year = {2026}, author = {Han, X and Zhang, L and Zhang, R and Liu, W}, title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1825002}, pmid = {42232626}, issn = {2296-2360}, abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.}, }
@article {pmid42232631, year = {2026}, author = {Gao, L and Wen, Y and Jing, X}, title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1795457}, pmid = {42232631}, issn = {2296-2360}, abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.}, }
@article {pmid42232653, year = {2026}, author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F}, title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1760647}, pmid = {42232653}, issn = {1662-4548}, abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.<br><br>METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.<br><br>RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.<br><br>CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.}, }
@article {pmid42232910, year = {2026}, author = {Oskolkov, N}, title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1603339}, pmid = {42232910}, issn = {1664-302X}, abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.}, }
@article {pmid42232914, year = {2026}, author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH}, title = {From microbial diversity to functional potential using dimensionality reduction.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786397}, pmid = {42232914}, issn = {1664-302X}, abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.}, }
@article {pmid42233252, year = {2026}, author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR}, title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42233252}, issn = {1758-0463}, support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; }, mesh = {Biocuration ; Humans ; *Autoimmune Diseases/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity/immunology ; *Antigens, Bacterial/immunology ; Animals ; *Databases, Protein ; }, abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.}, }
@article {pmid42233644, year = {2026}, author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M}, title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149825}, doi = {10.1128/msystems.01498-25}, pmid = {42233644}, issn = {2379-5077}, abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.}, }
@article {pmid42233648, year = {2026}, author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X}, title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0399325}, doi = {10.1128/spectrum.03993-25}, pmid = {42233648}, issn = {2165-0497}, abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.<br><br>IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.}, }
@article {pmid42233650, year = {2026}, author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM}, title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0339225}, doi = {10.1128/spectrum.03392-25}, pmid = {42233650}, issn = {2165-0497}, abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.}, }
@article {pmid42233654, year = {2026}, author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H}, title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0318325}, doi = {10.1128/spectrum.03183-25}, pmid = {42233654}, issn = {2165-0497}, abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.<br><br>IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.}, }
@article {pmid42233680, year = {2026}, author = {Grettenberger, CL and Macalady, JL and Hamilton, TL}, title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0070026}, doi = {10.1128/aem.00700-26}, pmid = {42233680}, issn = {1098-5336}, abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.}, }
@article {pmid42233768, year = {2026}, author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A}, title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.}, journal = {Journal of medical virology}, volume = {98}, number = {6}, pages = {e70997}, doi = {10.1002/jmv.70997}, pmid = {42233768}, issn = {1096-9071}, support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; }, mesh = {Humans ; *Papillomavirus E7 Proteins/genetics/metabolism ; *Human papillomavirus 11/genetics/pathogenicity ; Amino Acid Substitution ; Keratinocytes/virology ; *Polymorphism, Genetic ; *Host-Pathogen Interactions ; Protein Binding ; Oncogene Proteins, Viral ; }, abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.}, }
@article {pmid42234268, year = {2026}, author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M}, title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42234268}, issn = {1573-4978}, mesh = {Humans ; Myokines/metabolism ; *Exercise/physiology ; *Muscle, Skeletal/metabolism/physiology ; Signal Transduction ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism/physiology ; *Brain-Gut Axis/physiology ; Animals ; }, abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.}, }
@article {pmid42234577, year = {2026}, author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C}, title = {SNooPy: a statistical framework for long-read metagenomic variant calling.}, journal = {Nucleic acids research}, volume = {54}, number = {10}, pages = {}, pmid = {42234577}, issn = {1362-4962}, support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; }, mesh = {*Metagenomics/methods ; *Polymorphism, Single Nucleotide ; Humans ; *Software ; Algorithms ; Haplotypes ; Deep Learning ; Genome, Human ; }, abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.}, }
@article {pmid42234710, year = {2026}, author = {Liu, F and Lai, T and Xu, W and Li, G}, title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0349393}, pmid = {42234710}, issn = {1932-6203}, mesh = {*Wastewater/virology ; *Viral Proteins/genetics/chemistry/metabolism ; *SARS-CoV-2/genetics/isolation &amp; purification ; Humans ; COVID-19/virology ; Metagenomics/methods ; }, abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.}, }
@article {pmid42235107, year = {2026}, author = {Candia-Herrera, D and Guerra, M and Carrasco-Fernández, J and Campos-Quiroz, C and Garcia-Gomez, M and Igual, JM and Carro, L and Castro, JF}, title = {Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126734}, doi = {10.1016/j.syapm.2026.126734}, pmid = {42235107}, issn = {1618-0984}, abstract = {Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250[T], was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250[T] (=RGM 3146[T] = IMI 507634[T]).}, }
@article {pmid42235155, year = {2026}, author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY}, title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107186}, pmid = {42235155}, issn = {1525-3171}, abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.}, }
@article {pmid42235160, year = {2026}, author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X}, title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107187}, pmid = {42235160}, issn = {1525-3171}, abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.}, }
@article {pmid42235395, year = {2026}, author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W}, title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142574}, doi = {10.1016/j.jhazmat.2026.142574}, pmid = {42235395}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.}, }
@article {pmid42235463, year = {2026}, author = {Lin, Q and Mei, X and Zheng, H and Meng, J and He, F and Yang, B and Ru, X and Su, M and Wang, D and Tan, N and Fang, J and Fu, S and Ouyang, N and Yang, Z and Jiang, S and Zhang, Y}, title = {Optimisation and validation of capture mNGS for predicting antimicrobial resistance.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106319}, pmid = {42235463}, issn = {2352-3964}, abstract = {BACKGROUND: Antibiotic resistance critically compromises bacterial infection treatment. While antimicrobial susceptibility testing (AST) remains the standard for resistance assessment, its culture dependence is time-consuming. Clinical metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection and antibiotic resistance gene (ARG) profiling. However, low ARG detection sensitivity and unclear genotype-phenotype correlations limit its clinical utility.<br><br>METHODS: We developed capture mNGS approach with probe-based ARG enrichment and a host-attribution algorithm for precise ARG-bacteria linkage. Its ARG detection sensitivity was comparatively analysed against standard mNGS. Using phenotypic AST as reference, we then evaluated the clinical predictive value of capture mNGS-detected ARGs in a retrospective cohort from Sun Yat-sen Memorial Hospital (SYSMH) and an external cohort from Liuzhou Worker's Hospital (LWH). In addition, a prospective cohort from SYSMH was used to explore the clinical utility of ARG detection by mNGS.<br><br>FINDINGS: Compared to standard mNGS, capture mNGS significantly enhanced ARG detection sensitivity, achieving a 44-fold increase in sequencing depth. In our retrospective cohort, key resistance genes detected by capture mNGS accurately predicted phenotypic resistance: blaCTX-M achieved a sensitivity of 1.00 (95% CI: 0.86, 1.00) and specificity of 1.00 (95% CI: 0.59, 1.00) for ceftriaxone resistance prediction, with an area under the receiver operating characteristic curve (AUC) of 0.93 (95% CI: 0.87, 0.99). BlaKPC demonstrated a sensitivity of 0.94 (95% CI: 0.73, 1.00) and specificity of 1.00 (95% CI: 0.95, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.92, 1.00). Similarly, blaOXA-23 exhibited a sensitivity of 0.95 (95% CI: 0.82, 0.99) and specificity of 1.00 (95% CI: 0.69, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.94, 1.00), which was externally validated in the LWH cohort. In addition, mecA showed a sensitivity of 0.94 (95% CI: 0.71, 1.00) and specificity of 0.94 (95% CI: 0.81, 0.99) for oxacillin resistance (AUC = 0.94, 95% CI: 0.87, 1.00). Whereas blaTEM/blaSHV showed higher false-positive rates for cephalosporin resistance and ErmB/ErmC showed lower sensitivity (0.6, 95% CI: 0.32, 0.84) for macrolide-lincosamide-streptogramin (MLS) resistance. Capture mNGS reported results (median turnaround time (TAT): 24.71 h (IQR 22.74-41.00)) were shorter than AST (median TAT: 73.16 h (IQR 54.19-93.42)). In a prospective cohort, the time to guide antibiotic therapy based on reported positive ARGs was significantly shorter than that based on reported resistant phenotypes from AST.<br><br>INTERPRETATION: These results highlight that ARGs can be leveraged to rapidly and accurately predict bacterial resistance phenotypes with high sensitivity and specificity, thereby guiding antibiotic management in clinical practice.<br><br>FUNDING: The National Natural Science Foundation of China, the Guangdong Science and Technology Department, Science and Technology Projects in Guangzhou.}, }
@article {pmid42235671, year = {2026}, author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y}, title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128426}, doi = {10.1016/j.envpol.2026.128426}, pmid = {42235671}, issn = {1873-6424}, abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.}, }
@article {pmid42235696, year = {2026}, author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y}, title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135059}, doi = {10.1016/j.biortech.2026.135059}, pmid = {42235696}, issn = {1873-2976}, abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.}, }
@article {pmid42235698, year = {2026}, author = {Zhou, X and Yu, Z and Liao, H and Wang, Y and Zhuang, L and Zhou, S}, title = {Bacteria and viruses associated with antibiotic resistome in hyperthermophilic co-composting of cow manure and mushroom residue.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135075}, doi = {10.1016/j.biortech.2026.135075}, pmid = {42235698}, issn = {1873-2976}, abstract = {Antibiotic resistance in livestock-derived wastes represents a critical environmental and public health concern. Here, we applied genome-resolved metagenomic analysis to characterize antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and associated viral communities during co-composting of cow manure and mushroom residue. By day 20, hyperthermophilic composting (HTC) achieved markedly higher ARG removal (93%) than conventional thermophilic composting (TC, 84%). This enhanced performance was associated with the enrichment of thermophilic taxa (e.g., Bacillaceae and Sporolactobacillaceae) and the suppression of mesophilic ARG reservoirs (e.g., Enterobacteriaceae and Pseudomonadaceae). Genome-resolved analysis further revealed that a majority of multidrug-resistant ARB were eliminated during HTC, particularly Klebsiella pneumoniae and Escherichia coli harboring diverse ARGs and virulence factor genes. These high-risk pathogens were predicted to be targeted by a subset of lytic phages, including those affiliated with Autographiviridae and Schitoviridae, suggesting a potential role of lytic phages in suppressing resistance- and virulence-associated ARB. Collectively, these findings provide genome-resolved insights into the coordinated roles of thermophile-driven suppression and phage-mediated predation of ARB in ARG removal, highlighting HTC as a promising strategy for safer manure recycling and resistance risk mitigation.}, }
@article {pmid42235960, year = {2026}, author = {Chongdar, N and Goyal, A and Damare, SR}, title = {Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70375}, pmid = {42235960}, issn = {1758-2229}, support = {DST/INSPIRE/04/2021/002518//Department of Science and Technology, Govenrnment of India/ ; }, mesh = {Phylogeny ; *Seawater/microbiology ; *Aldehyde Oxidoreductases/genetics/metabolism ; Ecosystem ; Carbon Monoxide/metabolism ; *Multienzyme Complexes/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; *Aquatic Organisms/genetics/enzymology ; Oxygen/metabolism ; Oceans and Seas ; }, abstract = {Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.}, }
@article {pmid42236101, year = {2026}, author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A}, title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e111607}, pmid = {42236101}, issn = {2044-6055}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Anticonvulsants/therapeutic use ; *Brain/physiopathology ; Diet, Ketogenic ; *Drug Resistant Epilepsy/therapy/microbiology ; *Epilepsy/therapy ; *Gastrointestinal Microbiome/physiology ; Italy ; Longitudinal Studies ; Prospective Studies ; Quality of Life ; Vagus Nerve Stimulation ; }, abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.<br><br>METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-na&#xef;ve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.<br><br>ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.}, }
@article {pmid42236489, year = {2026}, author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, LM and Yeow, C and Valentin-Alvarado, L and Adams, PD and Banfield, JF and Siegel, JB and Prywes, N and Shih, PM}, title = {Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73982-5}, pmid = {42236489}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sample and synthesize a library of diverse rubisco sequences with an emphasis on clades that are sparsely represented in the biochemical literature. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily - in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize an unusually large catalytic subunit among characterized rubiscos, originating from a early-branching subclade with secondary structural elements not present in canonical rubisco architectures.}, }
@article {pmid42236734, year = {2026}, author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L}, title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07581-w}, pmid = {42236734}, issn = {2052-4463}, support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.}, }
@article {pmid42237168, year = {2026}, author = {Hou, X and Fu, Y and Jia, Z and Hou, L and Yin, Y and Xu, K}, title = {Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42237168}, issn = {2524-4671}, support = {CARS-35//China Agriculture Research System of MOF and MARA/ ; 2023JJ20043//Natural Science Foundation of Hunan Province Project/ ; 32372913//National Natural Science Foundation of China/ ; 2023RC3204//Science and Technology Innovation Program of Hunan Province/ ; }, abstract = {Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.}, }
@article {pmid42237383, year = {2026}, author = {Zhang, J and Shi, X and Peng, S and Zhang, C and Qiao, S and Yu, H}, title = {Icariin shapes post-withdrawal fecal resistome dynamics in layer hens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42237383}, issn = {1674-9782}, support = {B2024064//Hubei Provincial Department of Education Scientific Research Project/ ; 2025RZ026//Research and Innovation Initiatives of Wuhan Polytechnic University/ ; 202409//Open Fund of Hubei Province Key Laboratory of Animal Nutrition and Feed Science/ ; 32402807//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: While the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.<br><br>RESULTS: We designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.<br><br>CONCLUSIONS: Compared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.}, }
@article {pmid42237400, year = {2026}, author = {Liu, J and Huang, W and Wu, X and Ma, Y}, title = {Coronavirus disease 2019-associated encephalitis and concomitant subdural hematoma: a case report.}, journal = {Journal of medical case reports}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13256-026-06148-y}, pmid = {42237400}, issn = {1752-1947}, support = {82171350//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a global pandemic with evolving viral variants. In addition to respiratory symptoms, a growing trend of reports indicates that the central nervous system could also be affected in COVID-19 patients.<br><br>CASE PRESENTATION: Herein, we reported a case of a 61-year-old Chinese male with fever, psychiatric symptoms, and concomitant subdural hemorrhage. Although naso-oropharyngeal swab tests for SARS-CoV-2 ribonucleic acid detections were negative, the metagenomic next-generation sequencing from cerebrospinal fluid (CSF) samples showed the exclusive positive finding of SARS-CoV-2. The patient was diagnosed with probable COVID-19-associated encephalitis, and was recovered after receiving anti-infection medications, high-dose methylprednisolone pulses (1&#xa0;g/day for 5&#xa0;days), and subsequent intravenous immunoglobulin (0.4&#xa0;g/kg body weight for 5&#xa0;days) therapies.<br><br>CONCLUSION: Our case underscores the importance that for patients with fever and unexplained neuropsychiatric symptoms, it is recommended to conduct CSF testing to screen for possible pathogen infections, and to perform cranial imaging promptly to detect concomitant lesions.}, }
@article {pmid42237409, year = {2026}, author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X}, title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02433-6}, pmid = {42237409}, issn = {2049-2618}, support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; }, abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.<br><br>RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.<br><br>CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.}, }
@article {pmid42237424, year = {2026}, author = {Yang, L and Chen, J}, title = {mPower: a real data-based power analysis tool for microbiome study design.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02427-4}, pmid = {42237424}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.}, }
@article {pmid42237575, year = {2026}, author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT}, title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwag119}, pmid = {42237575}, issn = {1476-6256}, abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.}, }
@article {pmid42237904, year = {2026}, author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH}, title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {23}, pages = {16514-16525}, doi = {10.1021/acs.est.6c01505}, pmid = {42237904}, issn = {1520-5851}, mesh = {*Microbiota ; Halogenation ; Hospitals ; Disinfection ; *Virome ; Drug Resistance, Microbial/genetics ; }, abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.}, }
@article {pmid42237982, year = {2026}, author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC}, title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e37}, pmid = {42237982}, issn = {2048-6790}, mesh = {Animals ; Female ; Pregnancy ; *Dietary Fiber/administration &amp; dosage/pharmacology ; *Cecum/microbiology ; Rats, Sprague-Dawley ; *Prebiotics/administration &amp; dosage ; Male ; *Fatty Liver/prevention &amp; control ; *Maternal Nutritional Physiological Phenomena ; Fatty Acids, Volatile/metabolism ; Rats ; *Gastrointestinal Microbiome/drug effects ; Lactation ; Weaning ; *Obesity ; Liver/metabolism ; }, abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.}, }
@article {pmid42238272, year = {2026}, author = {Gallina, G and Pizzi, C}, title = {Reference-free k-mer based dissimilarity measures for metagenomes comparison.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1788907}, pmid = {42238272}, issn = {2673-7647}, abstract = {MOTIVATION: Metagenomics plays a crucial role in unraveling the relationship between microbial communities and the environment in which they live, allowing the development of food and environmental control techniques. Similarly, the study of microbial environments within the human body plays a crucial role towards precision medicine. In these contexts, the problem of metagenomic samples comparison is among the most challenging from the computational point of view due to the size of the datasets and to the incompleteness of microbial databases. Thus, the ability to define and efficiently compute reference-free dissimilarity measures is key to the development of effective and practical tools for metagenomes comparison.<br><br>RESULTS: In this work, we present a systematic experimental validation of reference-free k -mer-based dissimilarity measures. To this purpose, we investigate the correlation between two popular ecological dissimilarity measures, Bray-Curtis and Jaccard, computed using reference-free and reference-based k -mer approaches, for 12 &#x2264; k &#x2264; 31 . Our experiments cover both simulated and real metagenomics settings (samples from the human body and the oceans), and consider both linear and ranking correlation between the computed values. Our results support the hypothesis that the two definitions are indeed correlated for a wide range of values of k , and promote the development of efficient reference-free computational tools based on k -mer statistics for metagenomes comparison.}, }
@article {pmid42238651, year = {2026}, author = {Zhang, Q and Zhang, X and Cao, M and Ma, J and Yan, R and Wang, H and Jia, S}, title = {Study on the Role and Mechanism of γδ T Cells in Atherosclerosis Under a High-Fat Diet.}, journal = {Reviews in cardiovascular medicine}, volume = {27}, number = {5}, pages = {48002}, pmid = {42238651}, issn = {2153-8174}, abstract = {BACKGROUND: This study aimed to investigate the effects of γδ T cell inhibition under a high-fat diet (HFD) on metabolic function, immune inflammation, gut microbiota, and atherosclerosis (AS) progression in ApoE [-/-] mice.<br><br>METHODS: ApoE [-/-] mice were assigned to three groups: a control group (normal diet), a model group (HFD), and an intervention group (HFD + &#x3b3;&#x3b4; T cell receptor (TCR) monoclonal antibody). After 12 weeks, flow cytometry was used to assess &#x3b3;&#x3b4; T cell levels, and cytokines (interferon-gamma (IFN-&#x3b3;), IL-17A) were measured. Inflammatory markers in blood and adipose tissue were quantified, gut microbiota composition was analyzed via fecal metagenomics, and atherosclerosis was evaluated using Oil Red O, Masson's trichrome, and hematoxylin and eosin (HE) staining methods.<br><br>RESULTS: The HFD activated &#x3b3;&#x3b4; T cells and increased pro-inflammatory cytokines in ApoE [-/-] mice. Treatment with the &#x3b3;&#x3b4; TCR monoclonal antibody suppressed &#x3b3;&#x3b4; T cells, reduced IFN-&#x3b3; and IL-17A expression, improved lipid profiles, and decreased tumor necrosis factor-alpha (TNF-&#x3b1;), IL-1&#x3b2;, and IL-6 levels. Gut microbiota analysis showed an increase in beneficial bacteria, and histological staining (Oil Red O, HE, and Masson's trichrome) confirmed a reduction in atherosclerotic lesion burden.<br><br>CONCLUSION: The &#x3b3;&#x3b4; T cells contribute to AS development under the HFD. Inhibition of &#x3b3;&#x3b4; T cells reduces inflammation, improves gut microbiota composition, and attenuates atherosclerosis progression.}, }
@article {pmid42238901, year = {2026}, author = {Zhao, T and Chen, Y and Sun, H}, title = {A case of severe Legionella pneumonia treated with omadacycline and nemonoxacin.}, journal = {Respiratory medicine case reports}, volume = {62}, number = {}, pages = {102437}, pmid = {42238901}, issn = {2213-0071}, abstract = {Severe Legionella pneumophila pneumonia carries high mortality, and treatment is challenged by emerging resistance to conventional fluoroquinolones/macrolides and diagnostic delays. Novel agents such as omadacycline and nemonoxacin show theoretical promise, yet robust clinical evidence in legionellosis is lacking. We report a 59-year-old man with severe community-acquired pneumonia(sCAP) who initially received empiric ceftazidime-avibactam plus nemonoxacin. Respiratory failure did not improve, and the inflammatory markers did not decline. Subsequent bronchoalveolar lavage fluid metagenomic next-generation sequencing(BALF-mNGS) and urinary Legionella antigen confirmed Legionella pneumonia. We then switched to dual therapy with omadacycline and nemonoxacin. The combination led to rapid improvements in inflammatory markers, hypoxemia, and creatine kinase levels. This case provides a clinical rationale for using omadacycline plus nemonoxacin as salvage therapy in severe Legionella pneumonia when conventional regimens fail.}, }
@article {pmid42239023, year = {2026}, author = {Tang, F and Liu, H and Xi, L and Li, C and Wang, X and Wang, B}, title = {Solid-phase enrichment uncovers a hidden Salmonella transmission chain in a recurrent pediatric household cluster: a case report.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1820049}, pmid = {42239023}, issn = {2296-2565}, mesh = {Humans ; Male ; Child, Preschool ; *Salmonella Infections/transmission/diagnosis/microbiology ; Feces/microbiology ; Recurrence ; *Salmonella/isolation &amp; purification ; Family Characteristics ; Metagenomics ; Shotgun Sequencing ; }, abstract = {OBJECTIVES: To describe a household cluster of recurrent pediatric non-typhoidal Salmonella (NTS) infection and compare the yield of conventional culture, solid-phase enrichment, and shotgun metagenomic sequencing across symptomatic children and household contacts.<br><br>METHODS: Longitudinal fecal specimens from a 4-year-old boy (Mo) with three discrete NTS episodes in 2 months, his monozygotic twin (TB), and three adult co-residents were processed by conventional culture; specimens from Episode 2 onwards and all contact specimens additionally received solid-phase enrichment, and a subset shotgun metagenomics. Isolates were characterized by VITEK 2, XbaI-PFGE, and whole-genome sequencing.<br><br>RESULTS: None of Mo's episodes met sepsis criteria (peak WBC 12.52 &#xd7; 10?/L, CRP 5.46 mg/L, PCT 1.14 ng/mL); TB had one self-limited episode, both parents had brief symptomatic periods, and the grandmother was asymptomatic. Conventional culture was positive only at Mo's first episode, whereas solid-phase enrichment recovered Salmonella from three culture-negative pediatric acute-phase specimens (Mo 4.12, TB 4.16, Mo 5.1). Adult contacts were negative by both culture-based methods, but metagenomic sequencing detected Salmonella reads in all three. Mo_0412 and TB_0416 were S. enterica serovar Enteritidis ST11, with identical cgMLST, 99.9966% ANI, and 97% PFGE similarity, indicating a clonal household source. Mo received antibiotics across four classes during his recurrences, vs. two sequential agents in TB.<br><br>CONCLUSION: Conventional culture, solid-phase enrichment, and metagenomic sequencing functioned as complementary modalities, each recovering Salmonella the others missed, supporting a tiered diagnostic strategy for household NTS investigation. Cumulative antibiotic exposure may have contributed to Mo's differential susceptibility, a hypothesis warranting prospective study.}, }
@article {pmid42239051, year = {2026}, author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H}, title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.727306}, pmid = {42239051}, issn = {2692-8205}, abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.}, }
@article {pmid42239166, year = {2026}, author = {Ghadermazi, P and Emerson, JB and Olm, MR}, title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239166}, issn = {2692-8205}, abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain.}, }
@article {pmid42239183, year = {2026}, author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A}, title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.21.727052}, pmid = {42239183}, issn = {2692-8205}, abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.}, }
@article {pmid42239221, year = {2026}, author = {Keown, RA and Sikkema, AP and Barbone, VA and Ferrell, BD and Donnelly, OB and Iredell, SC and Zatopek, KM and Brumm, PJ and Mead, DA and Lohman, GJS and Wommack, KE and Polson, SW}, title = {Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239221}, issn = {2692-8205}, abstract = {Viruses constitute a significant proportion of Earth's genetic diversity, yet most remain uncharacterized beyond their sequences in viral metagenomes. Linking viral genotypes to phenotypes-especially enzyme function to phage infection dynamics-is challenging due to the lack of cultured virus-host systems. DNA polymerase I (PolA), essential for genome replication in ~25% of dsDNA phages, provides an opportunity to explore these connections. In phage T7, residue 526 is critical for nucleotide incorporation, with previous in vitro evidence indicating impacts on enzyme efficiency and fidelity. Previous analyses identified three substitutions at this position (Tyr/Y, Phe/F, Leu/L) linked with deeply rooted viral PolA clades. Mutation impacts at residue 526 were tested in vitro and in vivo. The Y526F protein exhibited a 50% reduction in specific activity, and when introduced via High Complexity Golden Gate Assembly into T7 demonstrated a 53% decrease in burst size and significantly longer latent period compared to wild type. The Y526L protein exhibited a 97% decrease in activity, and the Y526L phage was incapable of completing its lifecycle. These findings confirm historical biochemical data, provide in vivo context for these mutations in the T7-E. coli system, and offer experimental support for genotype-to-phenotype associations in viral PolA, informing viral metagenomics studies.}, }
@article {pmid42239239, year = {2026}, author = {Cho, Y and Tsuboyama, K and Litberg, TJ and Jung, MD and Obisesan, A and Wang, Q and Phoumyvong, CM and Thibeault, J and Ovchinnikov, S and Rocklin, GJ}, title = {Accurate protein stability prediction for small domains using mega-scale experiments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239239}, issn = {2692-8205}, abstract = {Predicting absolute protein folding stability is a long-standing challenge in biophysics, with broad applications in protein design and in understanding genetic variation and evolution. Physics-based simulations have shown limited success at predicting stability and are often computationally intractable, and machine learning methods have been constrained by the lack of sufficiently large experimental datasets. We recently introduced cDNA display proteolysis, a cell-free approach that can measure folding stability for nearly one million protein domains in parallel. Here, we applied this method to measure stability for 1.8 million diverse protein domains 60-80 amino acids in length primarily taken from the MGnify metagenomic database and spanning over 200,000 sequence families. Using this new "MGnify Stability dataset", we developed the predictive models SaProtΔG and ESM3ΔG, which accurately predict absolute folding stability for small domains with root mean squared error of 0.8 kcal/mol over a 6 kcal/mol range (Spearman rank correlation of 0.88). These predictors show high accuracy at predicting effects of substitutions, insertions, and deletions, successfully identify global trends toward higher stability in thermophilic organisms, and improve discrimination of stable and unstable computationally designed proteins. Our results illustrate how megascale biophysical measurements can complement existing evolutionary and structural data to enable accurate absolute stability prediction for small domains.}, }
@article {pmid42239480, year = {2026}, author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR}, title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.19.726352}, pmid = {42239480}, issn = {2692-8205}, abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.<br><br>RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .<br><br>CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.}, }
@article {pmid42239539, year = {2026}, author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L}, title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765801}, pmid = {42239539}, issn = {2235-2988}, mesh = {Humans ; Female ; Metagenomics ; Infant ; *Infectious Disease Transmission, Vertical ; *Microbiota/genetics ; *Genomic Structural Variation ; *Bacteria/genetics/classification ; Infant, Newborn ; Metagenome ; Mothers ; Longitudinal Studies ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.<br><br>METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.<br><br>RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.<br><br>DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.}, }
@article {pmid42239987, year = {2026}, author = {Zhao, C and Zhang, L and Wang, Y and Yang, G and Ren, C and Cao, X and Yu, Q and Jin, B and Men, Y and Liu, H and Zhang, J}, title = {Microbial Dehalogenation of 3,5,6-Trichlorooctafluorohexanoic Acid under Different Reducing Conditions.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {23}, pages = {16805-16817}, doi = {10.1021/acs.est.5c17496}, pmid = {42239987}, issn = {1520-5851}, mesh = {Halogenation ; Fluorocarbons ; Biodegradation, Environmental ; *Caproates/metabolism ; }, abstract = {Chlorinated polyfluoroalkyl substances (Cl-PFAS) have emerged as promising alternatives to legacy PFAS due to their enhanced microbial reactivity and improved environmental degradability. However, their transformation mechanisms under environmentally relevant reducing conditions remain poorly characterized. This study investigated the microbial dehalogenation of 3,5,6-trichlorooctafluorohexanoic acid (CTFE3), a representative Cl-PFAS, under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Microbial defluorination was observed across all reducing environments, with higher total defluorination efficiencies (∼60%) under nitrate- and sulfate-reducing conditions compared to iron-reducing and methanogenic conditions (∼30%) under the tested experimental conditions. Proposed biotransformation pathway analysis suggested that CTFE3 underwent more diverse and sequential hydrolytic dechlorination under nitrate- and sulfate-reducing conditions, which was associated with more extensive defluorination. Genes associated with hydrolytic dechlorination were consistently enriched under these conditions, but not in iron-reducing or methanogenic environments. Metagenomic binning further identified key taxa (e.g., Methyloversatilis discipulorum, Herbaspirillum seropedicae, Paracoccaceae, and Rhodobacteraceae-related bacteria) harboring both hydrolytic dechlorination and nitrate/sulfate-reduction genes, suggesting their involvement in CTFE3 hydrolytic dechlorination and subsequent defluorination. This study demonstrates that reducing conditions play an important role in shaping CTFE3 transformation patterns and highlight hydrolytic dechlorination as a viable pathway associated with extensive microbial defluorination, thereby offering insights for sustainable Cl-PFAS remediation.}, }
@article {pmid42240391, year = {2026}, author = {de Sousa, LP and Calderon Fajardo, AA and Brandão, MM and Maia de Oliveira, V and Romero, GQ}, title = {Metagenome-assembled genomes of four novel bacterial species from Atlantic rainforest stream sediments in Brazil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0033626}, doi = {10.1128/mra.00336-26}, pmid = {42240391}, issn = {2576-098X}, abstract = {Here, we report draft genome sequences of four novel bacterial species from Atlantic rainforest stream sediments in southeastern Brazil. The genomes represent distinct lineages within Nitrospirota and Pseudomonadota (average nucleotide identity <95% to known species) and encode diverse metabolic capabilities, including nitrification, denitrification, and aromatic compound degradation.}, }
@article {pmid42240519, year = {2026}, author = {Gharbi, M and Abbassi, MS}, title = {Bacteria as anticancer agents: bioactive metabolites, engineered platforms, and translational mechanisms.}, journal = {Letters in applied microbiology}, volume = {79}, number = {6}, pages = {}, doi = {10.1093/lambio/ovag050}, pmid = {42240519}, issn = {1472-765X}, mesh = {*Antineoplastic Agents/pharmacology/metabolism/chemistry ; Humans ; *Bacteria/metabolism/genetics/chemistry ; *Biological Products/pharmacology/metabolism ; *Neoplasms/drug therapy ; Drug Discovery ; Animals ; }, abstract = {Bacteria represent a vast and underexplored reservoir of bioactive compounds with significant anticancer potential. Numerous bacterial taxa, particularly actinomycetes, Bacillus, Pseudomonas, and marine-derived species, produce structurally diverse metabolites exhibiting cytotoxic, cytostatic, pro-apoptotic, immunomodulatory, and anti-angiogenic activities against cancer cells. Clinically established agents such as actinomycin D and bleomycin highlight the therapeutic relevance of bacterial natural products, while recent discoveries continue to expand the repertoire of bioactive polyketides, peptides, alkaloids, and proteins. These compounds act through multiple mechanisms, including DNA intercalation, induction of apoptosis, cell cycle arrest, metabolic disruption, and modulation of the tumor microenvironment. Advances in metagenomics, genome mining, and synthetic biology have enabled the identification and activation of previously silent biosynthetic gene clusters, significantly enhancing drug discovery potential. In addition to metabolite-based anticancer agents, advances in synthetic biology have enabled the development of engineered bacterial platforms capable of selectively colonizing tumors, delivering therapeutic molecules, and activating prodrug therapies within the tumor microenvironment. Despite ongoing challenges related to toxicity, limited yield, selectivity, and clinical translation, bacterial-derived compounds remain a promising frontier in oncology. This review summarizes bacterial sources, bioactive metabolites, molecular mechanisms, preclinical and clinical applications, and future prospects for developing effective and safe anticancer strategies.}, }
@article {pmid42240631, year = {2026}, author = {Hernández-Velázquez, R and Hernández-Avilés, JS}, title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {6}, pages = {}, pmid = {42240631}, issn = {1465-2080}, mesh = {*Lakes/microbiology/chemistry ; Metagenomics ; Mexico ; *Metagenome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Sulfur/metabolism ; Tropical Climate ; Carbon/metabolism ; Phylogeny ; Biodiversity ; Nitrogen/metabolism ; }, abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.}, }
@article {pmid42241759, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R}, title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107151}, pmid = {42241759}, issn = {1525-3171}, abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.}, }
@article {pmid42241815, year = {2026}, author = {Zhang, S and Liu, X and Cheng, R and Huang, C and Zhang, Z and Long, S and Yang, Q}, title = {Elucidating the Feammox nitrogen transformation pathway: Key intermediates and putative multi-species metabolic cooperation in a long-term Feammox-dominant system.}, journal = {Water research}, volume = {303}, number = {}, pages = {126223}, doi = {10.1016/j.watres.2026.126223}, pmid = {42241815}, issn = {1879-2448}, abstract = {The emerging Fe(Ⅲ) reduction coupled to anaerobic ammonia oxidation (Feammox) process offers a promising approach toward carbon neutrality in wastewater treatment. However, its nitrogen transformation pathway and metabolic mechanism remain unclear. This study established a Feammox-dominant sequencing batch reactor (Fe-SBR) and operated it for 515 days, achieving an ammonia removal efficiency of 97.9 ± 4.5% during the stable phase. Feammox was confirmed as the dominant process for NH4[+]-N conversion, accounting for 83.2% of ammonia transformation. NH2OH, NO, and N2O were identified as key intermediates in the Feammox nitrogen transformation pathway. By integrating metagenomic analysis of functional gene dynamics with metagenome-assembled genomes (MAGs), a potential coupled iron-nitrogen (Fe-N) metabolic pathway was proposed. This pathway suggested that the Feammox process might be accomplished through multi-species metabolic cooperation, with MtrC-mediated extracellular electron transfer potentially serving as the key link coupling nitrogen transformation to the iron redox cycle. These findings provide novel insights into the Feammox metabolic pathway and lay a theoretical foundation for the future precise control and optimization of this process.}, }
@article {pmid42241861, year = {2026}, author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L}, title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130128}, doi = {10.1016/j.jenvman.2026.130128}, pmid = {42241861}, issn = {1095-8630}, mesh = {Animals ; *Aquaculture ; *Nitrogen/metabolism ; Anti-Bacterial Agents ; *Probiotics ; Metagenomics ; China ; Microbiota ; Penaeidae ; }, abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.}, }
@article {pmid42241983, year = {2026}, author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M}, title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {459}, number = {}, pages = {111881}, doi = {10.1016/j.ijfoodmicro.2026.111881}, pmid = {42241983}, issn = {1879-3460}, abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.}, }
@article {pmid42242027, year = {2026}, author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M}, title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128569}, doi = {10.1016/j.micres.2026.128569}, pmid = {42242027}, issn = {1618-0623}, mesh = {Animals ; Male ; Mice ; *Bifidobacterium longum/physiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; *Fatty Liver/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function ; Liver/metabolism/pathology ; *Metabolic Diseases ; *Metabolome ; Metagenomics ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration &amp; dosage ; }, abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.}, }
@article {pmid42242076, year = {2026}, author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG}, title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142602}, doi = {10.1016/j.jhazmat.2026.142602}, pmid = {42242076}, issn = {1873-3336}, abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.}, }
@article {pmid42242079, year = {2026}, author = {Yang, F and Zhang, M and Tan, Y and Yuan, Z and Liu, W and Wu, Y and Li, F}, title = {Alkaline woody peat shifts CO2 emissions to CH4 by modulating microbial cross-feeding in Cd-contaminated paddy soil.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142498}, doi = {10.1016/j.jhazmat.2026.142498}, pmid = {42242079}, issn = {1873-3336}, abstract = {Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO2-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO2 (e.g., aceE), suggesting a reduced capacity for CO2 generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.}, }
@article {pmid42242448, year = {2026}, author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F}, title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.06.001}, pmid = {42242448}, issn = {1995-820X}, abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.}, }
@article {pmid42242497, year = {2026}, author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and ,  and Segre, JA and Sereti, I and Kong, HH}, title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.019}, pmid = {42242497}, issn = {1523-1747}, abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.}, }
@article {pmid42243106, year = {2026}, author = {Lee, M and Kim, D and Song, JH and Park, SJ and Chang, JY}, title = {Efficacy of Lactococcus lactis WiKim0124 in Fat-, Sucrose-, and Fat/Sucrose-Induced Obesity Models.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00915-3}, pmid = {42243106}, issn = {2396-8370}, support = {KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; }, abstract = {Lactococcus lactis WiKim0124 (WiKim0124), a probiotic strain isolated from kimchi, has previously shown anti-obesity effects in high-fat diet (HFD) models. This study investigated whether WiKim0124 and its formulated version, SW01, exert consistent anti-obesity efficacy across distinct diet-induced obesity models through modulation of host lipid metabolism and gut microbial function. In 3T3-L1 adipocytes and FFA-treated HepG2 cells, both treatments inhibited lipid accumulation and modulated lipid metabolism-related markers, indicating enhanced fatty acid oxidation and reduced lipogenesis. In C57BL/6 J mice fed HFD, high-sucrose (HSuc), or HFD + HSuc diets, daily oral administration of WiKim0124 or SW01 significantly reduced body weight gain, adipose tissue mass, and hepatic lipid accumulation. WiKim0124 and SW01 significantly enhanced fatty acid oxidation pathways, as evidenced by increased expression of the markers PPARα, CPT-1α, and UCP2. Gut microbiota analysis showed increased Bacteroidetes and enrichment of Akkermansia muciniphila in treated groups. Shotgun metagenomic functional profiling revealed enhanced short-chain fatty acid-related pathways and enzymes, with distinct patterns depending on treatment and dietary stressors. Microbial functional responses were most pronounced in the HFD + HSuc model, supporting a diet-dependent mode of probiotic action. Together, these findings demonstrate consistent anti-obesity efficacy of WiKim0124 and support the translational potential of its formulated application through integrated modulation of host metabolism and gut microbial function.}, }
@article {pmid42243452, year = {2026}, author = {Das, R and Medhi, MC and Tamang, B}, title = {Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02062-0}, pmid = {42243452}, issn = {2191-0855}, abstract = {Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.}, }
@article {pmid42243513, year = {2026}, author = {Yi, J and Zhao, Y and Li, Z and Chen, A and Tang, Z and Zheng, L and Ge, H and Yu, Q and Liu, W and Xiang, J and Tang, J}, title = {M.globosa promotes lung cancer progression and M2 macrophage polarization through oxidative phosphorylation.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01528-5}, pmid = {42243513}, issn = {2397-768X}, support = {2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2403084//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; }, abstract = {The lungs are colonized by a variety of microbes which play a significant role in lung cancer progression. In this study, we conducted an in-depth analysis of metagenomic sequencing data obtained from alveolar lavage fluid (ALF) samples of patients with non-small-cell lung cancer (NSCLC) at different clinical stages. The nested qPCR was used to validate the abundance of key fungi and establish a correlation between fungi abundance and patient prognosis. We found that elevated levels of M.globosa correlated with patients at stage1B-3 and worse prognosis. M.globosa enhanced the proliferation of lung cancer cells and promoted tumor growth in vivo by promoting M2-like macrophage polarization, which was primarily driven by oxidative phosphorylation (OXPHOS) activation. The inhibition of OXPHOS in tumor-bearing mice using metformin significantly retarded the tumor growth induced by M. globosa. Together, our clinical observations and experimental findings suggest that intracellular M. globosa infection may contribute to lung cancer progression through immunometabolic remodeling of macrophages.}, }
@article {pmid42243631, year = {2026}, author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW}, title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocag088}, pmid = {42243631}, issn = {1527-974X}, support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; }, abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.<br><br>MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.<br><br>RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.<br><br>DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.<br><br>CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.}, }
@article {pmid42243719, year = {2026}, author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS}, title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09123-3}, pmid = {42243719}, issn = {1471-2229}, support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; }, abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.<br><br>RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.<br><br>CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).}, }
@article {pmid42243998, year = {2026}, author = {Li, S and Sun, Y and Tong, X and Zhang, Z and Ma, X and Li, D and Min, L}, title = {Near-complete inhibition of rumen methanogenesis via microbial and enzymatic modulation using a low dose of Asparagopsis taxiformis combined with 3-nitrooxypropanol.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42243998}, issn = {1674-9782}, support = {SKXRC2025487//Youth S&amp;T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 2024CXTD13//Guangdong Modern Agro-industry Technology Research System/ ; 202408440440//China Scholarship Council/ ; NYQS202613//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; 2026A1515010802//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) from ruminants represents a major contributor to agricultural greenhouse gas emissions. The red seaweed Asparagopsis taxiformis (A. taxiformis) is a highly effective CH4 emission inhibitor, but its large-scale application is restricted by limited biomass availability. This study evaluated whether reducing the inclusion level of A. taxiformis (0.32% dry matter, DM) combined with 3-nitrooxypropanol (3-NOP; 0.05% DM) could maintain a high inhibitory efficacy, and elucidated the underlying microbial mechanisms through in vitro fermentation and metagenomics analysis.<br><br>RESULTS: The combined treatment decreased CH4 production by 98.21% (P&#x2009;<&#x2009;0.01) without impairing DM degradation, and markedly shifted rumen fermentation towards propionate, lowering the acetate-to-propionate ratio (1.59 vs. 2.65; P&#x2009;<&#x2009;0.01). Metagenomic profiling revealed substantial reductions in the abundance of Methanobrevibacter and Ruminococcus, along with increased levels of propionate-associated bacteria such as Prevotella, Treponema, Eubacterium, and Selenomonas (P&#x2009;<&#x2009;0.01). Functionally, the combined treatment downregulated key enzymes in hydrogenotrophic and methylotrophic methanogenesis, including methyl-coenzyme M reductase (EC:2.8.4.1) and tetrahydromethanopterin S-methyltransferase (EC:2.1.1.86), thereby blocking terminal methanogenic steps.<br><br>CONCLUSIONS: Collectively, these results demonstrate that co-supplementation with A. taxiformis and 3-NOP achieves near-complete methanogenesis inhibition at drastically reduced seaweed dosage through coordinated changes in fermentation patterns, microbial community structure, and methanogenic enzymatic pathways. This approach provides a practical strategy to overcome biomass limitations of A. taxiformis and warrants validation in long-term in vivo trials.}, }
@article {pmid42244002, year = {2026}, author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ}, title = {A diverse gut virome in natural populations of Drosophila melanogaster.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42244002}, issn = {2524-4671}, abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.<br><br>RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.<br><br>CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.}, }
@article {pmid42244030, year = {2026}, author = {Wang, Y and Zhang, Y and Feng, L and Han, Q and Yu, Q and Li, H}, title = {Host Ecology Shapes Gut Pathogen Evolution: An Eco-Evolutionary Trade-Off in Plateau Wildlife.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70344}, doi = {10.1111/1462-2920.70344}, pmid = {42244030}, issn = {1462-2920}, support = {32471575//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Lagomorpha/microbiology ; *Host-Pathogen Interactions ; *Biological Evolution ; Virulence Factors/genetics ; *Gastrointestinal Tract/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Animals, Wild/microbiology ; Ecosystem ; }, abstract = {The intestinal tracts of plateau wildlife function as crucial reservoirs for diverse pathogens. However, the mechanisms through which host ecology influences pathogen community assembly and their interactions remain unclear. By comparing the subterranean-living plateau zokor (Eospalax baileyi) with the aboveground plateau pika (Ochotona curzoniae) across a two-and-a-half-year study, this work provides evidence that the distribution and transmission dynamics of pathogens, virulence factor genes (VFGs), and pathogen-host interaction (PHI) genes are determined by animals' distinct niches. The results demonstrate a clear eco-evolutionary trade-off: the plateau zokor, inhabiting stable yet pathogen-enriched burrow systems, exhibited higher abundances of pathogens, VFGs, and PHI genes in its gut, and formed complex co-occurrence networks. In contrast, the plateau pika, under diverse environmental exposure, possessed higher pathogen and gene diversity but lower overall abundance, alongside simpler interaction networks indicative of opportunistic colonization. Metagenomic binning indicated a close association among VFGs, PHI genes, and mobile genetic elements (MGEs), pointing to their possible joint transfer. Additionally, animal weight and precipitation were identified as key drivers of pathogen dynamics. These findings indicate that the gut sits at the crossroads of animal and environmental health, highlighting how host-mediated pathogen evolution across distinct niches shapes the broader One Health dynamics of the plateau ecosystem.}, }
@article {pmid42244179, year = {2026}, author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H}, title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71330}, pmid = {42244179}, issn = {1469-8137}, support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; }, abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.}, }
@article {pmid42244577, year = {2026}, author = {Ettinger, CL and Eisen, JA}, title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.28.596327}, pmid = {42244577}, issn = {2692-8205}, abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.}, }
@article {pmid42244712, year = {2026}, author = {Iranzo, J and Wolf, YI and Koonin, EV}, title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.25.727639}, pmid = {42244712}, issn = {2692-8205}, abstract = {BACKGROUND: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome?<br><br>RESULTS: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors.<br><br>CONCLUSIONS: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.}, }
@article {pmid42244725, year = {2026}, author = {Steinberger, AJ and Nickodem, CA and Leite de Campos, J and Kates, AE and Goldberg, TL and Safdar, N and Sethi, AK and Shutske, JM and Ruegg, PL and Suen, G and Hite, JL}, title = {Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.726633}, pmid = {42244725}, issn = {2692-8205}, abstract = {Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, β-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.}, }
@article {pmid42244773, year = {2026}, author = {Espinoza, JL and Dupont, CL and Phillips, A}, title = {Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.07.14.664802}, pmid = {42244773}, issn = {2692-8205}, abstract = {Functional profiling of metagenomes and metatranscriptomes is essential for understanding microbial community capabilities, yet current methods require computationally expensive translated-search alignments that scale poorly to the large genome-resolved reference databases now common in the field. We introduce Leviathan, an open-source software package for integrated taxonomic and functional profiling that operates at both genome and pangenome resolution. Leviathan combines Sylph for ultra fast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against genome-resolved gene catalogs, bypassing the translated-search step that dominates runtime in existing approaches. For each (pan)genome, Leviathan functional profiling produces dual metrics: pathway abundance from aggregated gene-level quantification and pathway coverage from graph-based assessment of enzymatic step completeness. On CAMI-I and CAMI-II datasets, Leviathan achieved up to 74-fold faster runtimes and 14-fold lower memory usage compared to HUMAnN, while improving genome-level assignment accuracy by up to 12% and pangenome-level accuracy by up to 5%. We demonstrate Leviathan's applicability through two case studies: a marine plastisphere metagenomics dataset where differential coverage analysis revealed metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where pangenome-resolved co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.}, }
@article {pmid42245494, year = {2026}, author = {Hu, Z and Chen, C}, title = {Revealing gut microbiota profiles and their influencing factors in commercial boars of three breeds by a large-scale metagenome study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825304}, pmid = {42245494}, issn = {1664-302X}, abstract = {Boars play a critical role in pig production. Numerous studies have reported important effects of the gut microbiota on pig production traits. However, whether the gut microbiota is associated with reproduction traits in boars remains largely unknown. Understanding the gut microbial composition and its influencing factors in large-scale boar populations is an essential first step to investigate this association. In this study, shotgun metagenomic sequencing was performed on fecal samples of 1,651 commercial boars from three breeds raised in three pig farms to uncover their gut microbial structures. We observed significant differences in boar gut microbial compositions across three breeds, even when raised in the same farm. Permutational multivariate analysis of variance (PERMANOVA) within-farm breeds and with-age stages found that the effect size of each factor on boar gut microbial composition varied across farms and age stages. Breeds accounted for 2% ~ 9% of the variance of boar gut microbial compositions in different farms. We then identified gut microbial taxa enriched in each boar breed using MaAsLin2. Lactic acid and butyrate-producing taxa, such as Lactobacillus amylovorus and Faecalibacterium prausnitzii, were enriched in Duroc boars; Akkermansia muciniphila and Lactobacillus reuteri showed the enrichment in Landrace boars, accompanied by increased relative abundance of Enterobacteriaceae members. Meanwhile, the species from Bacteroides, Prevotella, and Treponema had higher abundances in the gut of Large White pigs than in the other two pig breeds. We also identified bacterial species enriched in each of the three age stages. These breed and age-associated microbial enrichment patterns might reflect the combined effects of long-term genetic selection of pig breeds, age, and differences in feeding diets. The results of this study provide important insights for further investigating the effects of gut microbiota on boar reproductive traits and for developing strategies to modulate the gut microbiota to improve boar health and production performance.}, }
@article {pmid42245495, year = {2026}, author = {Kuźniar, A and Das, AP and Goraj, W}, title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820854}, doi = {10.3389/fmicb.2026.1820854}, pmid = {42245495}, issn = {1664-302X}, }
@article {pmid42245502, year = {2026}, author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M}, title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825173}, pmid = {42245502}, issn = {1664-302X}, abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.}, }
@article {pmid42245511, year = {2026}, author = {Otto, SJG and McLeod, L and McCarthy, EL and Funk, T and Lacoste, SR and Chai, Z and Links, MG and Barlow, LD and Gow, SP and Ramsay, D and Zaheer, R and McAllister, TA and Stothard, P and Hill, JE and Waldner, CL}, title = {Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1806062}, pmid = {42245511}, issn = {1664-302X}, abstract = {INTRODUCTION: The risk to humans and animals from antimicrobial resistance (AMR) has increased the emphasis on antimicrobial stewardship in food animal agriculture. Current stewardship recommendations include increasing diagnostic laboratory testing to inform antimicrobial use for bovine respiratory disease (BRD) management in beef feedlot production, yet the performance of newer molecular and sequencing-based diagnostic tests in commercial settings remains poorly characterized.<br><br>METHODS: Using nasopharyngeal swabs collected from commercial feedlot calves as part of Canadian surveillance, this study evaluated diagnostic laboratory testing approaches for detecting key bacterial BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasmopsis bovis) and associated AMR genes. Bayesian latent class models (BLCMs) were applied to compare traditional culture and antimicrobial susceptibility testing (AST) or qPCR with long-read metagenomic sequencing and recombinase polymerase amplification (RPA). Differences in detection of target bacteria and phenotypic or genotypic AMR were assessed across the early feeding period and between age cohorts.<br><br>RESULTS: This represents the first large-scale field evaluation of a recently developed, long-read metagenomic sequencing protocol implemented by a commercial laboratory for detecting BRD bacteria and AMR in respiratory samples (n = 760) collected by private veterinarians from western Canadian beef feedlots. Detection patterns for BRD bacteria and AMR using culture/AST and metagenomics were often similar between fall-placed calves and yearlings, but with differences from RPA. Detection of BRD bacteria had low sensitivity (< 65% for most organisms/tests), but higher specificity (>90% for all organisms/tests). Detection of macrolide and tetracycline resistance had low but variable sensitivity, with higher estimates for AST compared to metagenomics and RPA, and higher but variable specificity (>90% for most resistance outcomes/tests). Despite not using any targeted enrichment, metagenomic sequencing detected M. bovis although with a sensitivity lower than qPCR or RPA. Estimates of predictive value were most informative across the largest range of prevalence for AST, followed by metagenomics and then RPA.<br><br>DISCUSSION: This work demonstrates the potential for large scale implementation of long-read metagenomic sequencing to support antimicrobial stewardship and AMR surveillance for feedlot cattle. The estimates of clinical diagnostic performance and predictive values provide evidence-based guidance for three different laboratory tests for BRD management.}, }
@article {pmid42245748, year = {2026}, author = {Li, JZ and Guan, SY and Zhang, JF and Zheng, JN}, title = {Acute Q Fever in an Elderly Traveler with Multiple Comorbidities Diagnosed by Blood mNGS and Resolved with Omadacycline.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {610202}, pmid = {42245748}, issn = {1178-6973}, abstract = {This article reports a case of acute Q fever in a 61-year-old man. The patient mainly presented with high fever and cough. Extensive multi-system investigations failed to identify an etiology. On the fourth day of admission, the diagnosis of acute Q fever was confirmed by rapid detection of Coxiella burnetii nucleic acid sequence by blood metagenomic Next-Generation Sequencing (mNGS). With the treatment of intravenous omadacycline, the fever was controlled within 24 hours and the clinical symptoms significantly improved. Subsequent sequential therapy with oral doxycycline was administered, and the patient was discharged successfully. This case highlights the value of mNGS in the rapid diagnosis of rare or zoonotic pathogens in patients with fever of unknown origin, especially in patients with potential exposure to endemic areas. Furthermore, the novel tetracycline antibiotic omadacycline, demonstrating favorable efficacy and safety despite the patient's liver dysfunction, offers a valuable treatment option for rapid control of acute Q fever symptoms, especially in severe cases or those intolerant to doxycycline.}, }
@article {pmid42245929, year = {2026}, author = {Yan, W and Wang, X and Shi, K and Wang, L}, title = {Atypical Legionella pneumophila encephalopathy lacking respiratory symptoms and radiographic lesions: A Case Report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1828042}, pmid = {42245929}, issn = {2296-858X}, abstract = {This report details an unusual case of Legionella pneumophila encephalopathy in a 29-year-old male who presented with acute altered consciousness and extreme agitation, notably lacking any respiratory symptoms or typical meningeal signs. Extensive imaging, including chest CT and cranial MRI, revealed no pulmonary infiltrates or structural brain lesions. Cerebrospinal fluid (CSF) analysis demonstrated an aseptic profile with elevated protein, and CSF metagenomic sequencing returned negative. The diagnostic dilemma was ultimately resolved using whole-blood targeted next-generation sequencing (tNGS), which detected Legionella sequences. The patient achieved a rapid and complete neurological recovery following a combined regimen of levofloxacin and high-dose glucocorticoids. This case underscores that Legionella infection can manifest as an isolated, toxin- and immune-mediated encephalopathy without preceding clinical pneumonia. It highlights the critical rescue value of early molecular screening (such as tNGS) in unexplained encephalopathy and supports the judicious use of early steroid intervention to halt the aseptic neurotoxic cascade.}, }
@article {pmid42246002, year = {2026}, author = {Ren, JM and Zhang, XY and Liu, XP and Pei, LH and Jiang, WP and Zhang, XM and Ding, H and Huang, JS}, title = {Specimen-specific differences in clinical metagenomic sequencing reporting patterns in hospitalized patients: a single-center retrospective observational study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823283}, pmid = {42246002}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Hospitalization ; Male ; Female ; Cerebrospinal Fluid/microbiology ; }, abstract = {Clinical metagenomic next-generation sequencing (mNGS) is increasingly used in hospitalized patients, but finalized reporting patterns vary across specimen types in routine practice. We conducted a single-center retrospective observational study using routine clinical mNGS data from January 1, 2024, to December 31, 2025. A specimen-specific first-order design retained only the first eligible mNGS order per patient within each specimen category during the study window. Orders were grouped as bronchoalveolar lavage fluid (BALF), blood, cerebrospinal fluid (CSF), and tissue for primary comparisons; heterogeneous "Other" specimens were described separately. The primary endpoint was report-interpreted any-positive at the order level. We summarized specimen-specific report-interpreted positivity, pathogen-group detection, the most frequently reported organisms ranked by order-level report presence, and mixed detections among positive orders. ICU-associated analyses were included as contextual descriptive stratification only. The cohort included DNA-only orders and a subset of PMseq-RNA-tested orders; RNA virus analyses were restricted to PMseq-RNA-tested orders, and DNA-only orders were treated as not tested for RNA virus fields. Among 1, 981 included specimen-specific first orders, BALF accounted for 973, blood 473, CSF 240, and tissue 122. Report-interpreted any-positive differed by specimen type, with BALF highest (876/973, 90.0%; 95% CI, 88.0-91.8%), followed by tissue (95/122, 77.9%; 95% CI, 69.7-84.3%), blood (343/473, 72.5%; 95% CI, 68.3-76.3%), and CSF (63/240, 26.2%; 95% CI, 21.1-32.2%). Among positive orders, at least 2 distinct standardized pathogens were reported in 672/876 BALF orders (76.7%), 182/343 blood orders (53.1%), 39/95 tissue orders (41.1%), and 8/63 CSF orders (12.7%). Across the four primary specimen groups, the most frequently reported organisms included Epstein-Barr virus (n = 485), Candida albicans (n = 285), and cytomegalovirus (n = 262), together with Klebsiella pneumoniae and Acinetobacter baumannii; these rankings reflect report-level frequency rather than adjudicated pathogenic roles, particularly for latency- or reactivation-prone viruses. Of included orders, 277 (14.0%) underwent PMseq-RNA testing. These findings characterize specimen-specific differences in clinical mNGS reporting patterns and provide a specimen-context-aware reference for interpreting routine inpatient reports.}, }
@article {pmid42246191, year = {2026}, author = {Das, D and Dixit, R and Pandey, M}, title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70462}, pmid = {42246191}, issn = {1440-1746}, abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.<br><br>METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.<br><br>RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7&#x3b1;-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.<br><br>CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.}, }
@article {pmid42247317, year = {2026}, author = {Zeng, Y and Wang, S and Zhang, Q and Miao, H and Xu, J and Li, W}, title = {Successful management of Legionella pneumonia in an immunocompromised infant presenting with generalized pustular rash: A case report.}, journal = {Science progress}, volume = {109}, number = {2}, pages = {368504261458101}, pmid = {42247317}, issn = {2047-7163}, mesh = {Humans ; Male ; *Immunocompromised Host ; Infant ; *Exanthema/drug therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; *Legionnaires' Disease/drug therapy/immunology/microbiology ; *Legionella/drug effects ; }, abstract = {Legionella infection is rare in children, and extrapulmonary manifestations are even less commonly reported. Cutaneous involvement, particularly in the form of generalized pustular eruptions, may present significant diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a male infant under 6 months with X-linked severe combined immunodeficiency (XL-SCID) who presented with a disseminated pustular rash as the predominant clinical feature. Initial blood and pus cultures were negative, and empirical antimicrobial therapy showed limited clinical response. Metagenomic next-generation sequencing (mNGS) was subsequently performed and identified Legionella as the causative pathogen. Based on this finding, the antimicrobial regimen was adjusted to include a macrolide antibiotic combined with trimethoprim-sulfamethoxazole (TMP-SMX), resulting in significant clinical improvement and eventual recovery. This case highlights the atypical presentation of Legionella infection with predominant cutaneous manifestations in children, particularly in the context of primary immunodeficiency, and underscores the diagnostic value of mNGS in cases with inconclusive conventional testing. Early application of advanced molecular diagnostics and timely optimization of targeted antimicrobial therapy are crucial for improving outcomes in rare and complex pediatric infections.}, }
@article {pmid42247440, year = {2026}, author = {Levade, I and Delisle, B and Fournier, &#xc9; and Therrien, C}, title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350663}, pmid = {42247440}, issn = {1932-6203}, mesh = {Animals ; Quebec ; *Metagenomics/methods ; Phylogeny ; *Culicidae/virology ; *Virome/genetics ; Genome, Viral ; Mosquito-Borne Diseases ; *Mosquito Vectors/virology ; *RNA, Viral/genetics ; Arboviruses/genetics/classification ; }, abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.}, }
@article {pmid42247515, year = {2026}, author = {Piñero, M and Librado, P}, title = {Genomic evidence for limited entomophagy in ancient Europeans.}, journal = {Science advances}, volume = {12}, number = {23}, pages = {eaec6939}, pmid = {42247515}, issn = {2375-2548}, mesh = {Animals ; Humans ; *Chitinases/genetics ; *DNA, Ancient/analysis ; Europe ; *European People/genetics/history ; *Insecta/classification/genetics ; Metagenomics ; *Diet/history ; History, Ancient ; }, abstract = {To meet the rising food demands of our growing population, the Food and Agriculture Organization proposed edible insects as sustainable sources of animal protein. Although hundreds of million people already consume insects around the tropics, western societies remain averse to entomophagy. To trace whether ancient Europeans consumed insects, we here apply two complementary genomic approaches. Metagenomic screening on 745 ancient anatomically modern human dental calculus returned limited insect DNA traces, with read abundances well below those observed in Neanderthals, western chimpanzees, and gorillas. In addition, genes encoding stomach-expressed chitinases show two of the most significant signatures of latitudinal differentiation genome-wide. Clines are consistent with evolutionary benefits of entomophagy in tropical regions and with expression quantitative trait locus data supporting low chitin digestibility in present-day Europeans. Ancient genomes confirm that both clines already existed at the onset of agriculture and persisted despite massive migrations. Together, our findings support occasional and possibly incidental insect consumption in Europe over the past ~9000 years.}, }
@article {pmid42247592, year = {2026}, author = {Boulay, A and Németh, V and Criel, B and Stock, M and De Baets, B and Galiez, C and Rousseau, E and Briers, Y and Vázquez, R}, title = {PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42247592}, issn = {1758-0463}, support = {#325947//FRQNT/ ; //NSERC/ ; 1S91526N//FWO/ ; 1S38519N//FWO/ ; #307935//FRQS/ ; 01P10022//BOF/ ; }, mesh = {*Bacteriophages/genetics/enzymology ; *Metagenomics/methods ; *Viral Proteins/genetics ; *Databases, Protein ; *Software ; *Metagenome ; }, abstract = {As biology becomes increasingly data-driven, so does the field of phage lysins, enzymes that degrade bacterial cell walls and offer promising alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for Phage Lytic Protein sequences and associated metadata to support global research efforts. Here, we present PhaLP 2.0, an enhanced database designed to address key challenges in computational lysin research by integrating newly identified lysins from thousands of metagenomes. To expand the known diversity of lysins beyond that of cultured phages, we developed SUBLYME, a protein-embedding-based machine-learning Software designed to Uncover and classify Bacteriophage Lysins from Metagenomic datasets. Using embeddings derived from the well-curated sequences of the original PhaLP database, we trained support vector machines to distinguish lysins from non-lysins in viromes and classify them as endolysins or virion-associated lysins. The models achieved an average F1 score of 98% on held-out clusters. SUBLYME enabled the discovery of 743 000 new lysin sequences from EnVhogDB, a virome-derived protein database, increasing the number of known lysin clusters 40-fold, from 1000 to 40 000. SUBLYME and PhaLP 2.0 are accessible online at https://github.com/Rousseau-Team/sublyme and https://phalp.ugent.be, respectively. Together, these advances establish PhaLP 2.0 as a comprehensive and scalable portal for lysin discovery, classification, and sequence analysis, paving the way for future antibacterial applications and evolutionary insights.}, }
@article {pmid42247807, year = {2026}, author = {Sadia, H and Amin, A and Khalid, N and Ahmed, I}, title = {Antimicrobial resistance and virulence in polymicrobial chronic wound infections: A metagenomic perspective.}, journal = {Journal of infection and public health}, volume = {19}, number = {8}, pages = {103280}, doi = {10.1016/j.jiph.2026.103280}, pmid = {42247807}, issn = {1876-035X}, abstract = {BACKGROUND: Chronic wound infections represent a significant clinical and public health challenge due to their polymicrobial nature and the increasing burden of antimicrobial resistance (AMR). Conventional culture-based diagnostics often fail to capture the full microbial diversity and resistance potential associated with these infections.<br><br>METHODS: Chronic wound samples persisting for more than 15 days were collected from patients at a tertiary-care hospital in Pakistan. Samples are categorized into five groups: lower leg (ll-H1), upper leg (ul-H2), foot (ft-H3), chest (ct-H4) and catheter (ca-H5). Shotgun metagenomic sequencing was employed alongside routine culture-based methods to characterize microbial communities, antimicrobial resistance genes, and virulence determinants. Taxonomic and functional profiling were performed to assess microbial diversity and resistance patterns across wound subgroups.<br><br>RESULTS: Metagenomic analysis revealed a predominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Clinically relevant pathogens, including Achromobacter xylosoxidans, Staphylococcus aureus, and Pseudomonas aeruginosa, were frequently detected, along with less commonly reported taxa such as Achromobacter insolitus and Stenotrophomonas maltophilia. Multiple antimicrobial resistance gene clusters and biofilm-associated virulence factors were identified, indicating substantial multidrug resistance potential. Site-specific analysis showed that Pseudomonas aeruginosa dominated ul-H2 (&#x223c;32%), while Enterobacter hormaechei was most abundant in ft-H3 (&#x223c;40%). Culture-based methods primarily recovered common aerobic pathogens, whereas metagenomics detected additional opportunistic and unculturable taxa, highlighting the limitations of routine diagnostics. Resistome analysis identified ARGs conferring resistance to &#x3b2;-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and macrolides.<br><br>CONCLUSIONS: Chronic wound infections in Pakistan harbor diverse polymicrobial communities with substantial antimicrobial resistance and virulence potential. Shotgun metagenomics provides a more comprehensive characterization than culture-based methods by detecting additional pathogens and resistance determinants across wound sites. These findings support the integration of metagenomic diagnostics to improve clinical decision-making, strengthen antimicrobial stewardship, and guide infection control strategies in resource-limited healthcare settings.}, }
@article {pmid42248018, year = {2026}, author = {Park, S and Shin, JH and Lee, HH and Lee, JG}, title = {Cover crop incorporation maintains the methane oxidation potential and lowers methane emissions in plastic-film-mulched upland arable soils.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130115}, doi = {10.1016/j.jenvman.2026.130115}, pmid = {42248018}, issn = {1095-8630}, mesh = {*Methane/metabolism ; *Soil/chemistry ; Oxidation-Reduction ; Soil Microbiology ; Zea mays ; Plastics ; *Agriculture/methods ; Crops, Agricultural ; Oxygenases ; }, abstract = {Plastic film mulching can transform upland arable soils from sinks for methane (CH4) into sources by limiting gaseous exchange and creating hypoxic microsites. We explored whether incorporating cover crops can help reduce CH4 emissions by maintaining methanotroph functional potential in the presence of mulching. We conducted a field experiment in an upland maize field to compare NPK fertilization and cover crop incorporation, both with and without mulching. We combined CH4 flux measurements with methane oxidation potential (MOP) assays and shotgun metagenomics to analyze CH4-cycling communities and functional gene profiles. Cover crop incorporation under mulching (M-CC) reduced cumulative CH4 emissions by 55% compared with NPK fertilization under mulching (M-NPK) and maintained 17% higher MOP. By contrast, particulate methane monooxygenase (pMMO) genes did not show a uniform enrichment under M-CC. However, M-CC demonstrated higher abundances of genes associated with hydrogenase activity, single-carbon (C1) metabolism, electron transport, and antioxidant biosynthesis. Specifically, there was a 21% to 67% increase in hydrogenase genes, a 14% to 55% rise in C1 metabolism genes, a 28% to 54% increase in electron transport genes, and a remarkable 280% elevation in the antioxidant biosynthesis gene egtD. Using plastic film mulching with incorporated cover crops maintained MOP and promoted greater microbial biomass and metabolic flexibility. These effects were linked to lower CH4 emissions and reduced yield-scale CH4 emissions, all without compromising maize yield.}, }
@article {pmid42248101, year = {2026}, author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD}, title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142573}, doi = {10.1016/j.jhazmat.2026.142573}, pmid = {42248101}, issn = {1873-3336}, abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.}, }
@article {pmid42248258, year = {2026}, author = {Guo, Y and Jia, X and Chen, Y and Xu, S and Ming, T and Kong, F and Xu, J}, title = {Inhibiting methanogenesis with medium-chain fatty acids: strategy for rapid start-up and stable operation of food waste chain elongation systems.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135078}, doi = {10.1016/j.biortech.2026.135078}, pmid = {42248258}, issn = {1873-2976}, abstract = {Converting food waste (FW) into medium-chain fatty acids (MCFAs) via chain elongation (CE) is an economical and eco-friendly approach, but methanogenic competition remains a key challenge limiting CE efficiency. Traditional inhibition methods (e.g., pH regulation, hydraulic/solids retention time control, chemical additives) require strict operation or external inputs, causing non-specific microbial inhibition, high costs and environmental risks. Innovatively, MCFAs can inherently suppress methanogens with obvious advantages. However, their inhibition mechanisms and dependence on concentration and carbon chain length remain unclear. This study investigated the effects of butyric acid (C4), caproic acid (C6), and caprylic acid (C8) at different concentrations on methane production, medium- and short-chain fatty acids accumulation, and microbial dynamics in FW anaerobic fermentation. The results indicated that the inhibitory effect was primarily driven by undissociated fatty acids, with the potency increasing with longer carbon chain lengths. Notably, C8 at a low undissociated concentration (0.05 mM) completely inhibited methanogenesis. Higher concentrations of C4, C6, and C8 effectively sustained hydrolysis and acidogenesis while promoting CE and leading to the accumulation of caproic acid and caprylic acid. Metagenomic analysis showed that a decline in methanogenesis-related functional genes was accompanied by an increase in reverse β-oxidation related functional genes. These findings provide a feasible strategy for rapid start-up and stable operation of FW-based CE systems, and present a sustainable route for FW valorization toward high-value biochemicals.}, }
@article {pmid42248259, year = {2026}, author = {Gai, T and Zhang, J and Zhang, S and Zhang, L and Li, X and Wu, Y and Yang, Y and Liu, X and Shi, G and Yang, M}, title = {Performance and mechanisms of a biochar-enhanced partial nitritation/anammox process for the treatment of silane tower wastewater.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135083}, doi = {10.1016/j.biortech.2026.135083}, pmid = {42248259}, issn = {1873-2976}, abstract = {The increasing discharge of silane tower wastewater, characterized by high ammonia (NH4[+]-N) and the presence of silane derivatives, poses significant challenges to biological nitrogen removal processes. In this study, a partial nitritation/anammox (PN/A) sludge system was enhanced through the addition of sludge-derived biochar (SBC). The results demonstrated that SBC effectively improved the nitrogen removal performance of PN/A sludge during the treatment of silane tower wastewater. Under low-proportion silane tower wastewater conditions, SBC rapidly promoted R2 sludge granulation within 19 d during phase I. During phase IV, when 100% silane tower wastewater was used as the influent, the NH4[+]-N and total nitrogen removal efficiencies of R2 were stably maintained at 80%-83%. These improvements were mainly attributed to the ability of SBC to promote sludge granulation, enrich functional microorganisms, and enhance extracellular electron transfer (EET) performance. SBC addition enabled the sludge to maintain higher levels of tightly bound extracellular polymeric substances rich in hydrophobic amino acids (HAAs). This study found that SBC-promoted EET was more strongly associated with anammox bacteria than with ammonia-oxidizing bacteria, resulting in a more pronounced enhancement of specific anammox activity than specific ammonia oxidation rate. Metagenomic and metatranscriptomic analyses further revealed that SBC enhanced the biosynthetic pathways and transcriptional expression of genes associated with HAA synthesis in PN/A sludge. Overall, this study provides a novel enhancement strategy for the application of PN/A processes in the treatment of complex industrial wastewater with high NH4[+]-N concentrations.}, }
@article {pmid42248305, year = {2026}, author = {Janes, VA and Stalenhoef, JE and van der Putten, BCL and Koster, LAM and Jakobs, ME and van Dissel, JT and de Jong, MD and Schultsz, C and Mende, DR}, title = {Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection.}, journal = {The Journal of infection}, volume = {93}, number = {2}, pages = {106783}, doi = {10.1016/j.jinf.2026.106783}, pmid = {42248305}, issn = {1532-2742}, abstract = {OBJECTIVES: The diagnosis of febrile urinary tract infection (fUTI) by urine culture is hampered by antibiotic pre-treatment. We investigated urine metagenomics to diagnose fUTI in patients with positive blood but negative urine cultures.<br><br>METHODS: We performed shotgun metagenomic sequencing on 41 culture-positive and 19 culture-negative urine samples from fUTI patients, comparing urine metagenomics to blood and urine culture including antimicrobial susceptibility testing (AST). mOTUs3.1 performed metagenomic pathogen detection and ResFinder2.0 antimicrobial drug resistance (AMR) gene detection (standard settings). Whole genome sequencing (WGS) was performed on blood culture isolates from culture-negative urine samples. BWA-MEM and sylph aligned metagenomic pathogen reads to their respective WGS assemblies.<br><br>RESULTS: Metagenomics detected the blood culture isolate in 39/41 culture-positive and 17/19 culture-negative urine samples. 11/19 urine culture-negative patients were pre-treated with antibiotics, versus 8/41 urine culture-positives. The blood culture isolate was the most abundant pathogen in 33/41 culture-positive and 15/19 culture-negative urine samples. A median of 93.2% of pathogen-specific metagenomic reads mapped to their WGS assemblies with a median ANI of 98.7% (n=11). Genotypic AMR detection and phenotypic AST matched in 38-96% of cases.<br><br>CONCLUSIONS: Urine metagenomics successfully detected the causative pathogen in urine culture-negative fUTI patients. Genotypic AMR prediction requires further investigation.}, }
@article {pmid42248407, year = {2026}, author = {Tan, Y and Sun, J and Chen, X and Wang, Y and Zhang, C and Gong, L and Cui, X}, title = {Chronic Papillary Conjunctivitis as a Novel Ocular Manifestation of Rickettsia felis Infection: A Case Report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108861}, doi = {10.1016/j.ijid.2026.108861}, pmid = {42248407}, issn = {1878-3511}, abstract = {PURPOSE: To report the first case of chronic papillary conjunctivitis caused by Rickettsia felis infection.<br><br>CASE: A 27-year-old man presented with a four-year history of unilateral papillary conjunctivitis refractory to multiple antibiotic courses. Examination revealed tarsal conjunctival injection, papillary hypertrophy, mucopurulent discharge, and eyelid laxity with entropion. The patient had a history of cat ownership for 5-6 years, suggesting possible exposure to the cat flea, and remained systemically asymptomatic without fever, rash, or lymphadenopathy. Metagenomic next-generation sequencing (mNGS), serology, and histopathology confirmed Rickettsia felis infection. Given the chronic intracellular nature of the infection, the patient received an extended 2-month course of oral doxycycline (100 mg twice daily) combined with topical therapy, with marked improvement observed by week 8 and subsequent entropion repair surgery.<br><br>CONCLUSION: This represents the first reported case of chronic, isolated rickettsial conjunctivitis without systemic involvement or Parinaud's oculoglandular syndrome features. This case highlights the importance of considering rickettsial infection in chronic, treatment-refractory conjunctivitis and demonstrates the value of metagenomic sequencing for diagnosis.}, }
@article {pmid42248728, year = {2026}, author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY}, title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.05.016}, pmid = {42248728}, issn = {1873-5010}, abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.<br><br>METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.<br><br>RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.<br><br>CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.}, }
@article {pmid42248819, year = {2026}, author = {Peng, D and Zhou, J and Xiong, M and Chen, Y and Zhang, Y and Hu, Y and Yang, Y and Xu, J and Zheng, Y and Xu, D}, title = {Gut Microbiota Dysbiosis Drives Lethal Bacterial Enteritis in Sturgeons: Insights From Ex Vivo Cultivation and Metagenomic Investigations.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70218}, doi = {10.1111/jfd.70218}, pmid = {42248819}, issn = {1365-2761}, support = {D-8006-25-0392//Shanghai Aquatic Wildlife Conservation and Research Center/ ; K2025-02-08-00-12-F00043//Shanghai Municipal Commission of Agriculture and Rural Affairs/ ; }, abstract = {The Chinese sturgeon (Acipenser sinensis) and Yangtze sturgeon (A. dabryanus) are critically endangered flagship species. To investigate the intestinal microbial changes associated with bacterial enteritis in captive populations, we integrated bacterial isolation with metagenomic sequencing to characterize both healthy and maladjusted gut microbiomes. Healthy sturgeons exhibited a stable microbiota dominated by the beneficial Cetobacterium. In contrast, enteritis was consistently associated with severe dysbiosis, characterized by the depletion of these commensals and the massive expansion of opportunistic pathogens, notably Aeromonas and Citrobacter. Culture-based analyses identified A. veronii, C. freundii and Plesiomonas shigelloides as the dominant cultivable bacteria from diseased individuals; these isolates harboured diverse virulence traits and were multidrug-resistant. Crucially, both sturgeon species showed highly similar microbial responses and pathogenic profiles during enteritis. These findings indicate that sturgeon enteritis is closely correlated with a dysbiosis-driven syndrome. Establishing the healthy baseline provides a critical theoretical foundation for screening autochthonous probiotics and developing targeted pathogen control strategies. Furthermore, the striking cross-species commonality validates the Yangtze sturgeon as a viable surrogate model for advancing disease management and conservation in the difficult-to-breed Chinese sturgeon.}, }
@article {pmid42248870, year = {2026}, author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F}, title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73437-x}, pmid = {42248870}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.}, }
@article {pmid42249277, year = {2026}, author = {Guanglin, W and Xiuwen, K and Rong, H}, title = {Awake VV-ECMO for severe pneumonia caused by Elizabethkingia anophelis: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13735-3}, pmid = {42249277}, issn = {1471-2334}, abstract = {BACKGROUND: Elizabethkingia anophelis is phenotypically similar to E. meningoseptica and is often misidentified by conventional methods, delaying appropriate therapy. Awake venovenous extracorporeal membrane oxygenation (VV-ECMO) avoids complications of deep sedation and mechanical ventilation, but its role in severe pulmonary infection with rare pathogens remains underexplored.<br><br>CASE PRESENTATION: We report a 62-year-old male with chronic hepatitis B who developed type I respiratory failure and septic shock unresponsive to conventional support. VV-ECMO was initiated on January 23, and awake ECMO management was implemented to preserve spontaneous breathing and cough reflex. Serial metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid revealed influenza A H1N1, Aspergillus fumigatus, and multidrug-resistant bacteria (Detailed mNGS results are provided in Supplementary Table 2). On day 32, sputum culture suggested E. meningoseptica, but subsequent mNGS identified E. anophelis (322,376 reads). The anti-infective regimen was adjusted to minocycline-based combination therapy. Under awake ECMO support, the patient's infection markers gradually improved, and he was successfully weaned from ECMO on day 38 and from mechanical ventilation thereafter. He was discharged after recovery.<br><br>CONCLUSION: This case demonstrates that awake ECMO can serve as an effective respiratory support platform in complex severe pneumonia. When conventional testing reports E. meningoseptica, clinicians should suspect possible E. anophelis infection, and timely mNGS is recommended for accurate species identification. Minocycline-based combination therapy appears promising for E. anophelis infections.<br><br>CLINICAL TRIAL: Not applicable.<br><br>CLINICAL PEARL: In critically ill patients with suspected Elizabethkingia infection, do not rely solely on phenotypic identification; use mNGS to distinguish Elizabethkingia anophelis from Elizabethkingia meningoseptica, and consider early minocycline-based therapy.}, }
@article {pmid42249286, year = {2026}, author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z}, title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05167-5}, pmid = {42249286}, issn = {1471-2180}, support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; }, abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.<br><br>METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.<br><br>RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM&#x2009;+&#x2009;HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM&#x2009;+&#x2009;HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.<br><br>CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H&#x2082;S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.}, }
@article {pmid42249504, year = {2026}, author = {Liu, Y and Xie, Y and Yang, J and Deng, Y and Liu, D and Chang, J and Tang, J and Zhao, H and Chen, X and Tian, G and Liu, G and Cai, J and Jia, G}, title = {Integrated gut metagenomic and muscle proteomic analysis reveals the role of dietary fermented extruded brewers' spent grain in enhancing pork quality through the gut-muscle axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42249504}, issn = {1674-9782}, support = {No. 2021ZDZX0009//Sichuan Science and Technology Program/ ; }, abstract = {BACKGROUND: The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.<br><br>METHODS: Sixty Duroc&#x2009;&#xd7;&#x2009;Landrace&#x2009;&#xd7;&#x2009;Yorkshire pigs (52.25&#x2009;&#xb1;&#x2009;2.10&#xa0;kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10&#xa0;weeks.<br><br>RESULTS: Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P&#x2009;<&#x2009;0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P&#x2009;<&#x2009;0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P&#x2009;<&#x2009;0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC I, MyHC IIa, PGC-1&#x3b1;, AMPK&#x3b1;1, TFAM, and SDH activity, and downregulated MyHC IIb and LDH activity (P&#x2009;<&#x2009;0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1&#x3b1;/TFAM signaling pathway.<br><br>CONCLUSIONS: Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1&#x3b1;/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.}, }
@article {pmid42249511, year = {2026}, author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H}, title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42249511}, issn = {2049-2618}, support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Aging/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Adaptive Immunity ; *Vitamin B 6/blood/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology/microbiology ; Immunity, Mucosal ; Ileum/immunology/microbiology ; }, abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.<br><br>RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced na&#xef;ve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of na&#xef;ve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.<br><br>CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.}, }
@article {pmid42249581, year = {2026}, author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W}, title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70397}, pmid = {42249581}, issn = {1751-7915}, support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; }, mesh = {*Escherichia coli/genetics ; *Polymorphism, Single Nucleotide ; *Colorectal Neoplasms/microbiology ; Humans ; Genome, Bacterial ; Genetic Markers ; Gastrointestinal Microbiome ; Case-Control Studies ; Chromosome Mapping ; Multilocus Sequence Typing ; }, abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.}, }
@article {pmid42249721, year = {2026}, author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W}, title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {11}, pages = {e70422}, doi = {10.1111/mec.70422}, pmid = {42249721}, issn = {1365-294X}, support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; Temperature ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota/genetics ; Seasons ; *Ecosystem ; Metagenomics ; }, abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.}, }
@article {pmid42250066, year = {2026}, author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W}, title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42250066}, issn = {1559-0291}, support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; }, abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.}, }
@article {pmid42250131, year = {2026}, author = {Gao, X and Qin, R and Li, S and Yang, Y and He, J}, title = {Congenital tuberculosis transmitted via the placenta: identification by metagenomic next-generation sequencing.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42250131}, issn = {1435-4373}, support = {grant number: kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; }, abstract = {BACKGROUND: Congenital tuberculosis (CTB) is a rare disease with high mortality in neonates. Early diagnosis is crucial but often delayed due to atypical clinical and imaging manifestations.<br><br>CASE PRESENTATION: We report a 36-day-old female infant presenting with recurrent fever. Laboratory data showed leukocytosis and neutrophilia with mildly elevated C-reactive protein. Chest computed tomography revealed extensive ground-glass opacities, multiple subpleural nodules, and necrotic hilar and mediastinal lymphadenopathy. The asymptomatic mother was subsequently found to have diffuse miliary nodules on chest CT. Conventional tuberculosis tests (acid-fast smear, culture, GeneXpert, T-SPOT.TB) were negative in both the infant and mother. Metagenomic next-generation sequencing (mNGS) of the placental tissue detected 10 specific Mycobacterium tuberculosis sequences, and Ziehl-Neelsen staining confirmed acid-fast bacilli. Both mother and infant responded well to anti-tuberculosis therapy.<br><br>CONCLUSIONS: CTB should be considered in neonates with persistent pulmonary infection unresponsive to broad-spectrum antibiotics. Examination of placental tissue using mNGS is a valuable diagnostic tool for confirming transplacental tuberculosis transmission.}, }
@article {pmid42250135, year = {2026}, author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M}, title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42250135}, issn = {1573-0972}, mesh = {*Agriculture/methods ; Soil Microbiology ; Climate Change ; Crops, Agricultural/microbiology/growth &amp; development ; Microbiota ; Stress, Physiological ; Ecosystem ; Biotechnology ; Mycorrhizae ; }, abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.}, }
@article {pmid42250463, year = {2026}, author = {Xia, L and Lu, L and Liu, M and Jiao, J and Liu, L and Meng, L and Liu, Y and Li, W and Lu, C and Ma, B}, title = {Proposal of Edaphobacterium genomatis gen. nov., sp. nov. within the family Casimicrobiaceae from metagenome-assembled genomes in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126735}, doi = {10.1016/j.syapm.2026.126735}, pmid = {42250463}, issn = {1618-0984}, abstract = {Casimicrobiaceae strains inhabit various environments, but their ecological roles in natural soils remain mostly unclear. By actively targeting specific high-altitude datasets during our Global Mollisols Genomic Atlas (GMGA) mining efforts, we discovered a previously unknown lineage within this family. This novel group is represented by five metagenome-assembled genomes (MAGs) recovered from oligotrophic soils in the Southern Brazilian Highland Grasslands, a unique environment within the broad Pampas black soil region. Phylogenetic and comparative genomic analyses showed these five MAGs form a distinct monophyletic clade within Casimicrobiaceae. Their novel taxonomic status is supported by Average Nucleotide Identity (ANI) thresholds, showing clear divergence from all known reference genomes. Functional annotations suggest a chemoorganotrophic lifestyle with microaerobic respiration capacity, while trace-gas scavenging genes indicate potential lithoheterotrophy for maintenance energy under nutrient limitation. Additionally, an autonomous ACC deaminase system and specialized nutrient scavenging pathways (organophosphonate and taurine utilization) highlight its adaptive capacity for rhizosphere interactions and survival in oligotrophic environments. Screening 22,976 public metagenomes demonstrated a widespread global distribution, primarily inhabiting diverse soil (86.4%) and plant-associated (7.0%) environments. Based on these analyses, we propose the name Edaphobacterium genomatis gen. nov., sp. nov. for this novel taxon following the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data) rules. Our results uncover hidden species diversity and highlight the specific functional roles of uncultured microbes in nutrient-limited highland niches within fertile black soil regions.}, }
@article {pmid42250813, year = {2026}, author = {Kadam, R and Jo, S and Panwar, NL and Kim, T and Park, J}, title = {Metagenomic insights into metabolic limitations and biosafety implications of rendered pig carcass anaerobic digestion.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135081}, doi = {10.1016/j.biortech.2026.135081}, pmid = {42250813}, issn = {1873-2976}, abstract = {Global livestock production has intensified, increasing the biosecurity and environmental risks associated with animal mortality management. This study evaluated the feasibility of anaerobic digestion (AD) as a sustainable valorization route for rendered pig carcasses using long-term performance monitoring and whole-metagenome shotgun sequencing. During operation at an organic loading rate (OLR) of 1.0-2.0 kg-VS/m[3]/d, the reactor achieved peak methane (CH4) yields of 400-430 mL-CH4/g-VS and an organic matter removal efficiency > 70%. The buffering capacity generated through carcass proteolysis contributed to maintaining reactor performance under increasing loading conditions. However, increasing the OLR to 3.0 kg-VS/m[3]/d triggered process instability, decreasing the CH4 yield and increasing the total volatile fatty acids (TVFAs) to > 6,000 mg/L, specifically dominated by propionic and butyric acids. Metagenomic analysis identified a specialized consortium dominated by the syntrophic acetogen Cloacamonas and acetoclastic methanogen Methanosaeta during reactor operation at moderate OLRs. Functional profiling revealed that although the community possessed efficient hydrolytic and syntrophic acetate oxidation pathways, propionic acid accumulation and lower completeness of propionate oxidation pathways suggested potential limitations in syntrophic propionate oxidation at elevated OLRs. Furthermore, biosafety-related assessments suggested that AD may offer potential biocontainment advantages over traditional carcass disposal methods based on reduced prevalence of antimicrobial resistance genes and virulence-associated factors. These findings provide a metabolic framework for optimizing carcass-based AD as a viable substrate for renewable energy recovery.}, }
@article {pmid42250815, year = {2026}, author = {Xie, C and Li, D and Li, J and Li, J and Yin, M and Wu, Y and Zhang, C and Luo, R and Zhu, Y and Zhang, Z and Zheng, Z and Peng, Y}, title = {Molecular mechanism of anammox granular sludge disintegration caused by polyethylene terephthalate micro/nanoplastics: a new perspective based on quorum sensing.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135060}, doi = {10.1016/j.biortech.2026.135060}, pmid = {42250815}, issn = {1873-2976}, abstract = {Quorum sensing (QS) regulates the synthesis and secretion of extracellular polymeric substances (EPS), which are essential for maintaining the structural stability of anaerobic ammonium oxidation (Anammox) granular sludge. However, the molecular mechanism linking polyethylene terephthalate micro/nanoplastics (PET-MNPs)-induced QS disruption to EPS inhibition remains unclear. This study investigated the effects of two PET-MNP sizes (80 μm and 300 nm) on Anammox granular sludge under different exposure concentrations. PET-MNPs significantly reduced nitrogen removal performance and caused surface cracking, structural loosening, and granule disintegration. EPS analysis showed that PET-MNPs decreased EPS content, altered protein secondary structure, and increased hydrophilic functional groups, thereby weakening sludge bioadhesion. Metagenomic and metatranscriptomic analyses indicated that PET-MNPs inhibited the abundance and expression of genes involved in the Anammox process, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and Wood-Ljungdahl pathway, resulting in insufficient ATP, NADH, and metabolic precursors required for EPS synthesis. Meanwhile, methionine and fatty acid metabolism were suppressed, limiting precursor supply for acyl-homoserine lactone (AHL) synthesis. Molecular docking showed that PET oligomers could stably bind to LuxR and potentially hinder AHL-LuxR complex formation. Exogenous AHL supplementation promoted EPS re-secretion, confirming the important role of QS imbalance in PET-MNPs-induced EPS reduction. Overall, PET-MNPs destabilized Anammox granular sludge through the combined effects of particle-induced physical damage and oligomer-mediated molecular interference. This study elucidates the molecular mechanism of MNP-induced Anammox granule disintegration and provides a theoretical basis for assessing the ecological risks of emerging pollutants in biological wastewater treatment.}, }
@article {pmid42250818, year = {2026}, author = {Liu, Y and Qian, Z and Peng, Y and Zhang, T and Li, Z and Shi, S and Gu, H}, title = {Enhancing ethanol-driven chain elongation via iron speciation: impacts on metabolic flux and dual FAB/RBO pathway activation.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135088}, doi = {10.1016/j.biortech.2026.135088}, pmid = {42250818}, issn = {1873-2976}, abstract = {Anaerobic chain elongation (CE) has emerged as a promising technology for upgrading low-value organic substrates into high-value medium-chain fatty acids (MCFAs); however, achieving targeted metabolic flux and efficient electron transfer remains challenging. To address this, this study explores the role of iron speciation in enhancing chain elongation (CE) driven by ethanol. Two iron-modified activated carbons, Fe3O4@AC and ZVI@AC, were evaluated to assess their impact on microbial metabolic networks. Results revealed that Fe3O4@AC significantly enhanced caproate production (4600.0 mg/L) and electron transfer efficiency (87.0 %), while ZVI@AC triggered a diversion towards alcohol production (940.61 mg/L n-butanol). The superior performance of Fe3O4@AC was attributed to its semiconductive properties, which facilitated interspecies electron transfer (potentially via DIET-like mechanisms) and balanced electron flow, promoting the activation of both fatty acid biosynthesis (FAB) and reverse β-oxidation (RBO) pathways. Metagenomic analysis revealed a shift in microbial community composition, with Massilibacterium enrichment under Fe3O4@AC, highlighting the importance of tailored material design for targeted MCFA production. These findings provide insights into optimizing microbial metabolism for enhanced CE efficiency.}, }
@article {pmid42250890, year = {2026}, author = {Ticho, AL and McRae, AN and Cifuentes, L and Fredrick, T and Anazco, D and Espinosa, MA and Garcia Cordova, JM and Romanos, M and Villamarin, J and Johnson, S and Lennon, R and Hurtado Andrade, MD and Chen, J and Camilleri, M and Acosta, AJ}, title = {A Subphenotype of Obesity With Reduced Enteroendocrine Glucagon-Like Peptide 1 Synthesis and Enhanced Tirzepatide Response.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.05.019}, pmid = {42250890}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Obesity is a heterogeneous disease characterized by different pathophysiological and behavioral traits that influence response to glucagon-like peptide 1 (GLP-1)-based therapies. We previously identified an obesity phenotype characterized by fast gastric emptying (GE) and increased postprandial hunger. We aimed to elucidate pathophysiological mechanisms in this phenotype by evaluating plasma enteroendocrine hormones and mucosal gene expression and to evaluate treatment response to tirzepatide across subphenotypes.<br><br>METHODS: A total of 483 adults with obesity underwent solid meal GE (SGE by scintigraphy), postprandial appetite assessment using a visual analogue scale, and plasma enteroendocrine hormone profiling. Gaussian mixed modeling identified phenotypic clusters. Associations with plasma short-chain fatty acids and fecal metagenomics were explored. A separate cohort (n = 31) underwent colonic mucosal biopsies with quantification of GCG (GLP-1) and PYY messenger RNA. Retrospective evaluation of weight loss in participants treated with tirzepatide among each cluster was performed (n = 61).<br><br>RESULTS: Three clusters were identified based on SGE and GLP-1. One cluster demonstrated fast SGE, increased postprandial hunger, and discordantly low postprandial GLP-1 (termed dc-GE/GLP-1; n = 130 [26.9%]), as well as lower plasma peptide YY and cholecystokinin. dc-GE/GLP-1 showed higher plasma short-chain fatty acid levels, without significant differences in fecal microbial composition. Compared with concordant clusters (c-GE/GLP-1; n = 353 [73.1%]), dc-GE/GLP-1 had decreased mucosal messenger RNA expression of GCG (GLP-1) and PYY. At 6 months of tirzepatide, dc-GE/GLP-1 was associated with greater weight loss compared with c-GE/GLP-1 (21.5% vs 11.7%).<br><br>CONCLUSIONS: We identified a subphenotype of obesity with fast GE and discordantly low GLP-1 plasma levels, reduced mucosal hormone synthesis, and enhanced weight loss to tirzepatide. Further studies are needed to identify mechanisms contributing to GLP-1 deficiency in this subphenotype of obesity.}, }
@article {pmid42251226, year = {2026}, author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR}, title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.}, journal = {Journal of natural medicines}, volume = {}, number = {}, pages = {}, pmid = {42251226}, issn = {1861-0293}, support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; }, abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.}, }
@article {pmid42251252, year = {2026}, author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE}, title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13715-7}, pmid = {42251252}, issn = {1471-2334}, support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.<br><br>METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.<br><br>RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n&#x2009;=&#x2009;24; n&#x2009;=&#x2009;8 previously diagnosed) and rhinovirus (n&#x2009;=&#x2009;18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.<br><br>CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.}, }
@article {pmid42251689, year = {2026}, author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X}, title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag090}, pmid = {42251689}, issn = {1536-4844}, support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; }, abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.<br><br>METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.<br><br>RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P&#x2009;=&#x2009;.040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P&#x2009;<&#x2009;.05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.<br><br>CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.}, }
@article {pmid42251704, year = {2026}, author = {Farace, PD and Marrero Diaz de Villegas, R and Mon, ML and Soria, MA and Talia, PM}, title = {Structural insights into predicted thermophilic GH5 cellulases for industrial lignocellulose bioconversion.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/07391102.2026.2683872}, pmid = {42251704}, issn = {1538-0254}, abstract = {Lignocellulosic biomass can be converted into biofuels and other valuable bioproducts, but it must first undergo physicochemical and enzymatic degradation. Among the various enzymes involved in lignocellulose degradation, thermophilic glycoside hydrolase family 5 (GH5) cellulases have gained significant attention given their ability to sustain enzymatic activity at temperatures exceeding 60 °C. These high temperatures not only accelerate enzymatic reactions, improving reaction rates and process efficiency, but also enhance substrate solubility and reduce the risk of microbial contamination, making them highly valuable for the paper, food, feed, pharmaceutical, and biofuel industries. In this work, we identified five GH5 cellulases with predicted thermophilic properties from termite gut metagenomes and evaluated their structural features using machine-learning classification, comparative structural modeling, interatomic contact analysis, and temperature-dependent flexibility simulations. The candidates, spanning GH5 subfamilies 2, 25, 37, 39, and 40, displayed high structural confidence (pLDDT > 90) and aliphatic indices comparable to those of thermophilic references. Analysis of amino acid composition analysis revealed enrichment in aromatic and charged residues. Hydrophobic contact densities were consistently higher than in mesophilic controls and aligned with thermophilic benchmarks. Temperature-dependent flexibility simulations showed restrained RMSF profiles, more closely resembling the thermophilic reference enzyme than to the mesophilic control. These findings are consistent with a thermophilic profile, pending experimental confirmation, and provide useful insights for the selection and engineering of GH5 cellulases for high-temperature biotechnological applications.}, }
@article {pmid42251735, year = {2026}, author = {Dennu, L and Devic, M and Rigonato, J and Falciatore, A and Lozano, JC and Vergé, V and Mariac, C and Joli, N and Jaillon, O and Sabot, F and Bouget, FY}, title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: insights into genetic diversity and function of outlier chromosomes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {126}, number = {5}, pages = {e70982}, pmid = {42251735}, issn = {1365-313X}, support = {ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; }, mesh = {*Phytoplankton/genetics ; *Genetic Variation/genetics ; Phylogeny ; Metagenome/genetics ; Genomics ; Metagenomics ; *Chromosomes/genetics ; }, abstract = {Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes (MAGs). Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78° N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: While MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the big outlier chromosome, a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome, associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish B. prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets.}, }
@article {pmid42251775, year = {2026}, author = {Sahnan, S and Morandini, V and Ferrer, M and Onrubia, A and Torralvo, C and Kaján, GL and Harrach, B and Varsani, A and Kraberger, S}, title = {Four lineages of adenoviruses identified in raptors sampled in Spain.}, journal = {Virology}, volume = {623}, number = {}, pages = {110990}, doi = {10.1016/j.virol.2026.110990}, pmid = {42251775}, issn = {1096-0341}, abstract = {Adenoviruses infect a wide range of vertebrate species from fish to humans, including an especially large number of avian species. This study utilized viral metagenomic workflow coupled with targeted PCR to identify and characterize adenoviruses from cloacal swabs collected from 50 black kites (Milvus migrans), 11 ospreys (Pandion haliaetus), and 35 common kestrels (Falco tinnunculus) sampled in Spain. A total of eleven adenoviral genomes were determined from black kites (n = 8) and common kestrels (n = 3). Amino acid pairwise comparison of the DNA polymerase protein coupled with phylogenetic analysis shows that these viruses fall into four adenovirus lineages: two in the genus Aviadenovirus (raptor adenovirus 2 and 3) and two in the genus Siadenovirus (raptor adenovirus 1 and 4). The genomes of raptor adenovirus 1 and raptor adenovirus 2 belong to the classified species Siadenovirus raptoris and Aviadenovirus falconis, respectively, whereas raptor adenovirus 3 and 4 represent putative new species. This study expands the known host range of raptor-infecting viruses in the species Siadenovirus raptoris and Aviadenovirus falconis to include black kites and common kestrels, respectively. We also expand on the diversity knowledge of adenoviruses in black kites.}, }
@article {pmid42251975, year = {2026}, author = {Chen, C and Wang, M and Sun, L and Cheng, X and Deng, H and Li, RH}, title = {Phosphorus metabolism regulates the trade-off between phosphorus removal and sludge reduction.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135096}, doi = {10.1016/j.biortech.2026.135096}, pmid = {42251975}, issn = {1873-2976}, abstract = {Sludge reduction decreases the phosphorus export flux through waste sludge discharge, thereby increasing the risk of effluent phosphorus instability. However, the regulatory role of phosphorus in sludge reduction remains unclear. Here, side-stream phosphorus recovery was introduced into an anaerobic side-stream reactor (ASSR) based sludge reduction system to redirect phosphorus export from sludge discharge to physicochemical recovery, enabling investigation of how phosphorus flux redistribution regulates sludge reduction. Two parallel systems, a conventional ASSR system (SBR-ASSR) and an ASSR system coupled with phosphorus recovery (SBR-ASSR-PR), were comparatively evaluated using phosphorus mass balance, endogenous respiration analysis, cryptic growth modeling, and metagenomic profiling. Phosphorus recovery increased total phosphorus removal from 77.8% to 97.3% and total nitrogen removal from 72.5% to 82.1%, while reducing the observed sludge yield by 28%. Phosphorus mass balance showed that 34.7% of influent phosphorus was rerouted through the recovery pathway, reducing phosphorus discharge via waste sludge from 74.9% to 57.5%. The resulting lower system phosphorus levels restructured microbial metabolic allocation, suppressing biosynthesis while enhancing decay and substrate reutilization, with the cryptic growth contribution increasing from 35.9% to 46.9%. Metagenomic profiling corroborated this metabolic shift, revealing significant changes in key genes and pathways related to phosphorus cycling, energy maintenance, and denitrification. These findings show that phosphorus metabolism can regulate microbial growth-decay allocation, and that side-stream phosphorus recovery can coordinate nutrient removal, phosphorus recovery, and sludge minimization by restructuring internal phosphorus fluxes and microbial metabolic allocation.}, }
@article {pmid42252081, year = {2026}, author = {Wang, F and Xie, J and Fu, T and Pu, K and Wu, Q and Li, Q}, title = {Negative CSF mNGS Results and Early Shunt Placement in Post-Infectious Hydrocephalus: A Retrospective Cohort Study.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {125104}, doi = {10.1016/j.wneu.2026.125104}, pmid = {42252081}, issn = {1878-8769}, abstract = {OBJECTIVE: To evaluate the impact of pre-shunt cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) guidance on the timing of ventriculoperitoneal (VP) shunt surgery and clinical outcomes in patients with post-infectious hydrocephalus (PIH), and to explore the value of mNGS in different clinical scenarios.<br><br>METHODS: In this retrospective cohort study, we included 42 patients with PIH who underwent VP shunt surgery at our institution between January 2019 and December 2025. Patients were divided into two groups according to whether pre-shunt CSF mNGS was performed: the mNGS group (n = 19) and the non-mNGS group (n = 23). Primary outcomes included recovery to shunt time (RTS), first negative to shunt time (NTS), decisional shunt to actual shunt time (DTS), and postoperative antibiotic time (PAT). Secondary outcomes included postoperative hospital stay (POHS), functional outcomes (mRS and GCS), POD 90 mortality, infection recurrence, and reoperation.<br><br>RESULTS: Compared with the non-mNGS group, the mNGS group demonstrated significantly shorter NTS (3 [IQR 1-4] days vs. 9 [IQR 4.5-17] days, P = 0.002), DTS (2 [IQR 1-3.5] days vs. 8 [IQR 6-18] days, P < 0.001), and PAT (0 [IQR 0-2] days vs. 4 [IQR 0-10] days, P = 0.010). No significant differences were observed between the two groups in RTS (P = 0.135), functional outcomes, mortality, infection recurrence, or reoperation.<br><br>CONCLUSIONS: Pre-shunt CSF mNGS testing significantly shortens NTS, DTS, and PAT in patients with PIH without compromising clinical outcomes. The mNGS-guided shunt strategy is safe and feasible, supporting its potential clinical application.}, }
@article {pmid42252233, year = {2026}, author = {Dou, ZX and Liu, C and Zhang, Y and Wang, ZQ and Zhao, L}, title = {[A case of microsporidial keratoconjunctivitis].}, journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology}, volume = {62}, number = {6}, pages = {468-472}, doi = {10.3760/cma.j.cn112142-20251002-00402}, pmid = {42252233}, issn = {0412-4081}, mesh = {Humans ; Male ; *Keratoconjunctivitis/microbiology/diagnosis/drug therapy ; *Microsporidiosis/diagnosis/drug therapy ; Adolescent ; *Eye Infections, Fungal/microbiology/drug therapy/diagnosis ; }, abstract = {A 15-year-old male patient presented with recurrent photophobia, lacrimation, and blurred vision in both eyes for 3 years. He had been repeatedly diagnosed with "bilateral keratitis (unknown etiology)"at other hospitals and failed to respond to multiple topical medications. Initially diagnosed as bilateral Thygeson superficial punctate keratitis, he was treated with 0.5% loteprednol etabonate suspension eye drops and other medications. However, his symptoms worsened after 3 weeks of treatment. Subsequently, corneal epithelial tissue metagenomic testing and scrape cytological examination were performed, confirming the diagnosis of bilateral microsporidial keratoconjunctivitis. The treatment regimen was adjusted to topical application of 1% voriconazole eye drops, 0.3% gatifloxacin ophthalmic gel, and 0.1% tacrolimus eye drops. After 3 weeks of treatment, the patient's visual acuity in both eyes recovered to 1.0, conjunctival hyperemia was alleviated, and corneal epithelial punctate infiltration and fluorescein staining improved. One month after treatment, his symptoms were basically relieved, with the corneal infiltration and palpebral conjunctival papillae resolved. No recurrence was observed during the one-year follow-up.}, }
@article {pmid42252320, year = {2026}, author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W}, title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-55351-w}, pmid = {42252320}, issn = {2045-2322}, support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; }, abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.}, }
@article {pmid42252423, year = {2026}, author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ}, title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05199-x}, pmid = {42252423}, issn = {1471-2180}, support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Qu&#xed;mica Valaner-MGI Mexico/ ; }, abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.}, }
@article {pmid42252476, year = {2026}, author = {Wei, C and Wang, Y and Chen, Z}, title = {Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02445-2}, pmid = {42252476}, issn = {2049-2618}, abstract = {BACKGROUND: The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood.<br><br>RESULTS: Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188&#xa0;kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems.<br><br>CONCLUSIONS: Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract.}, }
@article {pmid42252506, year = {2026}, author = {Galtier, A and Warinner, C and Velsko, IM}, title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag136}, pmid = {42252506}, issn = {1759-6653}, abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.}, }
@article {pmid42252693, year = {2026}, author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W}, title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag145}, pmid = {42252693}, issn = {1751-7370}, abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.}, }
@article {pmid42252802, year = {2026}, author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M}, title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {3}, pages = {e70324}, pmid = {42252802}, issn = {2190-6009}, support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; }, mesh = {Humans ; *Cachexia/etiology ; *Bacteriophages/genetics ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; *Neoplasms/complications ; Metagenomics/methods ; Metagenome ; Feces/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.<br><br>METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67&#x2009;&#xb1;&#x2009;8&#x2009;years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.<br><br>RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4&#x2009;kg/m2), WL (mean -6.5 vs. -0.2&#x2009;kg), survival (median 5 vs. 13&#x2009;months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p&#x2009;<&#x2009;0.001) but not for other clinical covariables (e.g., cancer type) (all p&#x2009;>&#x2009;0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p&#x2009;<&#x2009;0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p&#x2009;>&#x2009;0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial &#x3b2;-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p&#x2009;<&#x2009;0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p&#x2009;<&#x2009;0.05; 2025: Myoviridae, Siphoridae, p&#x2009;<&#x2009;0.05) but also single-stranded (2022: Inoviridae, Microviridae, p&#x2009;<&#x2009;0.05; 2025: Inoviridae; p&#x2009;<&#x2009;0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).<br><br>CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.<br><br>TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).}, }
@article {pmid42253890, year = {2026}, author = {Liu, Y and Xie, H and Song, Z and Huang, M and Li, M}, title = {Massive ascites and adnexal masses mimicking malignancy: A case report of Chlamydia trachomatis infection diagnosed by metagenomic next-generation sequencing.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02616}, pmid = {42253890}, issn = {2214-2509}, abstract = {OBJECTIVE: Chlamydia trachomatis (C. trachomatis) is the most commonly reported bacterial sexually transmitted infection among sexually active women. Although often asymptomatic or associated with non-specific clinical manifestations, it can cause inflammatory exudates and encapsulated fluid collections that are similar to adnexal masses on imaging. In rare cases, it may also present with massive ascites, a constellation of findings that may mimic ovarian malignancy.<br><br>CASE: We report the case of a 32-year-old female with a nearly 3-month history of abdominal pain, adnexal masses and massive ascites. The initial workup did not reveal obvious evidence of infection and cytological examination showed no malignant cells. However, advanced gynecological originated cancer could not be fully excluded. Metagenomic next-generation sequencing (mNGS), which detected C. trachomatis in ascitic fluid, facilitated the diagnosis. The patient showed satisfactory clinical improvement following doxycycline treatment.<br><br>CONCLUSION: For young, sexually active women presenting with unexplained ascites and adnexal masses, after excluding malignancy and common infectious diseases such as tuberculosis, C. trachomatis infection should be considered. Modern etiological detection methods, such as mNGS, can be employed to facilitate the diagnosis.}, }
@article {pmid42254105, year = {2026}, author = {Habib, E and Urooj, I and Barry, HD and Awais, M and Kumari, M and Hajj, F}, title = {AI-programmable therapeutics via metagenomic foundation models for rare phage-mediated autoimmune modulations: early translational risks and benefits.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3905-3906}, pmid = {42254105}, issn = {2049-0801}, }
@article {pmid42254157, year = {2026}, author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A}, title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3348-3359}, pmid = {42254157}, issn = {2049-0801}, abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.}, }
@article {pmid42254407, year = {2026}, author = {Liang, Y and Hu, J and Wang, Z}, title = {A case of severe psittacosis in a hemodialysis patient-the critical role of detailed medical history and next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1825118}, pmid = {42254407}, issn = {2296-858X}, abstract = {An 80-year-old male patient on maintenance hemodialysis was admitted with "high fever and cough." Pulmonary imaging suggested pneumonia, but his condition deteriorated rapidly despite empirical broad-spectrum antimicrobial therapy (covering bacteria, atypical pathogens, and fungi), progressing to respiratory failure and delirium. He was transferred to the intensive care unit for continuous renal replacement therapy. Routine microbiological tests (blood culture, sputum culture, respiratory pathogen PCR) were all negative. Detailed history revealed that the patient had kept a parrot for over a month prior to illness onset. Metagenomic next-generation sequencing of blood and sputum specimens detected abundant Chlamydia psittaci sequences. Following confirmation, treatment was adjusted to oral minocycline combined with intravenous azithromycin. The patient's temperature gradually normalized, neuropsychiatric symptoms resolved, and pulmonary imaging showed marked improvement, ultimately leading to successful discharge. This case highlights the importance of considering zoonotic pathogens in immunocompromised patients with refractory pneumonia. Detailed history-taking and metagenomic next-generation sequencing (mNGS) technology are crucial for early diagnosis. Early use of mNGS should be strongly considered in immunocompromised patients with severe pneumonia unresponsive to empiric therapy and negative routine workup, particularly when epidemiological clues such as bird exposure are present.}, }
@article {pmid42254409, year = {2026}, author = {Kong, H and Pan, J and Liu, J and Liang, M and Liu, L and Niu, H and Li, Y}, title = {Successful management of severe Pneumocystis jirovecii pneumonia with inhaled nitric oxide and individualized ventilatory strategies in an immunosuppressed patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1808578}, pmid = {42254409}, issn = {2296-858X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in extensive-stage small-cell lung cancer (SCLC) but may cause checkpoint inhibitor pneumonitis (CIP). Management of CIP often requires prolonged high-dose corticosteroids, leading to profound immunosuppression and increased risk of opportunistic infections. Among these, Pneumocystis jirovecii pneumonia (PJP) is a life-threatening complication in non-HIV patients and carries higher mortality than HIV-associated PJP. Early etiological diagnosis is therefore essential. We report a case of severe PJP diagnosed by metagenomic next-generation sequencing (mNGS) and successfully managed with comprehensive respiratory support.<br><br>CASE PRESENTATION: A 69-year-old HIV-negative man with extensive-stage SCLC received four cycles of etoposide-platinum chemotherapy plus adebrelimab. Subsequently, CIP developed and required prolonged high-dose methylprednisolone therapy. He was transferred to our hospital for progressive dyspnea. Evaluation showed severe hypoxemia (PaO&#x2082;/FiO&#x2082; 185&#x202f;mmHg) and markedly elevated serum 1,3-&#x3b2;-D-glucan (3327.99&#x202f;pg./mL). Bronchoalveolar lavage fluid mNGS identified P. jirovecii as the predominant pathogen, with Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans indicating mixed pulmonary infection. The patient received trimethoprim-sulfamethoxazole, cefoperazone-sulbactam, and caspofungin. Worsening respiratory failure required endotracheal intubation and mechanical ventilation. Lung recruitment maneuvers, individualized positive end-expiratory pressure titration, and adjunctive inhaled nitric oxide progressively improved oxygenation, allowing successful extubation and eventual discharge.<br><br>CONCLUSION: Severe PJP should be considered in non-HIV patients receiving corticosteroids for CIP. mNGS enabled rapid pathogen identification and targeted therapy. Comprehensive respiratory support, including optimized mechanical ventilation and inhaled nitric oxide, may be valuable in managing life-threatening opportunistic infections in immunosuppressed patients.}, }
@article {pmid42254474, year = {2026}, author = {Sparaciari, FE and Saylors, K and Chan, M and Perez, S and Firth, C and Horwood, PF and Karlsson, EA}, title = {Operationalizing metagenomic data from environmental surveillance for one health decision-making in live animal markets: Findings from a multisectoral workshop in Cambodia.}, journal = {Dialogues in health}, volume = {8}, number = {}, pages = {100312}, pmid = {42254474}, issn = {2772-6533}, abstract = {BACKGROUND: Live animal markets (LAMs) are recognized as hotspots for zoonotic disease emergence. Environmental surveillance (ES), particularly when paired with metagenomic sequencing, offers an advanced and actionable approach to pathogen detection in high-risk settings. However, the complexity of metagenomic data and the lack of user-friendly communication tools hinder its integration into routine public health decision-making.<br><br>METHODS: We conducted an exploratory qualitative participatory workshop study with descriptive analysis. A three-day multisectoral workshop was held in Phnom Penh, Cambodia, in May 2024, bringing together stakeholders from health, agriculture, and environment sectors to explore how metagenomic ES data can be visualized, understood, and applied. Through simulation exercises, surveys, and interviews, the workshop evaluated user preferences for data formats, thresholds for action, and decision-making strategies.<br><br>FINDINGS: In total, 52 participants attended the workshop and ten completed semi-structured interviews. Participants discussed their preferred familiar visualizations (bar, pie, and line charts) and intuitive color-coded thresholds (e.g., traffic-light schemes). While digital dashboards were welcomed, analog, printer-friendly formats remained essential due to infrastructure constraints. Key barriers to ES integration included limited bioinformatics capacity, lack of inter-ministerial coordination, and minimal ES prioritization at the provincial level.<br><br>INTERPRETATION: Metagenomic ES data can inform public health actions when visualization tools are tailored to end-user needs and embedded in multisectoral governance. This exploratory participatory workshop generated preliminary stakeholder-informed insights and an initial draft roadmap for future implementation planning in Cambodia. Further expert-led and funded work is needed to validate visualization tools, pathogen-specific thresholds, escalation pathways, and operational use under real-world surveillance conditions.}, }
@article {pmid42254492, year = {2026}, author = {Chang, Z and Wang, X and Zhao, M and Zhang, X and Li, S and Liu, Y and Zhang, S and Wang, J and Wang, X}, title = {MARM: a framework for malignancy risk prediction from host-derived CNV in bronchoalveolar lavage fluid mNGS data with microbial admixture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1846545}, pmid = {42254492}, issn = {1664-302X}, abstract = {Early identification and risk assessment of malignancy are essential for improving clinical decision-making and patient outcomes. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) data contain both microbial and host-derived signals, and a key challenge in extending such data to tumor-associated applications is the robust extraction of host features with discriminative value for malignancy from this complex, admixed background. To address this problem, we developed MARM, a malignancy risk prediction method centered on host-derived copy number variation (CNV). Using host-derived reads from BALF mNGS data, MARM performs genome-wide window-based coverage quantification, normalization and bias correction, reference baseline construction, and principal component-based denoising to derive window-level CNV features for malignancy risk modeling. In addition, a pseudo-label-based extension strategy was introduced to incorporate weakly labeled samples through high-confidence screening, and the performance of XGBoost, Random Forest, and generalized linear models (GLM) was systematically evaluated using CNV features, microbial features, and combined features. Models built on host-derived CNV features consistently outperformed those based on microbial features and achieved performance comparable to combined-feature models, while joint modeling did not provide a stable additional benefit. These findings indicate that, under the current data setting and feature construction strategy, CNV represents a more stable and informative discriminative signal than microbial features. Among the evaluated classifiers, XGBoost showed the best compatibility with window-level CNV features and outperformed Random Forest and GLM overall. On the independent validation set, the pseudo-label-enhanced MARM achieved the best overall performance, with a sensitivity of 0.686, specificity of 0.975, accuracy of 0.847, and Youden index of 0.671. By contrast, microbial features did not show stable independent discriminative ability, and combined modeling did not yield clear or sustained performance gains. Together, these results indicate that, in microbially admixed BALF mNGS data, host-derived CNV is more suitable than the evaluated microbial features as the core modeling signal for malignancy risk prediction. MARM provides a new methodological framework for malignancy prediction in complex clinical samples and offers a reference for deeper exploitation of host-derived signals in mNGS data and related auxiliary diagnostic applications.}, }
@article {pmid42254517, year = {2026}, author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P}, title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801806}, pmid = {42254517}, issn = {1664-302X}, abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.<br><br>METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.<br><br>RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC&#x202f;=&#x202f;0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7&#x3b1;,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.<br><br>CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.}, }
@article {pmid42254837, year = {2026}, author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM}, title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag082}, pmid = {42254837}, issn = {2730-6151}, abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.}, }
@article {pmid42255303, year = {2026}, author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W}, title = {Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1726191}, pmid = {42255303}, issn = {1664-462X}, abstract = {Biochar, a soil amendment with diverse regulatory functions, has been widely applied to enhance soil conditions. However, its underlying mechanism for alleviating continuous cropping obstacles, from the perspective of rhizosphere microbe-metabolite-plant coupling, remains to be further elucidated. Using cucumber (Cucumis sativus L.) as the model crop, this study explored the rhizosphere-mediated effects of biochar application under continuous cropping conditions via the analytical methods of metagenomics and metabolomics. Six biochar application rates (0, 5, 10, 20, 30, and 40 t ha[-][1]) were tested. All biochar treatments significantly improved cucumber yield by 20%-50%, with the C30 and C40 treatments producing the most pronounced yield enhancement. C10, C20, C30 and C40 treatments had a positive effect on cucumber quality, soil physicochemical properties and enzymatic activities. Vitamin C and soluble protein peaked in C20, whereas some sugar indicators decreased across all biochar treatments. Urease activity was significantly elevated under C20, C30, and C40 treatments. Notably, the C40 treatment led to marked increases in total nitrogen, available phosphorus, and sucrase activity. Biochar amendments also enriched key bacterial phyla involved in carbon and nitrogen cycling, including Actinobacteria, Bacteroidetes, Chloroflexi, and Bacillota. Medium to high application rates (C20, C30, C40) upregulated various secondary metabolic pathways associated with biotic stress resistance, including the biosynthesis pathways of phenylpropanoids, various alkaloids, and the metabolic pathway of phenylalanine. High biochar application rate (C40) characterized lipid metabolism as the core responsive pathway and significantly downregulated galactose metabolism. This study reveals that biochar application represents a promising strategy to mitigate continuous cropping obstacles of cucumber by enhancing nutrient cycling, enzyme activities, soil metabolite composition, and the rhizosphere microbial community in facility systems of the cold and arid northern regions of China.}, }
@article {pmid42255362, year = {2026}, author = {Sun, Y and Kei, K and Qiu, JW and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the feather duster worm, Sabellastarte sp. h YS-2021 (Sabellida: Sabellidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {274}, pmid = {42255362}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Sabellastarte sp. h YS-2021 (feather duster worm; Annelida; Polychaeta; Sabellida; Sabellidae). The genome sequence has a total length of 1 786.39 megabases. Most of the assembly (97.94%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.35 kilobases. From the metagenome data, we recovered 5 bins, of which one was a high-quality MAG.}, }
@article {pmid42255501, year = {2026}, author = {Huo, S and Liu, W and Lv, C and Liu, B and Xue, J and Hong, Y and Hao, Y and Chen, M and Xu, A and Tan, X and Feng, X and Li, S}, title = {The re-emergence of psittacosis in China: a scoping review of epidemiology, diagnostics, and One Health priorities.}, journal = {Science in One Health}, volume = {5}, number = {}, pages = {100158}, pmid = {42255501}, issn = {2949-7043}, abstract = {Psittacosis caused by Chlamydia psittaci has re-emerged in China as sporadic cases and localized outbreaks. However, current knowledge remains fragmented across the clinical, veterinary, epidemiological, and public health fields. This scoping review mapped studies on psittacosis in China, identified major knowledge gaps, and defined priorities for research, clinical management, and prevention and control. Following the Arksey and O'Malley framework and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), China National Knowledge Infrastructure (CNKI), Wanfang, PubMed, Web of Science, and Embase were searched for studies published between 1 January 1985 and 31 December 2025 and synthesized eligible studies with descriptive statistics and thematic analysis. A total of 424 studies were included. Research interest showed recent sharp increases and was concentrated in Eastern and Central China. Case reports and series dominated the literature, whereas analytic epidemiology, standardized surveillance, and high-resolution molecular studies remained limited. Reported cases were most often documented in middle-aged and older adults with avian exposure, including pet birds and poultry, and the reported occurrence showed a winter-spring pattern. Pneumonia was the predominant clinical presentation, and severe cases could progress to acute respiratory distress syndrome and multi-organ dysfunction. Metagenomic next-generation sequencing (mNGS) was the most frequently reported diagnostic method in recent studies, while PCR and serology remained important complementary tools. Overall, the literature is growing rapidly, but remains uneven in geographic coverage, study design, and integration across human, animal, and environmental sectors. These findings support broader One Health surveillance, stronger analytic and molecular epidemiology, and more standardized approaches to diagnosis, source investigation, and prevention in China.}, }
@article {pmid42256215, year = {2026}, author = {Li, C and Ye, X and Chen, Y and Shen, M and Zhou, Z and Jiang, H and Hu, L and Pan, H and Shen, D and Lin, Y and Wang, L}, title = {Pathogen spectrum of pulmonary infections in kidney transplant recipients and the diagnostic value of mNGS: a sputum and BALF study based on clinical decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1742153}, pmid = {42256215}, issn = {2235-2988}, mesh = {Humans ; *Sputum/microbiology/virology ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Kidney Transplantation/adverse effects ; Female ; Retrospective Studies ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Transplant Recipients ; *Clinical Decision-Making ; *Respiratory Tract Infections/microbiology/diagnosis ; Adult ; Bacteria/isolation &amp; purification/classification/genetics ; Metagenomics ; Fungi/isolation &amp; purification/classification/genetics ; Viruses/isolation &amp; purification/classification/genetics ; Coinfection/microbiology/diagnosis ; }, abstract = {BACKGROUND: Pulmonary infection is a common and severe post-transplant complication in kidney transplant recipients (KTRs). Their long-term immunosuppression results in an extremely complex pathogen spectrum. Compared with conventional etiological detection methods, metagenomic next-generation sequencing (mNGS) enables rapid and broad-spectrum pathogen identification. However, compared with bronchoalveolar lavage fluid (BALF), research on the diagnostic value of sputum - used as a non-invasive sample - for pulmonary infections in KTRs remains limited.<br><br>METHODS: A retrospective study included 77 kidney transplant recipients (KTRs) with pulmonary infections admitted from July 2021 to January 2025. BALF (n=37) or sputum (n=40) was collected for mNGS. Ninety-two non-immunosuppressed patients with pulmonary infections, treated during the same period and with BALF for mNGS, were also included. We compared pathogen profiles between the two groups and evaluated the diagnostic performance for KTRs pulmonary infections between BALF and sputum.<br><br>RESULTS: The pathogen spectrum in KTRs was dominated by viruses (43.0%) and opportunistic fungi (20.0%), whereas bacteria (67.97%) predominated in the non-immunosuppressed group. The co-infection rate was significantly higher in KTRs than in the non-immunosuppressed group (67.57% vs. 35.87%, P<0.001). In the KTRs cohort, the sputum group had a much higher prevalence of heart disease than the BALF group (52.5% vs. 2.7%, P<0.001). The positive detection rates of sputum and BALF mNGS showed no statistical difference (97.5% vs. 91.89%, P&#xa0;=&#xa0;0.268), but sputum mNGShad a higher concordance rate with the clinical composite diagnosis (95.0%) compared to BALF mNGS (81.08%). In both specimen types, mNGS achieved a significantly higher pathogen detection rate than conventional tests (P<0.001 for both), with poor agreement between the two approaches (Kappa < 0.2).<br><br>CONCLUSION: The pathogen spectrum of pulmonary infections in KTRs differs significantly from that in non-immunosuppressed patients. It is characterized by a predominance of viruses and opportunistic fungi. mNGS is superior to conventional methods for making an etiological diagnosis. Non-invasive sputum mNGS is a valuable diagnostic alternative in KTRs, particularly for patients unable or unwilling to undergo invasive procedures.}, }
@article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, mesh = {Animals ; Humans ; *Dysbiosis/complications/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/immunology/microbiology/therapy ; Intestinal Barrier Function ; Precision Medicine/methods ; *Probiotics/therapeutic use ; Diet Therapy ; Fatty Acids, Volatile/biosynthesis ; Plant Preparations/therapeutic use ; Antimicrobial Peptides/physiology ; Immunomodulation ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, }
@article {pmid42256253, year = {2026}, author = {Huang, W and Wang, S and Zhang, Y and Gao, M and Zhong, N and Hao, C and Janak, LP and Wang, L and Meng, S and Zhao, W and Zeng, S}, title = {Streptococcus mutans exacerbates gut microbiota dysbiosis in SHANK3 [-/-] autism model mice via the oral-gut axis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681259}, pmid = {42256253}, issn = {2000-2297}, abstract = {BACKGROUND AND OBJECTIVE: Autism spectrum disorder (ASD) is associated with gut microbiota dysbiosis, yet the impact of oral pathobiont translocation via the oral-gut axis remains unclear. This study investigated how Streptococcus mutans (S. mutans), a primary cariogenic pathogen, influences gut microbial structure and function in an ASD mouse model.<br><br>METHODS: SHANK3 knockout (SHANK3[-/-]) and wild-type (WT) mice were divided into four groups: WT control, WT S. mutans-gavaged (WT-S.m), SHANK3[-/-] control, and SHANK3[-/-] S. mutans-gavaged (SHANK3-S.m). Mice were gavaged with S. mutans UA159 twice weekly for five weeks, followed by fecal metagenomic sequencing (n&#x2009;=&#x2009;6 per group).<br><br>RESULTS: S. mutans translocated to the gut in both gavaged groups but did not achieve enhanced colonization in SHANK3[-/-] mice. S. mutans gavage significantly altered the gut microbiota structure in both WT and SHANK3[-/-] mice. In the ASD model, S. mutans gavage led to a significant enrichment of potential pathobionts (e.g. Duncaniella dubosii, Muribaculum gordoncarteri) and a decrease in beneficial bacteria (e.g. Bacteroides caecimuris, Bacteroides faecium). LEfSe analysis identified Parascardovia denticolens and Bacteroides heparinolyticus as specific biomarkers for the SHANK3-S.m group. Microbial networks showed reduced stability in SHANK3-S.m mice, with Enterocloster bolteae as a key node. Functional analysis revealed suppressed butanoate metabolism and enhanced neuroinflammation-related pathways.<br><br>CONCLUSION: Although S. mutans colonized only transiently, it provoked exacerbated ecological instability and pro-inflammatory metabolic alterations in ASD model mice, underscoring the role of the oral-gut-brain axis in ASD.}, }
@article {pmid42256259, year = {2026}, author = {Dewan, A and Mascellino, MT}, title = {Computational and multi-omics systems biology for precision microbiome therapeutics.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1842701}, pmid = {42256259}, issn = {2813-4338}, abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.}, }
@article {pmid42256958, year = {2026}, author = {Elendu, C and Debua, AT and Okolo, EH and Sadiq, HO}, title = {Immune Checkpoint Inhibitor Pneumonitis Complicated by Invasive Pulmonary Aspergillosis in COPD: Diagnostic and Therapeutic Challenges.}, journal = {Clinical case reports}, volume = {14}, number = {6}, pages = {e72755}, pmid = {42256958}, issn = {2050-0904}, abstract = {Checkpoint inhibitor-associated pneumonitis complicated by invasive pulmonary aspergillosis represents a diagnostic challenge in ICI-treated patients, particularly those with COPD receiving corticosteroid therapy. Persistent or worsening respiratory abnormalities despite immunosuppressive treatment should prompt reassessment for superimposed fungal infection, including bronchoscopy, BALF analysis, and microbiologic testing to facilitate diagnosis and targeted therapy.}, }
@article {pmid42257244, year = {2026}, author = {Moulignier, A and Heran, F and Lallemand, F and Bourdillon, P}, title = {Human Pegivirus Encephalitis With Brain Detection and Response to Sofosbuvir Ledipasvir.}, journal = {Annals of clinical and translational neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/acn3.70450}, pmid = {42257244}, issn = {2328-9503}, abstract = {Human pegivirus (HPgV-1) has been associated with severe encephalomyelitis in immunocompromised patients. Its neurological spectrum remains poorly defined. We report a slowly progressive encephalitis in a person living with well-controlled HIV, characterized by white matter abnormalities and inflammatory cerebrospinal fluid (CSF). HPgV RNA was detected in CSF and brain tissue by metagenomic sequencing, with no alternative pathogen identified. Following off-label treatment with sofosbuvir/ledipasvir, the patient showed sustained clinical improvement, normalization of CSF findings, and disappearance of detectable HPgV RNA. This observation expands the clinical context of HPgV-1 detection and supports further investigation of its role in central nervous system disease.}, }
@article {pmid42257696, year = {2026}, author = {Nebauer, DJ and Nelson, T and Romanis, C and Neilan, BA and Timms, VJ}, title = {Taxonomy bias in metagenome-assembled genome recovery.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42257696}, issn = {2057-5858}, mesh = {*Metagenome ; *Metagenomics/methods ; Shotgun Sequencing ; *Bacteria/classification/genetics ; Genome, Bacterial ; Phylogeny ; Base Composition ; Sequence Analysis, DNA/methods ; }, abstract = {The recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing is rapidly expanding the availability of representative genomes. However, this practice may skew the representation of specific taxa in real-world datasets. This bias is attributed primarily to the known inefficiencies of sequence-by-synthesis platforms in amplifying GC-rich and AT-rich sequence fragments. Here, we recover 216 medium- and high-quality MAGs from an Australian wetland site. Notably, no MAGs were recovered for some dominant cyanobacterial and proteobacterial species known to be present. A new protocol involving read-based classification and alignment to the MAG dataset demonstrated the highly efficient recovery of low-GC organisms in the Actinobacteria and Bacteroidota phyla. Additionally, the recovery of lost taxonomic information was demonstrated through unmatched sample mapping. The findings suggest a bias towards the recovery of smaller, low-GC organisms in MAG recovery, potentially skewing the global representation of microbial diversity. Our pipeline is made publicly available as a tool to help researchers estimate taxonomic losses following MAG recovery efforts.}, }
@article {pmid42258415, year = {2026}, author = {Pan, S and Chen, H and Sun, J and Xu, X and Gao, C}, title = {Species Identification And Antibiotic Susceptibility Testing Of The Nocardia Genus: Advances And Clinical Challenges.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/69977}, pmid = {42258415}, issn = {1940-087X}, mesh = {*Nocardia/drug effects/classification/genetics/isolation &amp; purification ; Humans ; *Anti-Bacterial Agents/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Microbial Sensitivity Tests/methods ; Nocardia Infections/microbiology/drug therapy/diagnosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The genus Nocardia comprises bacteria widely distributed in nature that can cause infections in both humans and animals. Due to their diverse clinical manifestations and prolonged culture time, infections are frequently misdiagnosed or overlooked. In recent years, advances in biological techniques have markedly improved molecular diagnostic methods, enabling more precise species identification. However, the increasing issue of antimicrobial resistance poses significant challenges for clinical management, particularly among immunocompromised patients, for whom treatment is more complex. Although multiple therapeutic agents are currently available, rising resistance rates highlight the critical importance of antibiotic susceptibility testing. This review discusses molecular identification methods for Nocardia species, including recent advances in 16S rRNA gene sequencing, multilocus sequence analysis (MLSA), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), and metagenomic next-generation sequencing (mNGS). The advantages and limitations of each technique are explored, with particular emphasis on their applications in detecting antibiotic resistance. The review also examines the clinical implementation of these molecular technologies, highlighting their contributions to rapid Nocardia identification, improved diagnostic accuracy, and reduced misdiagnosis. Finally, current limitations and future research directions are discussed, with particular attention to challenges related to cost, sensitivity, and standardization.}, }
@article {pmid42258525, year = {2026}, author = {Siegers, JY and Auerswald, H and Maquart, PO and Szentiványi, T and Guillebaud, J and Hoem, T and Li, X and Suor, K and Pum, L and Khun, L and Nuon, S and Chea, K and Heang, V and Bienes, KM and Su, YCF and Duong, V and Nouhin, J and Boyer, S and Karlsson, EA}, title = {Discovery of a novel coltivirus in a newly identified Bat Bug Species (Heteroptera: Cimicidae) in Cambodia.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {6}, pages = {e0014372}, pmid = {42258525}, issn = {1935-2735}, mesh = {Animals ; Cambodia ; Phylogeny ; *Chiroptera/parasitology ; *Coltivirus/isolation &amp; purification/genetics/classification ; Sequence Analysis, DNA ; Chlorocebus aethiops ; RNA, Viral/genetics ; Vero Cells ; Genome, Viral ; }, abstract = {Bats and their ectoparasites are significant reservoirs and potential vectors of emerging zoonotic pathogens, yet the viral diversity within bat-associated arthropods remains poorly characterized. This study reports the identification of a novel coltivirus (order Reovirales), provisionally designated Stricticimex coltivirus (SCCV), in a newly described bat bug species, Stricticimex phnomsampovensis, collected from cave-dwelling wrinkle-lipped free-tailed bats (Mops plicatus) in Cambodia. Metagenomic sequencing and phylogenetic analysis revealed that SCCV clusters within the Coltivirus genus, showing closest similarity to Tai Forest Reovirus (TFRV) previously isolated from African bats. SCCV was detected in 18.4% of examined bat bugs and successfully isolated in VeroE6 cells, with replication confirmed in multiple mammalian cell lines. The discovery of SCCV extends the known diversity and geographic range of coltiviruses and highlights bat ectoparasites as overlooked hosts of potentially zoonotic viruses. These findings underscore the importance of integrated One Health surveillance targeting both bats and their ectoparasites to better assess the risk of pathogen spillover in biodiverse regions with high human-animal contact.}, }
@article {pmid42258549, year = {2026}, author = {Vanhnollat, C and Chonephetsarath, S and Somlor, S and Vungkyly, V and Soulaphy, T and Vongsanga, S and Etobayeva, IV and Bigot, T and Wong, G and Letizia, AG and Brey, PT and Buchy, P and Vongphayloth, K}, title = {Detection and genetic characterization of Tembusu virus and other flaviviruses from mosquitoes in Lao PDR.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351023}, pmid = {42258549}, issn = {1932-6203}, mesh = {Animals ; *Flavivirus/genetics/isolation &amp; purification/classification ; Laos ; Phylogeny ; Female ; *Culicidae/virology ; Genome, Viral ; *Mosquito Vectors/virology ; Flavivirus Infections/virology ; Humans ; Mosquito-Borne Diseases ; }, abstract = {BACKGROUND: Lao People's Democratic Republic (Lao PDR), located in Southeast Asia and known for its rich biodiversity, is part of a region recognized as a hotspot for emerging and re-emerging infectious diseases. Among flaviviruses, dengue virus (DENV) and Japanese encephalitis virus (JEV) are recognized public health threats. However, other reemerging mosquito-borne flaviviruses may also infect humans and cause diseases. Despite that, their distribution and public health impact in Lao PDR are not well understood due to limited past surveillance.<br><br>METHODOLOGY: Mosquitoes were collected using CDC light traps from 2021 to 2024, as part of vector and pathogen surveillance studies conducted across six provinces. A total of 2,548 female mosquitoes, representing 100 species from 11 genera, were collected and morphologically identified. Of these, 1,622 mosquitoes were pooled into 1,008 "mini pools" according to species and collection site. The pools were screened for flaviviruses by nested RT-PCR. Positive samples were further analysed by metagenomic sequencing, and coding-complete genomes were recovered and subjected to phylogenetic analysis.<br><br>PRIMARY RESULTS: We recovered thirteen coding-complete genomes through metagenomic sequencing, which included one Tembusu virus (TMUV) strain (TMUV/Mos_L010) from Culex vishnui mosquitoes and 12&#xa0;other insect-specific flaviviruses (ISFVs). Phylogenetic analysis placed TMUV/Mos_L010 in cluster 3, closely related to a TMUV strain known to be pathogenic to dolphins in Thailand, with more than >99% bootstrap support for amino acid homogeneity. The detected ISFVs were part of the classical insect-specific flavivirus (cISFV) lineage and were further classified into five subgroups according to their associated mosquito genera: Aedes (1), Anopheles (1), Culex (2), and Uranotaenia (1).<br><br>CONCLUSIONS: This study documents the first detection of TMUV in Laotian mosquitoes and extends the known distribution of cluster 3 TMUV strains. The discovery of diverse ISFVs shows the rich and underexplored virome among Laotian mosquito populations. These findings highlight the need for enhanced arbovirus surveillance and ecological research to assess zoonotic risks of spillover infections in Southeast Asia.}, }
@article {pmid42258623, year = {2026}, author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN}, title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.}, journal = {Annals of the American Thoracic Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/annalsats/aaoag152}, pmid = {42258623}, issn = {2325-6621}, abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.<br><br>METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter&#xae; and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA&#x2122; proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.<br><br>RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10&#x2009;years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP&#x2011;1) profile (78%); neutrophilic recruiting, high&#x2011;Th17 (71%); eosinophilic dominant, high&#x2011;Th2 (51%); Th2/Th17&#x2011;high (47%), and Th2/Th17&#x2011;low (25%). PCD demonstrated increased neutrophil, and CD45&#x2011;related gene expression and activation of ten inflammatory pathways, including NF&#x2011;&#x3ba;B, oxidative stress, T&#x2011;cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P&#x2009;<&#x2009;.01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.<br><br>DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.}, }
@article {pmid42259326, year = {2026}, author = {Martins, MF and Govindan, R and Almaghlouth, NK and Kirby, JE and Kentoffio, KJ and Farmakiotis, D and Le-Mahajan, A}, title = {A fatal case of Legionella micdadei prosthetic valve endocarditis diagnosed by plasma microbial cell-free DNA metagenomic sequencing.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00223-9}, pmid = {42259326}, issn = {1474-4457}, abstract = {We report a fatal case of Legionella micdadei prosthetic valve endocarditis in a patient who was immunocompromised, characterised by an indolent outpatient course followed by rapid clinical deterioration into mixed shock secondary to valve dehiscence and sepsis. The diagnosis was made by plasma microbial cell-free DNA metagenomic next-generation sequencing (mcfDNA-mNGS) and confirmed by buffered charcoal yeast extract culture of valve tissue. This case underscores the diagnostic limitations of conventional methods in culture-negative endocarditis, the evolving role of mcfDNA-mNGS in culture-negative endocarditis, and the absence of current culture-negative endocarditis guidelines addressing timely diagnosis for patients who are at risk of rapid deterioration. In this Grand Round, we briefly review the state of diagnostics for culture-negative endocarditis and the particularities of Legionella endocarditis. We also propose a framework for deciding when to consider early metagenomic testing, balancing the potential strengths of this technology with its limitations and cost.}, }
@article {pmid42259450, year = {2026}, author = {Yang, W and Wang, X and Li, H and Liu, W and Chen, Z and Ren, B and Guo, T and Guo, J}, title = {Enhanced co-removal of nitrate and tetracycline from wastewater by iron-nitrogen-doped carbon: synergistic role of pyridinic nitrogen and iron.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135105}, doi = {10.1016/j.biortech.2026.135105}, pmid = {42259450}, issn = {1873-2976}, abstract = {Co-pollution of nitrate and tetracycline (TC) poses a critical barrier to efficient biological treatment due to impaired electron transfer, diminished microbial metabolic activity, and disrupted community structure. To address this challenge, this study synthesized an iron-nitrogen-doped carbon material (Fe-NC) featuring electron-withdrawing pyridinic nitrogen and Fe active sites. Under co-contaminated conditions, the nitrate and TC removal efficiencies of the TC/Fe-NC200 system were 100 % and 96 %, which were 21.27 and 2.18 times higher than those of the TC system. Material characterization indicated that Fe-NC might act as an electron transfer station, promoting the removal of nitrate and TC through Fe[3+]/Fe[2+] cycling. Electrochemical analyses showed that Fe-NC promotes the secretion of cytochrome c and flavin mononucleotide, accelerating extracellular electron transfer. Enzyme activity assays indicated that Fe-NC enhances intracellular electron transfer by activating key redox enzymes and upregulating associated gene expressions. Electron transfer system activity and metagenomic analysis further demonstrated that Fe-NC improves microbial respiration and increases the abundance of dominant taxa such as Bacteroidota (11.96 %) and Chryseobacterium (12.00 %), which support both TC degradation and microbial stress tolerance. These mechanistic insights establish a novel, bio-electroactive function for Fe-NC, in which the synergistic effects of Fe redox cycling and pyridinic nitrogen coordination led to improved electron flow, microbial function, and pollutant breakdown. This work not only reveals a previously unexplored pathway for biological co-removal of nitrate and antibiotics but also provides a scalable strategy for enhancing bioremediation efficiency in complex wastewater systems.}, }
@article {pmid42259455, year = {2026}, author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G}, title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135106}, doi = {10.1016/j.biortech.2026.135106}, pmid = {42259455}, issn = {1873-2976}, abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.}, }
@article {pmid42259841, year = {2026}, author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y}, title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01038-z}, pmid = {42259841}, issn = {2055-5008}, abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.}, }
@article {pmid42260308, year = {2026}, author = {Li, L and DU, L}, title = {[Clinical value of cerebrospinal fluid metagenomic next genera-tion sequencing in diagnosing neonatal intracranial infections].}, journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences}, volume = {}, number = {}, pages = {1-10}, doi = {10.3724/zdxbyxb-2025-0965}, pmid = {42260308}, issn = {1008-9292}, abstract = {OBJECTIVES: To evaluate the diagnostic performance of cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) for neonatal intracranial infections and its impact on clinical decision making.<br><br>METHODS: A retrospective observational study was conducted. Neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent CSF mNGS were enrolled. The sensitivity of mNGS and its concordance with CSF culture and PCR were calculated. Clinical impact was assessed using predefined criteria, and samples were categorized into positive impact and no impact groups to identify independent factors influencing the clinical utility of mNGS.<br><br>RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95% CI: 18.7%-46.3%), higher than that of culture PCR (18.8%, 95% CI: 8.9%-32.6%), but the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and culture PCR were 66.7% (95% CI: 29.9%-92.5%) and 76.9% (95% CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 37.7% (23/61) of patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, and 11 cases with negative results led to antibiotic de escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR = 22.127, P<0.01).<br><br>CONCLUSIONS: CSF mNGS provides valuable support in etiological diagnosis and clinical decision making for neonatal intracranial infections.}, }
@article {pmid42260359, year = {2026}, author = {Lu, F and Li, Y and Chen, X and Chen, Y and Li, C and Nong, G and Liu, J and Wei, Q}, title = {Community-acquired pseudomonas aeruginosa pneumonia in immunocompetent children: a study of 7 cases.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13768-8}, pmid = {42260359}, issn = {1471-2334}, support = {AD22035219//Guangxi Clinical Research Center for Pediatric disease/ ; 2025GXNSFAA069702//The National Natural Science Foundation of Guangxi/ ; }, abstract = {BACKGROUND: To characterize the clinical features and outcomes of community-acquired Pseudomonas aeruginosa (PA) pneumonia in immunocompetent children.<br><br>METHODS: A retrospective analysis was conducted on seven immunocompetent children with community-acquired PA pneumonia hospitalized between January 2015 and June 2025. Pneumonia was defined by acute respiratory symptoms with new radiographic infiltrates. PA infection was confirmed by culture from sterile sites/lower respiratory tract or metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid.<br><br>RESULTS: All patients were male (n&#x2009;=&#x2009;7). Age distribution was as follows: 1-12 months (n&#x2009;=&#x2009;3), 13-36 months (n&#x2009;=&#x2009;1), 37-60 months (n&#x2009;=&#x2009;1), and &#x2265;&#x2009;61 months (n&#x2009;=&#x2009;2). Median age at onset was 18.0 months (IQR: 8.0-123.0). All patients presented acutely with fever and cough; two developed respiratory failure within 72&#xa0;h. Additional clinical features included dyspnea (n&#x2009;=&#x2009;4), lung rales (n&#x2009;=&#x2009;4), hemoptysis (n&#x2009;=&#x2009;3), chest pain (n&#x2009;=&#x2009;2), and wheezing (n&#x2009;=&#x2009;1). Chest imaging showed lobar consolidation (n&#x2009;=&#x2009;5) or mass-like consolidation (n&#x2009;=&#x2009;2). A total of seven cases were identified, with PA confirmed by culture in four patients and by mNGS of bronchoalveolar lavage fluid in three patients. All isolates were susceptible to anti-pseudomonal &#x3b2;-lactam antibiotics except aztreonam. Complications included definite or suspected empyema (n&#x2009;=&#x2009;5), pyopneumothorax (n&#x2009;=&#x2009;3), and bacteremia (n&#x2009;=&#x2009;2). Three patients required pediatric intensive care, two received invasive mechanical ventilation, two underwent closed thoracic drainage, and one required decortication. There were no deaths, but 4 patients sustained significant residual lung injury secondary to necrotizing pneumonia.<br><br>CONCLUSION: Although rare, community-acquired PA pneumonia in immunocompetent children is associated with severe disease and pulmonary complications. Initial therapy with anti-pseudomonal &#x3b2;-lactam antibiotics appears effective in improving outcomes. Repeated cultures are recommended in the cases who remain symptomatic.}, }
@article {pmid42260652, year = {2026}, author = {Le Moigne, A and Andrei, A&#x15e; and Pernthaler, J}, title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02442-5}, pmid = {42260652}, issn = {2049-2618}, abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.<br><br>RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.<br><br>CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.}, }
@article {pmid42260783, year = {2026}, author = {Hao, M and Sha, Y and Gao, J and Niu, J and Xu, Y}, title = {Concurrent Spinal Dural Arteriovenous Fistula and Varicella-Zoster Virus Meningoencephalitis Unmasked by Corticosteroid-Associated Deterioration: A Case Report on the Diagnostic Value of Serial mNGS.}, journal = {Current medical imaging}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115734056496224260602072444}, pmid = {42260783}, issn = {1573-4056}, abstract = {BACKGROUND: Concurrent spinal dural arteriovenous fistula (SDAVF) and varicella-zoster virus (VZV) meningoencephalitis are exceptionally rare, and overlapping features can delay diagnosis. This case adds to the literature by illustrating how corticosteroid exposure before exclusion of vascular and infectious mimics may be followed by neurological deterioration, and by emphasizing the diagnostic value of serial metagenomic next-generation sequencing (mNGS).<br><br>CASE PRESENTATION: A 48-year-old man developed insidious bilateral lower-limb weakness that progressed to numbness, sphincter dysfunction, and near-paralysis. Initial spinal magnetic resonance imaging showed diffuse thoracolumbar cord lesions; cerebrospinal fluid studies were mildly inflammatory, and myelitis was suspected. He received methylprednisolone pulse therapy followed by oral corticosteroids without improvement. One month later, he presented with fever, severe headache, vomiting, worsening paralysis, and altered mental status. Cerebrospinal fluid demonstrated marked pleocytosis, hypoglycorrhachia, and elevated protein, and mNGS detected abundant VZV sequences. Brain imaging showed hydrocephalus, meningeal enhancement, multifocal ischemic lesions, and intracranial arterial stenoses, consistent with VZV meningoencephalitis and vasculopathy. After external ventricular drainage, intravenous acyclovir, dexamethasone for cerebral edema, and empirical anti-tuberculosis therapy, serial mNGS showed a reduced VZV burden. Repeat spinal imaging revealed tortuous perimedullary vessels and hemosiderin deposition, and angiography confirmed SDAVF from the left T10 intercostal artery. The fistula was coagulated. At 12-month follow-up, he regained slight right-leg movement and partial sensory recovery above L1.<br><br>CONCLUSION: Progressive myelopathy with atypical inflammatory features should prompt vascular evaluation and pathogen testing. Serial mNGS can identify coexisting infection, guide therapy, and help avoid hazardous empirical corticosteroid use when the diagnosis remains uncertain.}, }
@article {pmid42261054, year = {2026}, author = {Foster, NR and Holman, LE and Armbrecht, L and Courtin, J and Jensen, T and Pedersen, MW and Schreiber, L and Schroeder, H and Seersholm, FV and Zampirolo, G and Bohmann, K and Zimmermann, HH}, title = {A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70152}, pmid = {42261054}, issn = {1755-0998}, support = {101105307//European Union's Horizon Europe Marie Sklodowska-Curie Actions/ ; 856488//European Union's Horizon 2020 Research and Innovation Program/ ; //Independent Research Fund Denmark/ ; DP250100886//Australian Research Council (ARC)/ ; DP250103420//Australian Research Council (ARC)/ ; }, mesh = {*DNA, Ancient/isolation &amp; purification ; *Nucleic Acid Hybridization/methods ; *DNA, Environmental/isolation &amp; purification/genetics ; *Metagenomics/methods ; *Paleontology/methods ; }, abstract = {Recovering ancient DNA from environmental samples is transforming the way we understand historical ecosystems. While high-throughput sequencing of the total DNA in environmental samples (shotgun metagenomic sequencing) reveals the taxonomic contents of these samples, the genetic signals of some taxa (e.g., eukaryotes) can be weak compared to the background levels of DNA from organisms such as bacteria, requiring deep sequencing approaches that are costly. Thus, to increase cost-effectiveness, pre-sequencing enrichment of target DNA can be advantageous. One technique to enrich this target DNA is hybridisation capture, where short RNA or DNA baits are designed to match, bind and isolate specific stretches of DNA. Hybridisation capture has previously been applied to recover DNA from ancient skeletal remains, but it is only beginning to emerge as an approach to characterise organisms from ancient environmental samples. Thus, there is limited information on establishing hybridisation capture workflows for ancient environmental DNA applications, including the limitations and advantages. This mini review focuses on establishing a roadmap for the applications of hybridisation capture to ancient environmental DNA samples.}, }
@article {pmid42262077, year = {2026}, author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y}, title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0113225}, doi = {10.1128/spectrum.01132-25}, pmid = {42262077}, issn = {2165-0497}, abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.<br><br>IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.}, }
@article {pmid42262118, year = {2026}, author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P}, title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0050126}, doi = {10.1128/msystems.00501-26}, pmid = {42262118}, issn = {2379-5077}, abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.}, }
@article {pmid42262136, year = {2026}, author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G}, title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028426}, doi = {10.1128/msystems.00284-26}, pmid = {42262136}, issn = {2379-5077}, abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.<br><br>IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.}, }
@article {pmid42262316, year = {2026}, author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J}, title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.5c00556}, pmid = {42262316}, issn = {1520-5010}, abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.}, }
@article {pmid42262390, year = {2026}, author = {Weissman, JL and Walling, A and Ducklow, H and Zakem, EJ}, title = {Genomic Traits Associated with Copiotrophy Decouple from Maximum Growth Rate Predictions Along Temperature Gradients.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag147}, pmid = {42262390}, issn = {1751-7370}, abstract = {Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms, in part because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the world's oceans, where deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, leading to the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured along a temperature gradient. Our results suggest that, as a result of temperature's confounding effects, genomic signatures of growth optimization often better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as growth beyond a thermodynamic baseline maximum growth rate, rather than in relation to a static rate cutoff.}, }
@article {pmid42263510, year = {2026}, author = {Ergunay, K and Bourke, BP and Kamau, M and Fustec, B and Osborne, CJ and Mutura, J and Lebunge, R and Ochieng, G and Onyango, T and Cruz, A and Campos, M and Pott, MC and Romero, U and Deakins, AG and Paoli, J and Liao, HM and von Fricken, ME and McDermott, EG and Jiang, L and Grieco, JP and Achee, NL and Linton, YM}, title = {Unbiased long read metagenomic screening reveals diverse jingmen tick virus genomes across continents.}, journal = {Virology}, volume = {623}, number = {}, pages = {110999}, doi = {10.1016/j.virol.2026.110999}, pmid = {42263510}, issn = {1096-0341}, abstract = {Jingmen tick virus (JMTV) is an emerging tick-associated virus related to flaviviruses. Substantial information gaps remain on the epidemiology and public health impact of JMTV, despite evidence for symptomatic human infections, detection in potential zoonotic reservoirs and widespread global circulation. Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages. JMTV genome segments were assembled in 16.7% of the pools with initial virus detection. Adult ticks comprising Amblyomma gemma, Hyalomma rufipes, Rhipicephalus. evertsi and Rhipicephalus pulchellus from Kenya yielded complete JMTV genome assemblies. Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae. Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity. Further investigations and expanded screening are needed to elucidate JMTV and arbo-jingmenvirus global epidemiology.}, }
@article {pmid42263617, year = {2026}, author = {Chen, C and Li, J and Wang, F and Cheng, M and Sheng, T and Ahmed, Z and Hu, J and Zhou, Y}, title = {Auxiliary fermentation with Pediococcus acidilactici C1 reshapes flavor formation in sufu: An integrated metagenomic, flavoromic and non-targeted metabolomic deciphering.}, journal = {Food chemistry}, volume = {521}, number = {}, pages = {149979}, doi = {10.1016/j.foodchem.2026.149979}, pmid = {42263617}, issn = {1873-7072}, abstract = {Sufu, a traditional Chinese fermented soybean product, relies on spontaneous microbial succession for flavor, leading to high variability. Starter-assisted fermentation improves flavor; this study explores sufu flavor differences and mechanisms between spontaneous and Pediococcus acidilactici C1-inoculated processes. The findings demonstrated that inoculation with P. acidilactici C1 markedly enhanced the diversity and concentration of flavor compounds in sufu. Notably, 12 key taste-active free amino acids were detected, with glutamate up by 14% and aspartic acid showing an approximate 20-fold increase. A total of 15 key volatile flavor compounds were characterized, among which 8 were newly uncovered, namely ethyl 2-methylbutanoate, ethyl acetate, ethyl butyrate, ethyl caprylate, ethyl 2-ethylhexanoate, ethyl propionate, isoamyl acetate and 3-octanol. Metagenomics revealed enrichment of genes related to carbohydrate transport, amino acid/lipid metabolism, while non-targeted metabolomics confirmed metabolic remodeling. Multi-omics analyses showed P. acidilactici C1 reprogrammed carbon flux and boosted amino acid/lipid-derived volatile biosynthesis, enabling flavor-enhancing starter development.}, }
@article {pmid42263645, year = {2026}, author = {Xing, Y and Huang, X and Luo, J and Wei, D and Chen, H and Sun, X}, title = {Active carbon-fixing microbes and their role in carbon fixation in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119962}, doi = {10.1016/j.marpolbul.2026.119962}, pmid = {42263645}, issn = {1879-3363}, abstract = {Mangroves are vital blue carbon ecosystems, yet the microbial drivers of carbon fixation in their soils remain poorly understood. Here, this study investigated the patterns of drivers carbon-fixing microbes and their functional genes across three representative mangrove bays in the Beibu Gulf of the South China Sea (Lianzhou Bay, Maowei Sea and Zhenzhu Bay) using an integrated geochemical and metagenomic approach. The findings showed that: (1) the distribution of total organic carbon (TOC) in mangrove soils was significantly influenced by tidal zonation and mangrove plants, with TOC content in the mid-tidal zone consistently exceeding that in adjacent mudflats by 1.5- to 2.3-fold (p < 0.01); (2) potential dominant carbon fixation pathways inferred from soil microbial communities may vary significantly across different areas, including chemolithoautotrophic taxa (e.g., Nitrospira, Thiobacillus), phototrophic cyanobacteria (e.g., Synechococcus, Cyanobium), and mixotrophic assemblages. Correspondingly, the relative abundances of key functional genes (e.g., narH, narG, fabB, oadB) exhibited significant differences among these bays; (3) environmental factors including salinity, nutrients, and heavy metals jointly influenced the accumulation of carbon fixation genes and their microbial hosts, collectively explaining 63.9% of community variation at the species level. This study provides a mechanistic understanding of microbial functional diversity that underpins carbon cycling in mangrove soils, offering quantitative insights for the conservation and management of blue carbon ecosystems under anthropogenic pressures.}, }
@article {pmid42263665, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2026020270}, pmid = {42263665}, issn = {2473-9537}, abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).}, }
@article {pmid42263908, year = {2026}, author = {Figueroa-Ortiz, C and Schoninger, S and Chan, JL and Bermudez, TA and Li, Y and Cander, S and Mcgonagle, B and Bacon, CW and Kalchiem-Dekel, O and Chawla, M and Lin, R and Tamari, R and Shaffer, BC and Perales, MA and Redelman-Sidi, G and Shahid, Z and Loganathan, R and Kamboj, M and Papanicolaou, G and Lee, YJ}, title = {Tuberculosis After Allogeneic Hematopoietic Cell Transplant: A 15-Year Case Series Highlighting Diagnostic Challenges.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.06.007}, pmid = {42263908}, issn = {2666-6367}, abstract = {BACKGROUND: Tuberculosis (TB) is an uncommon but potentially fatal complication after allogeneic hematopoietic cell transplant (HCT). Diagnosis is often delayed due to nonspecific clinical presentations, limited sensitivity of screening tests for latent TB infection, and slow turnaround of conventional TB diagnostic methods.<br><br>OBJECTIVE: The study aim is to describe the clinical and diagnostic characteristics of allogeneic HCT recipients with TB in the era of molecular and sequence based diagnostic methods.<br><br>STUDY DESIGN: We conducted a retrospective review of microbiologically confirmed TB cases among HCT recipients at a tertiary cancer center from 2010 to 2025. We detail clinical, demographic, and diagnostic characteristics including metagenomic next-generation sequencing (mNGS) testing of bronchoalveolar lavage (BAL) and blood (Eurofins Viracor, Lenexa, KS) for two individuals.<br><br>RESULTS: Ten patients were diagnosed with active TB at a median of 122 days post-HCT (range: 36-2,557). The median age was 53 years, and 6 were males. Except for one patient, all patients were foreign-born. Pre-HCT TB screening was performed in 7 patients; however, only 3 had positive (tuberculin skin test, n=1; interferon-gamma release assay [IGRA], n=2), and 1 had indeterminate IGRA results. All patients had abnormal CT chest findings compatible with latent TB. Nine of 10 patients presented with either fever or cough, while one patient was asymptomatic with incidental radiographic abnormalities. TB was diagnosed by MTB PCR in 8 cases, 4 patients had disseminated TB, and 3 died. mNGS results were available in two patients. In both cases MTB was detected in BAL, and in one, MTB was detected in the blood. Among 9 patients with available susceptibility testing data, moxifloxacin resistance was identified in one case.<br><br>CONCLUSIONS: In our cohort, post-HCT TB occurred mainly in foreign-born patients. Infection was diagnosed early after transplant and was frequently disseminated, with high mortality. These results underscore the limitations of current screening methods, and the diagnostic challenges of post-HCT TB.}, }
@article {pmid42263990, year = {2026}, author = {Meng, Q and Zeng, W and Zhang, J and Liu, H and Li, S and Peng, Y}, title = {Efficient nutrient removal from low C/N municipal wastewater using a phototrophic biofilm system integrating simultaneous nitrification-denitrification and phosphorus removal (SND).}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {124859}, doi = {10.1016/j.envres.2026.124859}, pmid = {42263990}, issn = {1096-0953}, abstract = {Microalgae-bacteria systems based on phosphorus-accumulating organisms (PAOs) offer low-energy and low-carbon-emission solutions for wastewater treatment, but their performance declines with low carbon-to-nitrogen (C/N) ratios municipal wastewater. In this study, a phototrophic biofilm system capable of coupling simultaneous nitrification-denitrification with phosphorus removal (P-SNDPRB) was developed to enhance low C/N ratios (3.32-4.11) municipal wastewater treatment. Before biofilm integration, total nitrogen (TN) removal was below 75%. After integration, TN removal increased to over 82%, while organic matter and phosphorus removal efficiencies remained at 85% and 90% in the P-SNDPRB system, respectively. Microalgae photosynthesis supplied oxygen to the biofilm, enabling denitrification. Chemometric and metagenomic analyses revealed denitrification and phosphorus accumulating metabolism (PAM) as key pathways for nitrogen and phosphorus removal. Flow cytometry sorting showed that biofilm spatial distribution promoted synergistic interactions among Accumulibacter, Competibacter, Nitrosomonas, Chlorella, and Cyanobacteria, further enhancing nitrogen and phosphorus removal. This study provides a low-energy and sustainable approach for the treatment of municipal wastewater with a low C/N ratio.}, }
@article {pmid42264042, year = {2026}, author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H}, title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135134}, doi = {10.1016/j.biortech.2026.135134}, pmid = {42264042}, issn = {1873-2976}, abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.}, }
@article {pmid42264047, year = {2026}, author = {Xu, YY and Tan, X and Dang, CC and Zhao, ZC and Fang, R and Fan, L and Ren, NQ and Xie, GJ and Wu, YN}, title = {Metagenomic insights into Thermus-mediated sulfur oxidation, nitrogen cycling, and thermoadaptation in thermophilic autotrophic denitrification bioreactors.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135137}, doi = {10.1016/j.biortech.2026.135137}, pmid = {42264047}, issn = {1873-2976}, abstract = {Thermus species are widely recognized as a key group of heterotrophic denitrifiers mediating carbon, nitrogen, and sulfur cycling in geothermal habitats, and have attracted extensive research attention for their thermostable enzyme resources. However, their autotrophic denitrification potential remains poorly characterized, and the systems-level mechanisms underlying their thermal adaptation remain incompletely understood. This study presents three high-quality metagenome-assembled genomes (MAGs) of Thermus from autotrophic sulfur-based denitrification bioreactors. These MAGs encode the complete genetic potential for the Calvin-Benson-Bassham cycle, reductive tricarboxylic acid cycle, and 3-hydroxypropionate bicycle for inorganic carbon fixation. Thermus strains employ a distinct sulfide oxidation route: HS[-] is first oxidized to polysulfides or glutathione persulfide by fccAB, then condensed with sulfite to form thiosulfate via rhodanese, and finally completely oxidized to sulfate by complete sox cluster. T. scotoductus (MAG1) carries genes for nitrate reduction (narGHI) and dissimilatory nitrate reduction to ammonium (nrfA and nrfH). As conspecific strains, MAG2 and MAG3 harbor abundant denitrification genes (nar, nirK, norBC), indicating strong substrate-driven metabolic plasticity. A protein-protein interaction network further elucidated the systems-level thermoadaptive survival mechanisms of T. scotoductus, identifying chaperone-mediated protein homeostasis and DNA repair-dependent genomic stability as core adaptive strategies, alongside orphan nodes (e.g., aceE, lpd, nuoC) with potential independent functions. Collectively, these findings advance our understanding of Thermus' metabolic plasticity, offer valuable thermostable resources for high-temperature wastewater treatment and industrial applications, and bridge critical knowledge gaps in the autotrophic metabolism and thermoadaptive regulation of thermophilic bacteria-laying a robust genomic foundation for the development and optimization of high-temperature biotechnological processes.}, }
@article {pmid42264152, year = {2026}, author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TT}, title = {Enteral iron dose effect on iron storage, intestinal barrier, and gut microbiome in preterm infants: a randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {101389}, doi = {10.1016/j.ajcnut.2026.101389}, pmid = {42264152}, issn = {1938-3207}, abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.<br><br>OBJECTIVES: This study aimed to compare the effects of 2 enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.<br><br>METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/d, or a higher dose of 6 mg/kg/d of total enteral iron. The primary outcome was the fecal microbiome after 2 wk on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 wk postmenstrual age were also evaluated.<br><br>RESULTS: Among 151 randomly assigned infants who received study iron (77 low dose; 74 high dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In the subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/d had higher posttreatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/d. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.<br><br>CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/d was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/d dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants. This trial was registered at clinicaltrials.gov as NCT04497012.}, }
@article {pmid42264207, year = {2026}, author = {Laovechprasit, W and Avila-Reyes, VA and Stacy, BA and Young, KT and Harris, HS and Tuttle, AD and Sirpenski, G and Kennedy, AE and Innis, CJ and Norton, TM and Zirkelbach, B and Stanton, JB}, title = {Surveillance of gastrointestinal viruses of free-ranging and rehabilitated Sea turtles in the United States.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {142}, number = {}, pages = {105966}, doi = {10.1016/j.meegid.2026.105966}, pmid = {42264207}, issn = {1567-7257}, mesh = {Animals ; *Turtles/virology ; United States/epidemiology ; Phylogeny ; Genome, Viral ; *Viruses/classification/genetics/isolation &amp; purification ; *Gastrointestinal Diseases/veterinary/virology ; *Gastrointestinal Tract/virology ; }, abstract = {Sea turtle populations are imperiled globally, primarily due to anthropogenic threats. However, non-anthropogenic factors, such as infectious diseases, can affect their population stability. Viruses are common causes of gastrointestinal disease in many species, and gastrointestinal signs are regularly observed among sea turtles, but little is known about enteric viruses in sea turtles. Establishing basic knowledge of viral diversity and evolutionary relationships is a necessary step towards understanding potential health impacts. This study investigated the viral genome contents of seventy-seven gastrointestinal specimens from six species of sea turtles with varying health conditions from the Atlantic and Pacific coasts of the United States. Forty-eight, non-plant and non-bacteria infecting viruses were detected (≥5 viral-like reads per sample) through random RNA sequencing. Detected viral sequences were then confirmed and characterized by semi-targeted, strand-switching sequencing, which provided deeper sequencing metrics allowing for phylogenetic characterization (>10× depth) for nineteen viruses across eight viral families, including seven putative novel viral species, one putative novel genus, and eleven likely novel viral sequences from taxa that lack established species demarcation criteria. Sixteen RNA viruses were characterized: four double-stranded RNA viruses (Partitiviridae, Totiviridae, and Picobirnaviridae), eleven positive-sense single-stranded RNA viruses (Caliciviridae, Dicistroviridae, unclassified Hepelivirales, and unclassified Picornavirales), and one negative-sense bisegmented RNA virus (Chuviridae). Three DNA viruses were also identified (Parvoviridae, Circoviridae, and unclassified Cressdnaviricota). Viruses identified in this study were often genetically related to viruses previously known to infect aquatic invertebrates and fish. This study provides baseline knowledge of viral communities in sea turtles and will serve as a foundation for future hypothesis-driven research to understand their relevance to sea turtle health.}, }
@article {pmid42264211, year = {2026}, author = {Bhadelia, N and Gikandi, I and Lassmann, B}, title = {Regional Signals Preceding the 2026 Bundibugyo Virus Disease Outbreak.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108862}, doi = {10.1016/j.ijid.2026.108862}, pmid = {42264211}, issn = {1878-3511}, abstract = {BACKGROUND: The May 2026 Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo was declared a Public Health Emergency of International Concern after substantial undetected community transmission. We describe regional surveillance signals detected by the Biothreats Emergence, Analysis, and Communications Network (BEACON), our open access event based surveillance program, in the weeks preceding outbreak declaration.<br><br>METHODS: We reviewed BEACON reports of VHF-compatible illness clusters detected in the transboundary DRC-Uganda-Burundi-South Sudan region during March-April 2026, prior to the May 15 laboratory confirmation of BDBV.<br><br>RESULTS: BEACON detected four temporally proximal VHF-compatible illness signals: (1) March 9, North Kivu Province-suspected Ebola case under investigation with unresolved laboratory results; (2) March 10, Kasa&#xef; Province-fatal hemorrhagic illness with secondary cases and negative Ebola PCR; (3) March 30, Burundi-35-case undiagnosed cluster near the DRC border with 5 deaths, negative testing for major filoviruses and >200 pathogens, pending metagenomic sequencing; (4) April 22, South Sudan-three suspected VHF cases with negative initial testing. All four signals shared a similar diagnostic phenotype: VHF-compatible presentation, mobilization of investigation teams, negative initial testing, and no publicly reported confirmed etiology. None were formally reported to have been resolved.<br><br>CONCLUSIONS: Our detection of four unresolved VHF signals preceding the confirmed BDBV outbreak highlights gaps in formal follow-up mechanisms for negative cases and fragmented regional diagnostic coordination. In light of confirmed BDBV circulation and Africa CDC's identification of 10 countries at high risk for spread, these preceding signals warrant urgent retrospective investigation and laboratory.}, }
@article {pmid42264215, year = {2026}, author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and ,  and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH}, title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.024}, pmid = {42264215}, issn = {1523-1747}, abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.}, }
@article {pmid42264245, year = {2026}, author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J}, title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.}, journal = {International journal of biological macromolecules}, volume = {371}, number = {}, pages = {152899}, doi = {10.1016/j.ijbiomac.2026.152899}, pmid = {42264245}, issn = {1879-0003}, abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.}, }
@article {pmid42264341, year = {2026}, author = {Zhu, K and Sun, W and Wang, Z and Zha, Y and Qu, X and Wang, B and Zhang, H}, title = {Environmental ubiquity but limited host taxonomic distribution of co-occurring metal(loid)-resistance genes and persistent organic pollutant-transformation genes in global inland waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128552}, doi = {10.1016/j.envpol.2026.128552}, pmid = {42264341}, issn = {1873-6424}, abstract = {Human activities have transformed inland waters into reservoirs of co-contamination by heavy metals and persistent organic pollutants, driving microbial adaptation through metal-resistance genes (MRGs) and POP-transformation genes (POPTGs). However, the global biogeography and ecological drivers of these co-occurring functional genes and their hosts remain unresolved. Here, leveraging 1593 metagenomes, we investigate the global distribution, microbial hosts, co-occurrence patterns, and drivers of MRGs and POPTGs in inland waters. Key MRG subtypes (e.g., ruvB, pstB, arsB) and POPTGs (e.g., hdt, linJ, bphA) co-occurred in phylogenetically constrained hosts-predominantly Proteobacteria (e.g., Pseudomonas, Acidovorax)-exhibiting dual resistance to Cr/Cu and transformation of aromatic/chlorinated POPs. The positive correlations linked MRG-POPTG to mobile genetic elements, suggesting horizontal gene transfer accelerates multi-pollutant resistance. Our findings highlight known POPTGs and MRGs occur together, which is ubiquitous in the environment but restricted to a limited number of taxa (approximately 3.8% ratio of the total 4129 non-redundant MAGs). Finally, a global map of MRG-POPTG-carrying MAGs (MPCMs) abundance is generated, where climatic and anthropogenic factors explained MPCMs hot spots in South Asia, Southeast Asia, South America.}, }
@article {pmid42264402, year = {2026}, author = {Li, C and Tan, Y and Ma, S and Wang, J and Bai, W and Li, Z and Gao, S and Zhao, Q and Qin, J and Ye, Z}, title = {Concentration-dependent roles of hydrazine in immobilized denitrifying biofilm for industrial wastewater treatment.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135122}, doi = {10.1016/j.biortech.2026.135122}, pmid = {42264402}, issn = {1873-2976}, abstract = {Hydrazine-bearing industrial wastewater is challenging to treat biologically because hydrazine can simultaneously act as a reducing substrate and a microbial inhibitor. In this study, an immobilized denitrifying biofilm system was used to evaluate the concentration-dependent effects of hydrazine on denitrification performance, electron contribution, and microbial response under anoxic conditions. Under sufficient co-substrate conditions, 5-10 mg/L hydrazine was effectively removed, with a maximum removal efficiency of approximately 94%, while stable denitrification was maintained. Nitrogen-15 isotope tracing showed that approximately 31% of the electrons released from hydrazine oxidation were transferred to denitrification-coupled nitrate reduction, indicating that hydrazine can partially contribute reducing equivalents in the denitrifying biofilm. However, elevated hydrazine concentrations impaired hydrazine oxidation and denitrification, induced nitrite and ammonium accumulation, and reduced carbon utilization. Mechanistic analyses showed that this deterioration was associated with oxidative stress, membrane damage, and inhibition of key enzymes, particularly nitrite reductase and hydroxylamine oxidoreductase. Metagenomic analysis further revealed a stress-induced shift in the microbial community from central carbon metabolism toward compensatory pathways. Overall, this study provides mechanistic and process-level insights into the feasibility and operational limitations of using immobilized denitrifying biofilms for treating hydrazine-bearing industrial wastewater.}, }
@article {pmid42264404, year = {2026}, author = {Li, Z and Wang, L and Wang, B and Wang, S and Liu, T and Peng, Y}, title = {Controlled transition from anammox to partial denitrification-anammox system enhanced nitrogen removal: Microbial community succession and organic matter management.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135121}, doi = {10.1016/j.biortech.2026.135121}, pmid = {42264404}, issn = {1873-2976}, abstract = {Integrated partial denitrification-anammox (PDA) offers a sustainable strategy for mainstream wastewater treatment. However, the dynamic transitions and microbial mechanisms during the shift from anammox to coupled PDA remain inadequately characterized. In this study, a PDA system was systematically established by the gradual replacement of nitrite with nitrate and controlled increases in acetate concentrations. Subsequently, acetate was replaced with sludge fermentation liquor (SFL) as the organic carbon source. The process achieved progressive enhancement in nitrogen removal, which stabilized at 93.9%-96.1%. The contribution of anammox in nitrogen removal accounted for > 74% of influent total nitrogen. Concurrently, the mean particle size increased from 85.6 μm to 387.5 μm, and this granulation process significantly improved the stability of the PDA system. 16S rRNA sequencing revealed a marked enrichment of Candidatus Brocadia (0.3% to 4.6%) and Thauera (5.8% to 17.3%). Furthermore, metagenomic analysis confirmed the high abundance of anammox-related genes (hdh, hzs) and higher abundance of the genes encoding nitrate reductase (narG/H/I, napA/B) compared to nitrite reductase genes (nirS/K). This metabolic bias reinforced the PD ecological niche, ensuring stable PDA functionality when SFL was used as the carbon source. Notably, enhanced activity of polysaccharide and protein hydrolase highlighted the critical roles of hydrolysis and acidogenesis in sustaining non-competitive PD performance, particularly under SFL conditions. This study provides a potentially reproducible strategy for the cultivation of PDA communities from anammox inoculum, elucidating microbial dynamics and functional stability during process transitions. These findings provide valuable insights for efficient wastewater treatment by replacing external chemical carbon sources to improve the recovery and utilization of sludge resources.}, }
@article {pmid42264456, year = {2026}, author = {Wildbur, C and Dawson, RA and Roy, S and Ah-Peng, C and Espenberg, M and Hernández, M}, title = {Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {7}, pages = {}, doi = {10.1093/femsec/fiag062}, pmid = {42264456}, issn = {1574-6941}, support = {DHF\R1\211076//Royal Society Dorothy Hodgkin Research Fellowship/ ; RF\ERE\210050//Royal Society Research Fellows Enhanced/ ; RF\ERE\231066//Royal Society Research Fellows Enhanced/ ; NE/X018180/1//NERC Discipline Hopping for Discovery Science/ ; //European Union/ ; GA 101075426//ERC/ ; }, mesh = {*Soil Microbiology ; *Carbon Monoxide/metabolism ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenome ; *Volcanic Eruptions ; Phylogeny ; Aldehyde Oxidoreductases/genetics/metabolism ; Multienzyme Complexes/genetics/metabolism ; Soil/chemistry ; }, abstract = {Volcanic soils provide a unique environment for studying microbial colonization and succession due to their extreme conditions and distinct geochemical profiles. This study focused on carbon monoxide (CO)-oxidizing microbial communities in volcanic soils at Piton De La Fournaise, Réunion Island. Soil samples from three sites (corresponding to eruptions in 1401, 1559, and 2007) were analysed to assess microbial community structure using 16S rRNA gene sequencing and metagenomic analysis to identify functional genes involved in CO oxidation. Phylum-level analysis showed higher relative abundance of Acidobacteriota and Chloroflexota, lower abundances of Actinomycetota and Bacteroidota, and relatively stable levels of Pseudomonadota, while class-level patterns included rising Alphaproteobacteria and Acidobacteriia, with Ktenobacteria emerging in the 1401 site. CO dehydrogenase-related genes were found in 17 metagenome-assembled genomes across all sites. The CO consumption rate by microbes in soils was measured. CO-oxidizing microbes were present across soil ages, with detectable activity in the 2007 site and greatest activity in the 1401 site, suggesting that these microbes actively use CO as an energy source even in soils with primary vegetation, contrary to general understanding. The findings suggest intricate dynamics of microbial succession in volcanic soils and may challenge conventional expectations about community complexity over time.}, }
@article {pmid42265111, year = {2026}, author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and ,  and Iudicone, D}, title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07571-y}, pmid = {42265111}, issn = {2052-4463}, support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; }, abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.}, }
@article {pmid42265123, year = {2026}, author = {Murchie, TJ and Cocker, SL and Baleka, S and Vogel, NA and Natola, L and Karpinski, E and Tirlea, D and Barrera, MA and Grant, DM and Morien, E and Long, GS and Rutledge, LY and Zazula, GD and Jensen, BJ and Froese, DG and Poinar, HN}, title = {Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42265123}, issn = {2041-1723}, mesh = {Animals ; *DNA, Ancient/analysis ; *Sciuridae/genetics ; *DNA, Environmental/genetics/analysis ; Fossils ; Permafrost ; Phylogeny ; Mammoths/genetics ; Ecosystem ; Yukon Territory ; DNA, Mitochondrial/genetics ; Bison/genetics ; Genome, Mitochondrial ; Metagenomics ; *Feces/chemistry ; Plants/genetics ; }, abstract = {Permafrost-preserved ground squirrel (Urocitellus) burrows in Yukon, Canada contain coprolites (palaeofaeces) that span from the Holocene to at least the Middle Pleistocene (~700 kya). Using shotgun metagenomics and targeted enrichment, we recover a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including: plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. These coprolites consistently preserve an abundance of eukaryotic DNA, enabling the assembly of >18 mitochondrial genomes (ground squirrel, snowshoe hare, steppe bison, horse, and mammoth), and revealing previously unrecognized diversity within Arctic Urocitellus, including a ~700 kya lineage that predates divergence among several extant clades. Characteristic damage patterns, positive/negative controls, and in silico taxon validations strongly support aDNA authenticity, and comparisons with regional permafrost datasets indicate minimal post-depositional leaching. These results show that permafrost coprolites can yield high-resolution records of Quaternary ecosystems and multi-organism population histories, providing a powerful complement to sedimentary and skeletal ancient DNA.}, }
@article {pmid42265319, year = {2026}, author = {Gionchetta, G and Lee, J and Hansen, O and Beck, K and Bürgmann, H}, title = {Invasion dynamics of antimicrobial-resistant E. coli in river biofilms: impacts on the resistome, microbiomes, and horizontal gene transfer.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00232-5}, pmid = {42265319}, issn = {2731-8745}, support = {ID 100010434//La Caixa Foundation/ ; 186531/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {River biofilms are frequently exposed to invasion by antibiotic-resistant bacteria (ARB) due to episodic or chronic wastewater inputs, yet the ecological processes governing the fate of invaders and their resistance plasmids remain poorly understood. We experimentally exposed river-grown biofilms from sites differing in microbial diversity and wastewater impact to a genetically tagged ARB Escherichia coli carrying a transferable IncPα plasmid with the nptII resistance gene. Over two weeks, we tracked invader and plasmid dynamics using qPCR and plasmid-to-genome ratios as a proxy for horizontal gene transfer (HGT), complemented by 16S rRNA gene sequencing and metagenomics. Both quantification approaches yielded consistent results: the invader transiently established in all biofilms, peaking within 48 h and declining to near-background levels after 14 days. Decreasing plasmid-to-genome ratios indicated limited HGT and progressive plasmid loss. Biofilms impacted by wastewater showed slower declines, suggesting greater plasmid persistence in disturbed environments and increased abundance of specific indigenous antimicrobial resistance genes of public health concern. While the overall resistome exhibited short-lived shifts, and indigenous resistomes remained largely stable. These findings demonstrate that invader-biofilm interactions are dynamic and shaped by community context, supporting the One Health framework and highlighting how environmental conditions modulate antimicrobial resistance risks in freshwater ecosystems.}, }
@article {pmid42265550, year = {2026}, author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Wajnberg, G and Laing, C}, title = {MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06497-x}, pmid = {42265550}, issn = {1471-2105}, support = {CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; }, abstract = {BACKGROUND: Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species.<br><br>RESULTS: A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively.<br><br>CONCLUSIONS: MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the 'mnbc-me' package in bioconda.}, }
@article {pmid42265587, year = {2026}, author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S}, title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05281-4}, pmid = {42265587}, issn = {1471-2180}, support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; }, abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.}, }
@article {pmid42265917, year = {2026}, author = {Nakamura, K and Okazaki, A and Motooka, D and Matsumoto, N and Hasegawa, Y and Fukuda, S and Yabe, M and Sugiura, A and Yatsuka, Y and Fushimi, T and Onuki, T and Aida, Y and Ohtake, A and Murayama, K and Okazaki, Y}, title = {Nanopore-based haplotype-resolved X-chromosome inactivation analysis for clinical severity assessment in X-linked disorders: an AIFM1 family study with proof-of-concept application to a mosaic PDHA1 carrier.}, journal = {HGG advances}, volume = {}, number = {}, pages = {100632}, doi = {10.1016/j.xhgg.2026.100632}, pmid = {42265917}, issn = {2666-2477}, abstract = {X-chromosome inactivation (XCI) modifies disease severity in females with X-linked variants, but clinically applicable high-resolution assessment remains limited. We report a family with an AIFM1 variant showing marked intrafamilial phenotypic variability and evaluated whether haplotype-resolved nanopore sequencing can inform clinical interpretation. Targeted long-read sequencing was performed in a severely affected hemizygous male, his asymptomatic heterozygous mother, and a severely affected heterozygous sibling. In the hemizygous male, the sample served as a technical control, with all reads mapping to a single haplotype, consistent with a hemizygous X chromosome. Among heterozygous carriers with the identical variant (c.506C>T; p.Pro169Leu), XCI correlated with severity: the affected sibling showed 84% skew favoring activation of the pathogenic allele, whereas the mother showed preferential inactivation (20%). This family-based study shows that using nanopore sequencing for haplotype-resolved X-inactivation (XCI) analysis may provide a practical framework for selected X-linked disorders with variable expressivity.}, }
@article {pmid42266244, year = {2026}, author = {Lin, X and Du, Y and Mai, H and Zhang, X}, title = {Voriconazole-Induced Agranulocytosis in a Cirrhotic Patient with Influenza-Associated Pulmonary Aspergillosis: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {607868}, pmid = {42266244}, issn = {1178-6973}, abstract = {The diagnosis and treatment of influenza-associated pulmonary aspergillosis (IAPA) present significant challenges, and voriconazole, as the first-line treatment for IAPA, rarely causes the serious adverse event of agranulocytosis. We first report a case of voriconazole-associated agranulocytosis in a patient with IAPA complicated by cirrhosis and systematically describe the complete process of diagnosis, treatment, and adverse event management. A 68-year-old male with a history of liver cirrhosis presented with cough, dyspnea, and fever. Testing confirmed influenza A, and chest computed tomography (CT) showed diffuse bilateral pulmonary inflammation. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and culture detected Aspergillus fumigatus, confirming the diagnosis of IAPA. The patient received voriconazole. On Day 20 of hospitalization, agranulocytosis developed and resolved after voriconazole discontinuation and granulocyte colony-stimulating factor (G-CSF) administration, consistent with voriconazole-associated agranulocytosis. After neutrophil recovery, voriconazole was resumed with leukocyte support and close monitoring of complete blood counts (CBC) and drug levels. At one-month follow-up, no recurrence of infection or agranulocytosis was observed. This case emphasizes the value of mNGS in timely diagnosis of IAPA, underscores the importance of closely monitoring CBC in such patients during triazole antifungal therapy, and proves the feasibility of resuming antifungal treatment-including the cautious re-administration of the initially sensitizing agent under strict monitoring-after the correction of agranulocytosis. These findings contribute to a better understanding of the disease and may help to optimize its clinical management.}, }
@article {pmid42266457, year = {2026}, author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ}, title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf079}, pmid = {42266457}, issn = {2730-6151}, abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.}, }
@article {pmid42266956, year = {2026}, author = {Lu, J and Zhong, J and Qiu, W and Zhang, Q}, title = {Intrathecal combined with intravenous eravacycline for the treatment of multisite carbapenem-resistant Acinetobacter baumannii infections (intracranial, pulmonary, and bloodstream) in a post-trauma adolescent female: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829527}, pmid = {42266956}, issn = {2296-858X}, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of hospital-acquired infection among critically ill patients, with extremely limited therapeutic options, particularly for central nervous system (CNS) infections. Eravacyline, a novel fully synthetic fluorocycline, demonstrates potent in vitro activity against CRAB but exhibits poor penetration across the blood-brain barrier (BBB).<br><br>CASE PRESENTATION: A 17-years-old female with severe traumatic brain injury developed concurrent intracranial, pulmonary, and bloodstream CRAB infections. Initial systemic antimicrobial therapy, including intravenous colistin and eravacycline, failed to control the intracranial infection. After switching to a regimen incorporating intrathecal eravacycline (initial dose 2 mg, followed by 5 mg daily) combined with high-dose intravenous cefoperazone-sulbactam and nebulized colistin, the patient showed rapid clinical and microbiological improvement. Serial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) revealed a dramatic reduction in pathogen load, with eventual eradication of CRAB.<br><br>CONCLUSION: This case highlights the potential role of intrathecal eravacycline as a salvage therapy for CRAB meningitis, particularly in cases of multifocal, extensively drug-resistant infection. Further pharmacokinetic and safety studies are warranted to optimize its use in CNS infections.}, }
@article {pmid42267106, year = {2026}, author = {Wu, Y and Gao, Q and Yang, H and Wang, Y and Lang, L and Liu, B and Jiang, X and Li, D and Wang, X and Xun, J and Zhang, Q}, title = {Multi-omics analysis identifies gut microbiota-glutamine axis contributing to the pathogenesis of reflux esophagitis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1805181}, pmid = {42267106}, issn = {1664-302X}, abstract = {BACKGROUND: Reflux esophagitis (RE), a common gastroesophageal reflux disease characterized by esophageal mucosal inflammation, is closely associated with gut microbiota dysbiosis and metabolic abnormalities. The glutamine-glutamate metabolic pathway regulates inflammation and mucosal barrier function, but its role in RE and association with gut microbiota remain unclear. This study aimed to characterize gut microbiota and serum metabolites in RE patients via integrated multi-omics (focusing on the gut microbiota-glutamine axis), and verify the activation status of this pathway in RE inflammatory models and the anti-inflammatory effect of its targeted inhibition.<br><br>METHODS: RE patients and healthy controls (HCs) were enrolled. Fecal metagenomic sequencing and serum untargeted metabolomics (LC-MS/MS) were performed to identify differential gut microbiota and serum metabolites between the two groups, followed by Pearson correlation analysis to explore their associations. In vitro experiments were conducted on human esophageal epithelial cells (HEECs) divided into four groups: normal, inflammatory, glutamine-supplemented, and inflammatory + glutamine + glutaminase inhibitor (BPTES) groups. qPCR was used to detect the mRNA expression of glutamine-glutamate pathway molecules (GLS, c-Myc, SLC1A5), mucosal barrier markers (ZO-1, Occludin), and pro-inflammatory cytokines (IL-8, IL-6, IL-1&#x3b2;, TNF-&#x3b1;). Intracellular concentrations of glutamine, glutamate, and &#x3b1;-ketoglutarate were measured, and the anti-inflammatory effect of BPTES was verified.<br><br>RESULTS: RE patients showed significant differences in gut microbiota diversity and composition compared with HCs, with Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae as dominant taxa. Serum metabolomics revealed elevated glutamine and glutamate in RE patients, which were identified as key differential metabolites related to RE pathogenesis. Pearson analysis revealed that alterations in serum metabolite profiles of RE patients were significantly correlated with changes in gut bacterial abundance. Notably, glutamate-glutamate (Glu-Glu) metabolism exhibited negative correlations with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). In vitro, inflammatory HEECs exhibited increased intracellular glutamine, glutamate, and &#x3b1;-ketoglutarate, upregulated glutamine-glutamate pathway molecules and pro-inflammatory cytokines, and downregulated mucosal barrier markers. Exogenous glutamine alone failed to alleviate inflammation, while combined with BPTES significantly reversed pathway activation and mitigated inflammation in inflammatory HEECs.<br><br>CONCLUSION: RE patients exhibit significant gut microbiota dysbiosis (dominated by Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae) and abnormal glutamine metabolism (elevated serum glutamine and glutamate). Pearson analysis reveals that the glutamine-glutamate pathway correlates negatively with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). The glutamine-glutamate pathway is activated in inflammatory esophageal epithelial cells, and targeted GLS inhibition by BPTES reverses pathway activation and mitigates inflammation. These findings highlight the gut microbiota-glutamine axis as potential diagnostic biomarkers and therapeutic targets for RE, providing new insights into pathogenesis and a basis for novel clinical interventions.}, }
@article {pmid42267107, year = {2026}, author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S}, title = {Parabolic flight induces site specific microbiome changes in women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1817099}, pmid = {42267107}, issn = {1664-302X}, abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.<br><br>METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.<br><br>RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p&#x202f;<&#x202f;0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.<br><br>CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.}, }
@article {pmid42267128, year = {2026}, author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K}, title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1832403}, pmid = {42267128}, issn = {1664-462X}, abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.}, }
@article {pmid42267141, year = {2026}, author = {Hardies, SC and Park, J and Cho, BC and Hwang, CY}, title = {Alishewanella Phage LSH1 from the Sea Surface Microlayer Provides a Novel Minimalistic View of the Siphoviral Hub Structure.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0131}, pmid = {42267141}, issn = {2001-0370}, abstract = {LSH1 is a novel lytic siphovirus isolated, together with its host in the genus Alishewanella, from the surface microlayer of a brackish tidal reservoir in South Korea and characterized with respect to growth properties, genome sequence, gene annotation, mass spectrometry, and electron microscopy. Sequence analysis shows that LSH1 shares only distant similarity to other cultured phages, although a closer metagenomic neighborhood can be defined. LSH1 represents the first isolate from a large, previously unsampled family-level sector of the viral tree. Transmission electron microscopy revealed a tail end distinct from the best structurally characterized siphoviral prototypes and similar in appearance to Salmonella phage Jersey, the prototype of a large structurally uncharacterized group named Guernseyvirinae. Therefore, Jersey was included in the comparative analysis with LSH1. A combination of hidden Markov model comparisons and AlphaFold reconstruction was used to clarify the structural relationships of these phages. Both have structural homologs of portions of the canonical bacteriophage lambda tail hub but lack the lambda components associated with receptor recognition linked to ejection triggering in that system. The LSH1 and Jersey tail hubs are of different sequence lineages, but each represents a relatively minimalistic version of the siphoviral tail hub, with distinct candidates for the structural location of their antireceptors. This study explores the capability of AlphaFold to rapidly augment the relatively few structurally characterized phages with models for diverse variants, fleshing out how much variation there is and perhaps leading to a better treatment of how this variation is evolving.}, }
@article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {811-826}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, mesh = {Animals ; *beta-Thalassemia/genetics/complications/veterinary/microbiology ; *Macaca fascicularis ; *Gastrointestinal Microbiome/physiology ; Mutation ; *Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics ; *beta-Globins/genetics/metabolism ; Male ; }, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, }
@article {pmid42267811, year = {2026}, author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P}, title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0080726}, doi = {10.1128/aem.00807-26}, pmid = {42267811}, issn = {1098-5336}, abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.<br><br>IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.}, }
@article {pmid42267859, year = {2026}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70307}, pmid = {42267859}, issn = {2045-8827}, support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; }, mesh = {*Rhizosphere ; *Metagenomics ; Soil Microbiology ; *Allium/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fertilizers/analysis ; Soil/chemistry ; }, abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.}, }
@article {pmid42268526, year = {2026}, author = {Mohit,  and Verma, S and Yadav, A and Venkatesh, V}, title = {Multi-omics insights into immunometabolic dysregulation in neonatal sepsis for precision medicine.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42268526}, issn = {1573-4978}, mesh = {Humans ; *Neonatal Sepsis/metabolism/immunology/genetics/therapy ; Multiomics ; Infant, Newborn ; *Precision Medicine/methods ; Metabolomics/methods ; Proteomics/methods ; Genomics/methods ; Biomarkers/metabolism ; }, abstract = {Neonatal sepsis remains a major global health challenge, contributing substantially to morbidity and mortality despite many advances. Conventional diagnostics often fail to capture the disease complexity and immune dysregulation, leading to delayed diagnosis and sub-optimal treatment. Recent advances in multiomics, including genomics, transcriptomics, proteomics, metabolomics and metagenomics are transforming molecular understanding by enabling a precise view of host-pathogen interactions. These approaches also provide critical insights into metainflammation, a state of chronic, low-grade immune and metabolic dysregulation, playing a pivotal role in neonatal immune vulnerability. Integrating multi-omics with meta-inflammatory profiling may support future risk stratification, biomarker discovery, and precision-oriented neonatal sepsis care. However, clinical translation requires further validation, platform standardization, and feasibility assessment in NICU settings. Such insights may establish the foundation of P4 medicine by emphasizing prediction, prevention, personalisation, and participation in neonatal care. Multi-omics integration may support endotype identification, and data-driven clinical communication after adequate validation. Overall, this review highlights how multiomics and metainflammation driven frameworks may improve mechanistic understanding of neonatal sepsis and guide future development of clinically feasible precision-medicine approaches.}, }
@article {pmid42268876, year = {2026}, author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR}, title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351562}, pmid = {42268876}, issn = {1932-6203}, mesh = {Humans ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/immunology ; Aged ; Healthy Volunteers ; Metagenomics ; Case-Control Studies ; Bacteria/genetics/isolation &amp; purification/classification ; COVID-19 ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.<br><br>METHODS: BAL specimens from healthy control volunteers (n&#x2009;=&#x2009;20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n&#x2009;=&#x2009;52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).<br><br>RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p&#x2009;<&#x2009;0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p&#x2009;=&#x2009;0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q&#x2009;<&#x2009;0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.<br><br>CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.}, }
@article {pmid42269300, year = {2026}, author = {Lo, HY and Hsiao, YT and Wu, YJ and Whang, LM and Chen, WH and Tung, HH}, title = {Persistence and dynamics of antibiotic resistome in a drinking water supply system with booster chlorination.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142622}, doi = {10.1016/j.jhazmat.2026.142622}, pmid = {42269300}, issn = {1873-3336}, abstract = {Due to the extensive use of antibiotics worldwide, the prevalence of antibiotic resistance genes (ARGs) in aquatic environments has become a major public health concern. This study investigated the ARGs in a drinking water supply system, with particular emphasis on booster chlorination in the distribution network. To elucidate the dynamics of the antibiotic resistome, environmental DNA was extracted from water collected from five different sections, and the resistome profiles were subsequently reconstructed with metagenome assembly. Our findings revealed that 35 core ARGs persisted but decreased in concentration during water treatment and early distribution, with genes resistant to bacitracin, multidrug, and rifamycin being the most prominent. However, a notable surge of ARGs was observed at the terminal distribution segment. This increase was linked to changes in the resistome structure, which were primarily associated with shifts in the microbial community and, within the DWDS specifically, also linked to horizontal transfer mediated by mobile genetic elements (MGEs) under chlorine stress from booster chlorination. Microbial communities within the drinking water distribution system (DWDS) shifted distinctly from those in the water treatment plant. Under re-chlorination pressure, the chlorine-tolerant Mycobacteriales and the biofilm-forming Hyphomicrobiales and Rhodobacterales became the predominant taxa. Additionally, metagenome-assembled genomes (MAGs) reconstruction further identified that Hyphomicrobium and Mycobacterium were the main ARG carriers in the DWDS, with the latter as the main putative host for the core ARGs. Overall, this study demonstrated that booster chlorination in the water distribution system while controlling microbial regrowth, may simultaneously facilitate ARG dissemination. These findings highlight the need to optimise re-chlorination practices to balance microbial growth control while minimising ARG proliferation in DWDS.}, }
@article {pmid42269354, year = {2026}, author = {Petersen, J and Ringel, V and Päuker, O and Frühling, A and Rohde, M and Jarek, M and Spröer, C and Bunk, B and Huber-Fischer, K and Pradella, S and Freese, HM and Koblitz, J and Neumann-Schaal, M and Brinkmann, H}, title = {Think pink 2.0 - Description of Roseobacter cerffii sp. nov., isolated from the chromerid alga Vitrella brassicaformis, and reclassification of Sulfitobacter sabulilitoris as Billmartinia sabulilitoris, gen. nov., comb. nov.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126731}, doi = {10.1016/j.syapm.2026.126731}, pmid = {42269354}, issn = {1618-0984}, abstract = {A Gram-stain-negative, aerobic, pink-pigmented bacterial strain A03A-229[T] was isolated from a non-axenic culture of the chromerid alga Vitrella brassicaformis CCMP3155, which originates from the Great Barrier Reef in Australia. Complete genome sequencing revealed the presence of seven circular replicons, representing one chromosome, two chromids and four plasmids. The 142-kb DnaA-like I chromid, which contains the photosynthesis gene cluster (PGC), traces of ubiquinone-11 and the ability to reduce nitrate are diagnostic for A03A-229[T]. Genomic, physiological, and chemotaxonomic data provided clear evidence that strain A03A-229[T] (= DSM 112523[T] = CECT 31310[T]) represents a new species of the genus Roseobacter, for which the name Roseobacter cerffii sp. nov. is proposed. R. cerffii A03A-229[T] represents the tenth described species of the genus Roseobacter, but phylogenetic (meta-)genome analyses indicated the presence of at least 27 different species. Reconstruction of the metabolic pathways of the genus Roseobacter revealed a highly conserved metabolism with lineage specific adaptations for the formation of compatible solutes and a surprising abundance of four GAPDH genes. The ability to perform aerobic anoxygenic photosynthesis, which is mediated by the PGC, is responsible for the eponymous pink color of this genus, while it only occurs scattered in the sister genus Sulfitobacter. Our phylogenomic analyses provided clear evidence for a distinct taxonomic status of strain Sulfitobacter sabulilitoris HSMS-29[T] (= KACC 19870[T] = NBRC 113549[T]). Based on its phylogenetic position, low average amino-acid identities (AAI) and a PufC-type PGC, we propose the reclassification of this strain as Billmartinia sabulilitoris gen. nov., comb. nov.}, }
@article {pmid42269462, year = {2026}, author = {Riveros, A and Kwon, H and Impellitteri, CA and Jiang, D}, title = {Nitrate reshapes electron partitioning and Se[0] formation during continuous electro-microbial treatment of mixed selenium oxyanions.}, journal = {Water research}, volume = {303}, number = {}, pages = {126244}, doi = {10.1016/j.watres.2026.126244}, pmid = {42269462}, issn = {1879-2448}, abstract = {Selenium in flue-gas-desulfurization (FGD) wastewater occurs as mixed selenate and selenite oxyanions, and requires both aqueous removal and reduction to elemental selenium to prevent secondary waste generation. Here, we introduce a continuous-flow electro-microbial platform that couples flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) to achieve voltage-driven removal and bio-mediated reduction within a compact reactor configuration. During 41 days of operation treating mixed selenium oxyanions (10 mg Se L[-1] each) in fortified water samples with FGD-relevant nitrate concentrations (20 mg L[-1]), the system achieved removal efficiencies of 84-95% for selenite and 54-78% for selenate. Nitrate unexpectedly enhanced apparent elemental selenium yield from 70% to 99% under 2 V, but decreased selenium-specific Faradaic efficiency from 20% to 8%, likely due to a combination of electron flux diversion and co-respiration between nitrogen and selenium oxyanions. Metagenomics suggested that genes associated with indirect selenium transformation (cysIJ, trxA/B, gshA/B, and ybbN) were 45-115x more abundant than genes encoding dedicated selenate reductases. Together, these results demonstrate FCDI-BES as a promising platform for treating selenium and potentially other redox-active oxyanions and highlight the importance of studying electron-acceptor competition in similar systems.}, }
@article {pmid42269501, year = {2026}, author = {Ghose, M and Parab, AS and Manohar, CS}, title = {Metagenome-based analysis of xenobiotic degradation potential in urban mangrove sediments under chronic anthropogenic impact.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119970}, doi = {10.1016/j.marpolbul.2026.119970}, pmid = {42269501}, issn = {1879-3363}, abstract = {Urban mangrove sediments receive continuous inputs of industrial and domestic pollutants, yet the microbial basis of pollutant transformation in these chronically impacted systems remains insufficiently resolved. This study investigated xenobiotic degradation potential in sediments from two urban mangrove locations along the Mandovi estuary, Goa, India, through reanalysis of previously generated shotgun metagenomic data. The assembled metagenomes showed enrichment of degradation pathways associated with aromatic and aliphatic pollutants commonly linked to urban contamination. A high representation of oxidoreductases and related aromatic transformation functions indicated that xenobiotic processing is closely linked to redox regulation and central carbon metabolism. Pathway completeness did not consistently correspond with relative abundance, suggesting that lower-abundance pathways may still retain structurally coherent degradation capacity. Hydrocarbon-specific annotation revealed the coexistence of aerobic and anaerobic activation strategies, consistent with adaptation to the redox heterogeneity of mangrove sediments. Xenobiotic- and hydrocarbon-associated functions were linked mainly to Pseudomonadota, Actinomycetota, Shewanella, and a substantial fraction of unresolved bacterial lineages, indicating that undercharacterized taxa may contribute importantly to pollutant-processing potential. Supportive metagenome-assembled genome analysis showed that recovered genomes encoded complementary subsets of degradation functions, although these genomes should be treated as illustrative examples rather than representatives of the whole community. Comparison between locations revealed similar core degradation functions but variation in secondary pathways, likely reflecting differences in local pollutant inputs and sediment conditions. These results show that urban mangrove microbiomes retain a functionally structured and redox-adapted metagenomic repertoire for xenobiotic and hydrocarbon degradation, highlighting their relevance to pollutant transformation, environmental monitoring, and native community-based bioremediation.}, }
@article {pmid42269618, year = {2026}, author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M}, title = {Variations in the latitudinal diversity gradients of the ocean microbiome.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.016}, pmid = {42269618}, issn = {1934-6069}, abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.}, }
@article {pmid42269619, year = {2026}, author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y}, title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.009}, pmid = {42269619}, issn = {1934-6069}, abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.}, }
@article {pmid42269751, year = {2026}, author = {Sun, X and Li, S and Liang, J and Wang, C and Bai, Y and Mao, J and Qu, J}, title = {From correlation to causality: Identifying potential environmental drivers of pathogenic antibiotic-resistant bacteria in river water using causal machine learning.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128570}, doi = {10.1016/j.envpol.2026.128570}, pmid = {42269751}, issn = {1873-6424}, abstract = {Pathogenic antibiotic-resistant bacteria (PARB) pose a serious public health threat within the One Health framework, yet identifying their potential environmental drivers in complex aquatic systems remains a challenge. This study systematically compared correlation analysis, explainable machine learning, and causal machine learning within a unified framework. Both Spearman correlation and explainable machine learning identified numerous potentially important factors, notably non-antibiotic pharmaceuticals such as carbamazepine and bezafibrate. However, causal inference via double machine learning, which controls for confounders and interaction effects, revealed a distinctly different driver profile. Under predefined assumptions, this approach estimated potential causal effects for dissolved oxygen, the nitrate-to-ammonium ratio, specific antibiotics (roxithromycin, azithromycin), and non-antibiotic compounds (acenaphthene, 2-chloroanthracene). Taxon-specific analysis further showed that Aeromonas aligned closely with the overall PARB causal profile, whereas Pseudomonas responded primarily to oxidation-reduction potential. Functional profiles suggested potential stress-adaptation mechanisms related to signal transduction and metabolic regulation pathways. By shifting from associative prediction to causal inference, this causal machine learning-guided framework provides a robust analytical basis for identifying environmental drivers and informing targeted management of PARB risks in aquatic ecosystems.}, }
@article {pmid42270066, year = {2026}, author = {Shi, H and Wang, L and Wu, Y and Cai, B}, title = {Synergistic mechanisms by which arbuscular mycorrhizal fungi regulate hyphosphere bacterial communities and functional genes to suppress potential N2O production under tetracycline stress.}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {125020}, doi = {10.1016/j.envres.2026.125020}, pmid = {42270066}, issn = {1096-0953}, abstract = {Tetracycline (TC), a widely used veterinary antibiotic, frequently accumulates in agricultural soils and disrupts nitrogen (N) cycling, thereby enhancing nitrous oxide (N2O) emissions. However, biologically based mitigation strategies and their underlying mechanisms remain poorly understood. In this study, a soybean pot experiment was conducted with four treatments: control, arbuscular mycorrhizal fungi (AMF) inoculation, TC addition, and AMF combined with TC. By integrating hyphosphere-specific sampling, potential N2O production rate measurements, 16S rRNA gene sequencing, quantitative PCR, metagenomics, and partial least squares path modeling, we systematically elucidated AMF-mediated regulation of N2O production under TC stress. TC significantly increased potential N2O production rate (+21.2%), primarily by selectively suppressing the terminal denitrification step, as evidenced by reduced nitrous oxide reductase (NOS) activity and decreased abundance of the nosZ gene, resulting in denitrification pathway disruption and N2O accumulation. In contrast, AMF inoculation under TC stress reduced potential N2O production rate by 29.5%, restoring it to control levels. Mechanistically, AMF improved hyphosphere soil properties (e.g., increased SOC and TN and enhanced TC dissipation) and selectively enriched functionally competent and TC-tolerant denitrifiers, particularly nosZ-harboring taxa such as Streptomyces, thereby repairing denitrification pathway completeness. Path modeling further demonstrated that AMF mitigated N2O production both directly by enhancing N-cycling microbial functional capacity and indirectly by optimizing soil physicochemical conditions. Our findings reveal the microbial and molecular mechanisms underlying antibiotic-enhanced N2O emissions and highlight AMF as a low-input, nature-based environmental biotechnology strategy to simultaneously remediate antibiotic-contaminated soils and mitigate agricultural greenhouse gas emissions.}, }
@article {pmid42270094, year = {2026}, author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B}, title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {33}, number = {}, pages = {10732748261460118}, pmid = {42270094}, issn = {1526-2359}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation &amp; purification/genetics ; Aged ; Fungi/isolation &amp; purification ; }, abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.}, }
@article {pmid42270219, year = {2026}, author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y}, title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119489}, doi = {10.1016/j.foodres.2026.119489}, pmid = {42270219}, issn = {1873-7145}, mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; }, abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.}, }
@article {pmid42270261, year = {2026}, author = {Vandana,  and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP}, title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119548}, doi = {10.1016/j.foodres.2026.119548}, pmid = {42270261}, issn = {1873-7145}, mesh = {Animals ; *Polyphenols/pharmacology ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Fruit/chemistry ; *Cognitive Dysfunction/chemically induced/prevention &amp; control/drug therapy ; *Arsenic/toxicity ; Male ; *Rubus/chemistry ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; Disease Models, Animal ; }, abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.}, }
@article {pmid42270391, year = {2026}, author = {Nakaya, Y and Hashimoto, K and Fukushima, K and Fatimah, M and Matsumoto, Y and Funauchi, A and Tsukaguchi, A and Yamauchi, K and Miyazaki, A and Iwahashi, Y and Tone, M and Naito, M and Shiroyama, T and Hirata, H and Takeda, Y and Nakamura, S and Kumanogoh, A}, title = {Mycobacterium brisbanense Pulmonary Disease Treated with a Macrolide-Based Multidrug Regimen: A Case Report.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, doi = {10.2169/internalmedicine.7351-26}, pmid = {42270391}, issn = {1349-7235}, abstract = {A 73-year-old woman with a history of tracheostomy for tracheomalacia and bronchiectasis developed a worsening productive cough with progressive nodular/bronchocentric opacities on computed tomography. She was diagnosed with Mycobacterium brisbanense pulmonary disease based on repeated sputum culture results. Antimicrobial susceptibility testing revealed a low minimum inhibitory concentration for clarithromycin, and whole-genome sequencing confirmed the absence of the erm gene. Owing to repeated smear positivity and clinical progression, macrolide-based multidrug therapy was initiated, resulting in both clinical and radiographic improvements. To our knowledge, this is the first reported case of M. brisbanense pulmonary disease in Japan, thus highlighting its potential pathogenicity.}, }
@article {pmid42270613, year = {2026}, author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J}, title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74161-2}, pmid = {42270613}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.}, }
@article {pmid42270686, year = {2026}, author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ}, title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53382-x}, pmid = {42270686}, issn = {2045-2322}, abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.}, }
@article {pmid42271018, year = {2026}, author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG}, title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10447-x}, pmid = {42271018}, issn = {2399-3642}, support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; }, abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.}, }
@article {pmid42271211, year = {2026}, author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q}, title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05231-0}, pmid = {42271211}, issn = {1471-2180}, support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; }, abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.}, }
@article {pmid42271238, year = {2026}, author = {Bi, JG and Wang, YH and Li, PK and Liu, Q and Zheng, X}, title = {Metagenomic insights into regional gut microbiota variation of invasive Spodoptera frugiperda across the Gaoligong Mountains.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05259-2}, pmid = {42271238}, issn = {1471-2180}, support = {202102AA310055//the Supported by the Major Science and Technique Programs of Yunnan Province/ ; YNWRQNBJ2020101//the Young Top Talents of the High-level Talents Training Support Program in Yunnan Province/ ; 202305AM340031//the Lower Nu River, Mountain Agroecosystem, Observation and Research Station of Yunnan Province/ ; 2026J1054//the Yunnan Provincial Department of Education Science Research Fund Project/ ; }, abstract = {BACKGROUND: The invasive pest Spodoptera frugiperda poses a potential threat to the ecological security of western Yunnan, using the Gaoligong Mountains as an important cross-border corridor and overwintering site. However, the potential role of gut microbiota in the local adaptation of S. frugiperda during its invasion remains poorly understood.<br><br>METHODS: Adult populations were monitored using sex pheromone traps, and metagenomic sequencing was performed on larval gut microbiota from different regions of the Gaoligong Mountains. The gut microbial composition and functional potential were analyzed, with specific focus on the microbial traits potentially associated with host adaptation and invasion.<br><br>RESULTS: S. frugiperda populations persisted year-round in the Gaoligong Mountains, with adult activity peaking from January to May. Microbial diversity was highest in southern samples. Enterococcus, typically dominant in S. frugiperda, displayed low abundance in the central and northern regions. In contrast, Providencia emerged as the dominant genus specifically at the Pianma site (PM, along the China-Myanmar border), where the gut microbiota exhibited higher abundance of site-specific functional genes compared to other regions. These genes encoded proteins including type 1 subunit membrane proteins and outer membrane-targeting proteins. Additionally, the PM samples showed a higher relative abundance of genes K07345, K07347, and K15125. Functional annotation highlighted a strong potential for vancomycin degradation and an enrichment of diverse antimicrobial resistance-associated genes, with adeL being the most abundant.<br><br>CONCLUSIONS: These findings suggest that the PM area may represent an important gateway or a priority monitoring site for the transboundary invasion of S. frugiperda, underscoring the urgency of strengthening local management of invasive pests.}, }
@article {pmid42271362, year = {2026}, author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D}, title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42271362}, issn = {1479-5876}, support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Metagenomics ; *Fungi/genetics ; Cohort Studies ; *Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.<br><br>METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.<br><br>RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.<br><br>CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.}, }
@article {pmid42271421, year = {2026}, author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED}, title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01336-4}, pmid = {42271421}, issn = {1475-2891}, abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.<br><br>METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[&#xae;] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.<br><br>RESULT: Thirty-four Australian adults (mean age: 38.4&#x2009;&#xb1;&#x2009;18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.<br><br>CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.<br><br>TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).}, }
@article {pmid42271469, year = {2026}, author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N}, title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.}, journal = {Annals of general psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12991-026-00686-x}, pmid = {42271469}, issn = {1744-859X}, abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.<br><br>METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.<br><br>RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P&#x2009;<&#x2009;0.001); a significantly prolonged immobility time in the forced swim test (P&#x2009;<&#x2009;0.01); and a significantly decreased total movement distance in the open field test (P&#x2009;<&#x2009;0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P&#x2009;=&#x2009;0.018) and Pielou's evenness index (P&#x2009;=&#x2009;0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R&#x2009;=&#x2009;0.145, P&#x2009;=&#x2009;0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F&#x2009;=&#x2009;1.675, R&#xb2; = 0.0897, P&#x2009;=&#x2009;0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P&#x2009;<&#x2009;0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P&#x2009;<&#x2009;0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.<br><br>CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.}, }
@article {pmid42271556, year = {2026}, author = {Kaushik, S and Borck, J and Flatow, E and Frishman, WH and Aronow, WS}, title = {Blood Culture-Negative Infective Endocarditis: A Review.}, journal = {Cardiology in review}, volume = {}, number = {}, pages = {}, pmid = {42271556}, issn = {1538-4683}, abstract = {Blood culture-negative infective endocarditis (BCNIE) represents a diagnostically challenging subset of infective endocarditis in which routine blood cultures remain negative despite fulfillment of Duke-ISCVID diagnostic criteria. BCNIE arises primarily from prior antibiotic exposure, infection with fastidious or nonculturable organisms, or noninfectious conditions that mimic endocarditis. Common fastidious pathogens include Coxiella burnetii, Bartonella species, Brucella species, Tropheryma whipplei, fungi, and nutritionally variant streptococci. Because delayed pathogen identification may postpone targeted therapy, BCNIE is associated with increased diagnostic complexity and substantial morbidity and mortality. Modern evaluation relies on a multimodal strategy integrating serologic testing, prolonged culture incubation, histopathology, advanced molecular diagnostics, and multimodality imaging. Emerging molecular techniques, including 16S/18S polymerase chain reaction and metagenomic next-generation sequencing, have significantly improved microbiologic yield, particularly from excised valve tissue, and are now incorporated into updated Duke-ISCVID criteria. Echocardiography remains central to diagnosis, while cardiac computer tomography and 18 fluoro-2-deoxy-D-glucose positron emission tomography/computer tomography provide complementary value in prosthetic valve disease and detection of periannular complications. Management requires empiric antimicrobial therapy followed by organism-directed treatment once a pathogen is identified, with surgery frequently necessary for heart failure, uncontrolled infection, fungal disease, or structural complications. Multidisciplinary endocarditis teams are increasingly recognized as essential to optimizing outcomes in this complex disease process.}, }
@article {pmid42271557, year = {2026}, author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K}, title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42271557}, issn = {2524-4671}, support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; }, abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.<br><br>RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.<br><br>CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.}, }
@article {pmid42271572, year = {2026}, author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E}, title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42271572}, issn = {1574-6941}, support = {//CNRS/ ; ANR-24-CE01-6539-01//French National Research Agency/ ; }, mesh = {*Groundwater/microbiology/chemistry ; *Caves/microbiology/chemistry ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; South Africa ; *Geologic Sediments/microbiology ; Metagenome ; Oxidation-Reduction ; }, abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.}, }
@article {pmid42272236, year = {2026}, author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T}, title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70630}, pmid = {42272236}, issn = {1365-2125}, support = {//Micreos Human Health B.V./ ; }, abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.<br><br>METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10&#xa0;&#x3bc;g/g, XZ.700 30&#x2009;&#x3bc;g/g, XZ.700 100&#x2009;&#x3bc;g/g or vehicle twice daily for 7&#xa0;days on nonlesional skin and on all lesions (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;10%). In Part B, subjects received XZ.700 100&#x2009;&#x3bc;g/g or vehicle on all lesions twice daily for 14&#x2009;days (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.<br><br>RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100&#x2009;&#x3bc;g/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.<br><br>CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100&#x2009;&#x3bc;g/g for 14&#x2009;days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.}, }
@article {pmid42272618, year = {2026}, author = {Top, FK and Boussiengui, LG and Sall, NC and Faye, M}, title = {First identification of Molluscum contagiosum poxvirus from human in Senegal.}, journal = {Journal of public health in Africa}, volume = {17}, number = {1}, pages = {1586}, pmid = {42272618}, issn = {2038-9922}, abstract = {Herein, we report on the first identification of a human case of Molluscum contagiosum virus (MOCV) in Senegal. In 2024, a male child living in Diamniadio, Dakar region, with no history of travel, tested positive for MOCV. The aetiology was identified using metagenomic sequencing in the framework of the ongoing preparedness activities for the 2024 mpox public health emergency of international concern (PHEIC). Given the overlapping clinical features of MOCV infection and mpox, further research on MOCV is warranted in the West African region, particularly in the current context of high mpox circulation.}, }
@article {pmid42272701, year = {2026}, author = {Luo, L and Guo, Z and Chen, W and Zheng, Y and Chen, C and Li, Q and Wang, N and Ji, Y and Hua, J}, title = {Mycobacterium abscessus infection in a young man with cystic fibrosis: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1737211}, pmid = {42272701}, issn = {2296-2360}, abstract = {BACKGROUND: Cystic fibrosis (CF) is a rare autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although relatively common in Caucasian populations, CF is rare in China, where it frequently presents with non-specific respiratory symptoms, leading to delayed diagnosis and frequent coinfections with multidrug-resistant pathogens.<br><br>CASE REPORT: A 21-year-old man presented with a 6-year history of recurrent productive cough and intermittent fever over the past 6 months. Imaging revealed bronchiectasis with evidence of infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Staphylococcus aureus and Mycobacterium abscessus. Further investigations revealed pancreatic lipomatosis, congenital absence of seminal vesicles, and fat-soluble vitamin deficiencies. CF diagnosis was confirmed by elevated sweat chloride concentration (88&#x2005;mmol/L) and biallelic CFTR mutations. Clinical stability was achieved through a quadruple antimycobacterial regimen (linezolid, moxifloxacin, azithromycin, and minocycline) combined with systemic supportive care. CFTR modulator therapy was deferred due to limited access and financial constraints.<br><br>CONCLUSION: We report a case of CF in a Chinese patient presenting with nontuberculous mycobacterial infection, a condition rarely documented in East Asian populations. We provide a review of the relevant literature, aiming to emphasize the importance of early recognition of CF, personalized antimicrobial strategies, and improved access to essential medications.}, }
@article {pmid42272754, year = {2026}, author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C}, title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779298}, pmid = {42272754}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Metabolomics ; *Constipation/microbiology/immunology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; *Rhinitis, Allergic/microbiology/immunology/metabolism/complications ; Child ; Female ; Feces/microbiology ; Male ; Amino Acids/metabolism ; Multiomics ; Bacteria/classification/genetics ; Metabolome ; }, abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.<br><br>METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.<br><br>RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P&#xa0;=&#xa0;0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and &#x3b3;-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC&#xa0;=&#xa0;0.946).<br><br>CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.}, }
@article {pmid42272841, year = {2026}, author = {Qiu, X and Qiang, L and Wang, Y and Li, B and Lei, Z and Wang, J}, title = {Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1834558}, pmid = {42272841}, issn = {1663-9812}, abstract = {BACKGROUND: Staphylococcus aureus (SA) remains a global health threat due to its increasing drug resistance and intracellular persistence, which compromise the conventional antibiotic efficacy. Host-directed therapy (HDT) has emerged as a promising alternative by modulating host immunity. With multi-targeting and immunomodulatory properties, traditional Chinese medicine (TCM) monomers represent ideal candidates for HDT. However, their ability to promote host immunity-mediated SA clearance remains largely unexplored.<br><br>METHODS: Forty-one TCM monomers potentially regulating host apoptosis, a core mechanism of the host innate immune defense against intracellular pathogens, were screened to identify a compound that promotes the clearance of intracellular SA and methicillin-resistant SA (MRSA). The mechanism was investigated in infected macrophages using transcriptomics, proteomics, molecular dynamics simulations, and biochemical assays. The physiological function of the TCM monomer was examined in infected mice through lung pathology and multi-omics analysis, including transcriptomics, proteomics, metagenomics, and metabolomics.<br><br>RESULTS: Triptolide was identified as a potent facilitator of host immunity-mediated intracellular clearance of SA and MRSA, without exerting direct bactericidal effects. Mechanistically, triptolide directly binds to the X-linked inhibitor of apoptosis protein (XIAP), disrupting its interaction with caspases to relieve their inhibition and thereby induce apoptosis. Furthermore, in murine infection models, triptolide treatment reduced bacterial loads, alleviated inflammation, and induced macrophage apoptosis in lungs, concurrently maintaining microbiota homeostasis and improving metabolic function.<br><br>CONCLUSION: This study establishes a proof of concept for triptolide as a HDT candidate against SA and MRSA infections, which not only enhances host apoptosis-mediated pathogen clearance but also maintains host microbiota and metabolic homeostasis.}, }
@article {pmid42272967, year = {2026}, author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM}, title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.}, journal = {Bioengineering &amp; translational medicine}, volume = {11}, number = {3}, pages = {e70124}, pmid = {42272967}, issn = {2380-6761}, abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.}, }
@article {pmid42273068, year = {2026}, author = {Moradi, Z and Alinizi, HR and Mehrvar, M}, title = {Genomic characterization of broad bean wilt virus 1 (Fabavirus alphaviciae) from Iran including phylogenetic relationships.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {256}, pmid = {42273068}, issn = {2190-572X}, abstract = {UNLABELLED: The complete genome of a broad bean wilt virus 1 (BBWV1; Fabavirus alphaviciae) isolate (BBWV1-IR) was recovered from an uncultivated Plantago lanceolata plant in Iran by viral metagenomics and validated by RT-PCR. RNA1 (5,779 nucleotides) contains a single ORF encoding replication-associated proteins (Pro-Co, HEL, VPg, Pro, RdRp), while RNA2 (3,414 nucleotides) harbors two overlapping ORFs encoding the large and small coat proteins (LCP and SCP) and two additional proteins (VP47 and VP37). Comparative analyses revealed that BBWV1-IR shared 81-92% and 79.5-83% nucleotide identity in RNA1 and RNA2, respectively, with global isolates. No intragenic recombination was detected; however, reassortment analysis identified three distinct events, including one involving BBWV1-IR, whose RNA1 segment likely originated from Austrian (major) and UK (minor) parental lineages. ORF1 and ORF2a showed substantial variability and high haplotype diversity, with VP37 displaying the greatest nucleotide diversity. Evolutionary analyses indicated that BBWV1 genes were predominantly shaped by negative selection, with essential replication proteins (HEL and Pro) under strong purifying pressure, while VP47 and VP37 experienced more relaxed constraints. A few codons in ORF1 and ORF2a were under episodic positive selection. Phylogenetic analysis clustered 19 non-recombinant isolates into two major clades (A and B), with BBWV1-IR positioned in subclade I of clade A alongside geographically distant isolates, reflecting human-mediated long-distance dispersal. Incongruent clustering of ORF1 and ORF2a in several isolates supports RNA segment reassortment as a key driver of novel variant emergence. Collectively, these findings highlight the roles of mutation, selection, reassortment, and gene flow in shaping BBWV1 evolution, exemplified by the Iranian isolate.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04905-w.}, }
@article {pmid42273206, year = {2026}, author = {Montgomery, A and Nupp, S and Gray, CR and Jay, ZJ and Edgcomb, V and Hatzenpichler, R}, title = {Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag111}, pmid = {42273206}, issn = {2730-6151}, abstract = {The marine deep biosphere harbors microbial communities that drive organic matter transformations and biogeochemical cycles. Previous work on these communities has focused either on genomic characterization or metabolic activity measurements. However, to understand microbial ecophysiology in the deep biosphere, taxonomic identity and metabolic function must be connected on both single-cell and ecosystem scales. In this work, we optimized a bioorthogonal noncanonical amino acid tagging fluorescence-activated cell sorting (BONCAT-FACS) workflow for low-biomass deep-biosphere sediments obtained during International Ocean Discovery Program Expedition 385 (IODP 385). BONCAT-FACS with 16S rRNA gene amplicon sequencing as well as metagenomics of sediment communities was applied to characterize translationally active communities in hydrothermally altered subsurface sediments of the Guaymas Basin. Our results revealed a heterotrophic microbial population throughout all sediments examined, with taxa translationally active down to our deepest sampling point, 154 m below the seafloor. Based on 16S rRNA gene identities, the translationally active microbial community was dominated by heterotrophic members of the Gammaproteobacteria, Bacilli, Deinococci, and Alphaproteobacteria. These taxa are likely key contributors to cycling the large quantities of hydrothermally altered organic matter in Guaymas Basin sediments. To further elucidate the metabolic capacity of active taxa, we mapped 16S rRNA gene amplicons to metagenome assembled genomes (MAGs) previously obtained from IODP 385. These MAGs contained genes associated with C1 metabolism, carbohydrate degradation, and fermentation, indicating that active taxa leverage these metabolisms for energy conservation. Our results demonstrate that BONCAT-FACS provides high-throughput and single-cell insights into the metabolic activity of microbes in the low-biomass marine subsurface.}, }
@article {pmid42274245, year = {2026}, author = {Christian, WC and Jay, ZJ and Tolic, N and Nicora, CD and Livingstone, R and Trimmer, S and McDermott, TR and Hatzenpichler, R}, title = {Proteomic stress response by a novel methanogen enriched from the Great Salt Lake.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0041226}, doi = {10.1128/spectrum.00412-26}, pmid = {42274245}, issn = {2165-0497}, abstract = {Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity, more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase the expression of energy-conservation or osmotolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus. 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.IMPORTANCEMethanogens are microbes that affect the climate through their production of the greenhouse gas, methane. Changes in climate and land-use patterns are drying up saline lakes, damaging their unique economic and ecological value. As lake levels across the globe fall, it is unclear how methanogens and the amount of methane they produce will concurrently shift. In this study, we measured high methane output from the Great Salt Lake (GSL) across seasons and identified a novel methanogen as part of a larger methanogenic community that is responsible for these emissions. We cultured this novel methanogen from GSL sediments and determined that its methane production was largely unaffected by stress conditions. Our findings indicate that methanogens in saline environments, including a novel cultivated species, may be important and continued sources of methane as salinity increases.}, }
@article {pmid42274374, year = {2026}, author = {Madi, N and Sayeed, A and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, IU and Islam, T and Khan, ZH and Bhuiyan, TR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ}, title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag286}, pmid = {42274374}, issn = {1537-6613}, abstract = {Virulent bacteriophages (phages) can kill bacterial prey, potentially reducing burden of infection. In cholera, a high phage to Vibrio cholerae ratio is associated with mild dehydration, yet the relative importance of this ratio in disease severity remains unclear. We used machine learning to rank select host, microbial, and environmental factors as determinants of dehydration severity in over 600 cholera patients from across Bangladesh. We found the phage:pathogen ratio ranked among the top classifiers for mild dehydration, behind age and location. We advocate that phage predation be included as a key factor in cholera characterization for scientific, clinical and epidemiological applications.}, }
@article {pmid42275101, year = {2026}, author = {Zhu, XY and Hopkins, FE and Airs, R and Widdicombe, CE and Wilkinson, B and Tarran, GA and Woodward, EMS and Carrión, O and Curson, ARJ and Ma, Q and Hanwell, L and Yang, GP and Christie-Oleza, JA and Lea-Smith, DJ and Zhang, XH and Todd, JD}, title = {Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag141}, pmid = {42275101}, issn = {1751-7370}, abstract = {Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolise it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.}, }
@article {pmid42275884, year = {2026}, author = {Zhao, J and Zuo, M and Cao, L and Li, Q and Zhang, R and Wu, H and Yuan, J and Lv, C and Yu, Y and Lu, J}, title = {The neutral and acidic polysaccharides from Ginseng are metabolized by specific gut microbial taxa and confer immunomodulatory effects.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {158}, number = {}, pages = {158400}, doi = {10.1016/j.phymed.2026.158400}, pmid = {42275884}, issn = {1618-095X}, mesh = {*Panax/chemistry ; *Polysaccharides/pharmacology/metabolism/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Immunologic Factors/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Fermentation ; }, abstract = {BACKGROUND: Ginseng (Panax ginseng C. A. Mey.) exerts immunomodulatory effects partly mediated by its polysaccharides and interactions with gut microbiota. However, due to the structural complexity of ginseng polysaccharides, knowledge of their oral fate and direct microbiota interactions remains limited.<br><br>PURPOSE: This study aims to elucidate the oral fate of neutral and acidic polysaccharides in ginseng, analyze core gut microbiota genera and their immunomodulatory effects mechanisms.<br><br>METHODS: Structural analysis was conducted on neutral and acidic polysaccharides from ginseng. Thereafter, in vitro digestion and fermentation were performed, with metagenomic and metatranscriptomic profiling. The results were validated in conventional and pseudo&#x2011;germ-free immunosuppressed mouse models, and the immunomodulatory mechanisms of the core gut microbiota were investigated.<br><br>RESULTS: The in vivo and in vitro findings indicated that neutral and acidic polysaccharides exhibit different digestive properties and gut microbiota degradation patterns, differ in short-chain fatty acid production tendencies, bind to GPR-41/43 receptors, upregulate MAPK-p38 phosphorylation, and promote proliferation of intestinal immune cells.<br><br>CONCLUSION: This work systematically elucidated the digestive characteristics of ginseng polysaccharides and laid the groundwork for future studies on the specificity and structure-function relationships of plant-derived polysaccharides.}, }
@article {pmid42275949, year = {2026}, author = {Zheng, Y and Su, F and Li, H and Wu, H and Cui, P and Song, F}, title = {Wetland succession reshapes microbial degradation of plant- and microbial-derived carbon.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130154}, doi = {10.1016/j.jenvman.2026.130154}, pmid = {42275949}, issn = {1095-8630}, mesh = {*Wetlands ; *Carbon/metabolism ; *Soil Microbiology ; Bacteria/metabolism ; Biodegradation, Environmental ; Fungi/metabolism ; China ; Plants/metabolism ; Soil/chemistry ; }, abstract = {Plant- and microbial-derived organic carbon require distinct microbial enzymes, but how wetland succession regulates these substrate-specific degradation pathways in estuarine soils remains unclear. We collected 0-10 cm soils from four wetland types in the Liaohe River Estuary, China-tidal flat, restored wetland, Suaeda salsa wetland, and reed wetland-with three independent replicate sites per type. Shotgun metagenomic sequencing, CAZy annotation, taxonomic annotation, co-occurrence networks, and Mantel tests were used to examine CAZyme genes targeting plant-, fungal-, and bacterial-derived carbon. We identified 16,346,752 CAZyme-encoding sequences assigned to 749 families. Carbon-cycling gene composition differed significantly among wetland types (ANOSIM R = 0.37, p = 0.034). Gene diversity was higher in early to mid-successional stages, whereas the abundances of plant-, fungal-, and bacterial-derived carbon degradation genes increased along succession. Lignocellulose-degrading genes were most enriched in reed wetland, including AA3, CBM9, and CE1. Microbial hosts shifted markedly, with Bacteroidota increasing from 8.53% to 38.28% among plant-derived carbon degraders. Plant-derived carbon degrader networks were densest in tidal flat soils, suggesting a transition from stress-associated microbial associations to resource-specialized assemblages. Environmental controls were substrate-specific: plant-derived genes correlated only with nitrate, fungal-derived genes with moisture, nitrogen, salinity, and electrical conductivity, and bacterial-derived genes with none of the measured variables. These findings reveal substrate-specific microbial mechanisms linking wetland succession to carbon turnover and identify Bacteroidota, AA3, and nitrate availability as candidate indicators for restoration assessment and carbon-sequestration management.}, }
@article {pmid42276429, year = {2026}, author = {Kang, X and He, P and Zhang, H and Lü, F}, title = {Multi-omic insights into thermal regulation of the resistome through composting-simulating microcosm system.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135119}, doi = {10.1016/j.biortech.2026.135119}, pmid = {42276429}, issn = {1873-2976}, abstract = {Composting is a crucial biosecurity practice that stabilizes organic waste and reduces biological hazards prior to land application, with temperature as a major driver of resistome succession. However, compost temperature is a dependent, composite factor jointly determined by microbial metabolism and management practices. The regulatory pathways of temperature on resistome remain unclear. In this study, temperature gradients from 50°C to 65°C were applied to biowaste in a composting-simulating microcosm system to investigate the genomic and functional regulatory pathways of antimicrobial resistance genes (ARGs) using high-temporal-resolution metagenomic and metatranscriptomic analyses. The succession dynamics of ARGs under temperature-controlled incubation were demonstrated from the ecological niche perspective. Our results revealed that the genomic potential and transcriptional activity of ARGs responded asynchronously to temperatures. ARG sensitivity to temperature was category-specific, with 60°C representing a critical threshold for genomic-level removal of ARGs. The context-anchored members drove the resistome's response trends during temperature-controlled incubation, while abundance-based dynamics did not show significant kinetic shift under elevated temperatures. Temperature shaping the resistome through intra-lineage ARG reduction within context-anchored members rather than community succession. Unassociated fragment members showed transient abundance fluctuations at 55°C. Both context-anchored and unassociated fragment ARG carriers maintained transcriptional homeostasis during temperature-controlled incubation. Viruses had a limited impact on the community resistome. Our study demonstrated temperature-driven regulation of the resistome, providing a basis for optimizing ARG management in composting.}, }
@article {pmid42276430, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Pan, X}, title = {Industrial red mud establishes redox-active interfaces to steer metabolic pathways toward chain elongation in sludge anaerobic fermentation.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135151}, doi = {10.1016/j.biortech.2026.135151}, pmid = {42276430}, issn = {1873-2976}, abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) provides a promising route for sludge valorization, but is often limited by inefficient hydrolysis and restricted interspecies electron transfer. This study evaluated industrial red mud (RM) as a conductive and alkaline regulator to enhance anaerobic chain elongation (CE). With 5 g/L RM addition, MCFAs yield reached 12.6 g COD/L, representing a 164% increase over the control. Spectroscopic analysis showed that the strong alkalinity of RM altered protein secondary structures, facilitating substrate hydrolysis while maintaining stable pH favorable for CE. Increased release of humic-like substances was observed, and electrochemical evidence suggested that the adsorption of these redox mediators onto the RM surface potentially facilitated the formation of redox-active interfaces, which contributed to the enhanced electron transfer capacity. Microbial network analysis demonstrated that RM acted as a topological hub, restructuring the community into a synchronized syntrophic consortium (hydrolysis-acidogenesis-CE) and highly enriching key CE bacteria. Metagenomic analysis revealed an increase in the abundance of genes encoding conductive membrane proteins (cytochromes and Mtr-associated), suggesting a potential enhancement in direct interspecies electron transfer. Meanwhile, RM increased the gene abundance of the CE key pathway (reverse β-oxidation pathway), thereby favoring the genetic potential for MCFAs accumulation. These findings establish a sustainable 'waste-treating-waste' framework, utilizing RM-driven electron reservoirs to facilitate the high-value conversion of WAS in anaerobic systems.}, }
@article {pmid42276515, year = {2026}, author = {Hassanien, A and Saadaoui, I and Sayadi, S}, title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2026.06.006}, pmid = {42276515}, issn = {1638-6183}, abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.}, }
@article {pmid42276765, year = {2026}, author = {Diao, Y and Li, J and Wang, L and Zhang, Q and Xu, C and Peng, A and Lu, C and Lai, B and Chen, R and Chen, J and Pei, X}, title = {Microbiological characteristics of granulomatous lobular mastitis revealed by metagenomic sequencing.}, journal = {Journal of clinical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1136/jcp-2026-210744}, pmid = {42276765}, issn = {1472-4146}, abstract = {AIMS: Granulomatous lobular mastitis (GLM) is a rare, chronic, benign inflammatory disease of the breast with an unclear aetiology. This study aimed to characterise the microbial features of GLM using metagenomic next-generation sequencing (mNGS) and to provide potentially relevant microbial clues for clinical evaluation.<br><br>METHODS: Twenty fresh lesion tissue samples were collected from 15 female patients with GLM, including one representative sample per patient and five additional deep tissue samples. Clinical data collection, mNGS, bioinformatics analysis and data interpretation were performed to characterise the microbial profiles of GLM lesions.<br><br>RESULTS: In this study, all patients presented with palpable breast masses, breast pain and abscess formation. More than half showed increased white blood cell counts, neutrophil percentages, C reactive protein levels and erythrocyte sedimentation rates together with decreased lymphocyte percentages. Based on genus-level filtering, mNGS identified 16 bacterial genera, 14 fungal genera and 3 viral genera, revealing a complex but bacteria-dominated microbial profile. The most frequently detected bacterial genera were Corynebacterium, Cutibacterium, Acinetobacter, Staphylococcus and Hathewaya, with marked interpatient variation in relative abundance, while fungal profiles were relatively more concentrated. In five patients with both superficial and deep tissue samples, microbial profiles differed across sampling depths, particularly for bacterial composition.<br><br>CONCLUSIONS: mNGS revealed a complex, bacteria-dominated microbial profile in GLM lesions and indicated that sampling depth may influence the detected microbial profiles. These findings may provide useful clues for clinical evaluation, but the pathogenic significance of these micro-organisms remains to be elucidated.}, }
@article {pmid42277004, year = {2026}, author = {Clark, JR and Chirman, D and Prakash, H and Terwilliger, A and McNeese, M and Ross, M and Tisza, M and Javornik Cregeen, SJ and Hopkins, L and Deegan, J and Troisi, CL and Boerwinkle, E and Mena, K and Wu, F and Kimata, JT and Johnson, M and Gregory, D and Fletcher, FE and Giordano, TP and Maresso, AW}, title = {Statewide multi-year wastewater sequencing reveals dual origins of HIV-1 signal.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74140-7}, pmid = {42277004}, issn = {2041-1723}, support = {U19AI14429//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30AI161943//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01DA059394//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; }, abstract = {Human immunodeficiency virus 1 (HIV-1) is a retrovirus which has infected 90 million people and resulted in over 40 million deaths. Despite advances in diagnostics, treatment, and prophylaxis, HIV-1 continues to spread due to undiagnosed and untreated infections. Traditional monitoring methods are ineffective when access to testing is limited or people do not seek care, particularly given the long period between infection and symptom onset, allowing undetected transmission to continue. Here, we use a hybrid-capture sequencing approach to track HIV-1 signal in municipal wastewater in 15 different cities over nearly 3 years. We obtain near-complete genomic coverage of HIV-1, enabling detailed genomic analysis. Surprisingly, there are a substantial number of research-associated retroviral vector sequences recovered. Using computational competitive mapping, we identify specific genomic regions that differentiate authentic HIV-1 from vector-derived inputs. In an exploratory analysis of sites with available clinical data, wastewater-derived circulating HIV-1 reads show a positive correlation with community-level HIV diagnosed prevalence that was robust to exclusion of individual high-prevalence sites. This study identifies lentiviral vector contamination as a confounding factor in wastewater HIV-1 detection, recovers authentic circulating HIV-1 signal through an original classification framework, and provides initial evidence that the resulting signal tracks community HIV burden.}, }
@article {pmid42277027, year = {2026}, author = {Wacker, EM and Rühlemann, MC and Franke, A and Ellinghaus, D}, title = {TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42277027}, issn = {2041-1723}, support = {EL 831/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Metagenome/genetics ; *Software ; Humans ; *Metagenomics/methods ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/methods ; Shotgun Sequencing ; Workflow ; }, abstract = {Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI's Sequence Read Archive (SRA). Technically advanced and easy-to-use best-practice metagenome software workflows for raw data pre-processing, assembly of metagenome-assembled genomes, and taxonomic and functional annotation of metagenome-assembled genomes are needed for reproducible analysis and harmonization of large-scale metagenomic datasets. We introduce TOFU-MAaPO (Taxonomic Or FUnctional Metagenomic Assembly and PrOfiling), a portable, automated single-command Nextflow pipeline for large-scale analysis of metagenomic short-read sequencing data. It analyzes metagenome files locally or directly from the SRA using accession or study IDs. In a benchmark against three established metagenome software pipelines, the TOFU-MAaPO workflow yielded 12%, 42% to 77% more high-quality metagenome-assembled genomes, likely reflecting the integration of multiple complementary binning tools with a unified refinement strategy. Using its assembly-free taxonomic abundance profiling module, we also automatically downloaded 16,462 uniquely identifiable and accessible human gut metagenome samples from the SRA and taxonomically annotated them against the Genome Taxonomy Database on a high-performance cluster in less than 55 hours, including download time. TOFU-MAaPO makes large metagenome projects more accessible to individual research groups and is freely available at https://github.com/ikmb/TOFU-MAaPO .}, }
@article {pmid42277260, year = {2026}, author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C}, title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {42277260}, issn = {1546-1718}, abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.}, }
@article {pmid42277454, year = {2026}, author = {Amoia, SS and Giampetruzzi, A and Antònio, LF and Tomàs Pais da Cunha, A and Minafra, A}, title = {A new putative carlavirus identified by metagenomic analysis in a wild weed in Angola.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42277454}, issn = {1432-8798}, mesh = {Genome, Viral ; Metagenomics ; *Plant Diseases/virology ; Phylogeny ; *Carlavirus/genetics/isolation &amp; purification/classification ; Angola ; *Plant Weeds/virology ; High-Throughput Nucleotide Sequencing ; Open Reading Frames ; RNA, Viral/genetics ; }, abstract = {A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery of a putatively novel carlavirus, tentatively named 'Seles weed carlavirus'. The complete genome sequence, consisting of 8,597 nucleotides, poly-A tail excluded, exhibited the typical organization of members of the genus Carlavirus, including the replicase polyprotein (ORF1); the triple gene block (ORFs 2-4); the coat protein (ORF5) and an RNA-binding protein (ORF6). The replicase polyprotein and coat protein gene regions of the newly described virus shared the highest amino acid sequence identity with the corresponding sequences of cowpea mild mottle virus (51.40%) and Hainan betaflexivirus (63.08%), respectively. The infection was further confirmed by RT-PCR with multiple specific targeted primer pairs, whose related amplicons were cloned and sequenced.}, }
@article {pmid42277703, year = {2026}, author = {Cumley, N and Quick, J and Brier, T and Wilkinson, S and Kent, C and Hassan-Smith, Z and Loman, N and Hassan-Smith, G}, title = {Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13276-9}, pmid = {42277703}, issn = {1471-2334}, abstract = {BACKGROUND: Central nervous system infections (CNSI) contribute significantly to global disability and mortality, but the causative agent is often undetected. Metagenomic sequencing offers the potential to enhance diagnostic sensitivity, particularly in cases of unusual or partially treated infections. However, caution is required in interpretation of metagenomics data due to technical artefacts from contamination or non-specific read mapping which can reveal a broad spectrum of biologically plausible but diagnostically unlikely organisms.<br><br>METHODS: This study compares the performance of metagenomic sequencing with standard clinical microbiology methods using cerebrospinal fluid (CSF) from patients with CNSI and non-infected control samples. To evaluate sensitivity of different laboratory approaches, we sequenced DNA and RNA metagenomic libraries extracted from CSF, using both cell-free and cellular fractions. We then devised a set of simple, easily interpreted yet rigorous filters tailored for clinical metagenomics to generate a framework for result interpretation that can be readily applied by clinical scientists.<br><br>RESULTS: We demonstrate that composite filtering strategies are essential to reduce misleading signals and support standardised workflows. Additionally, our results suggest that a cell-free sample preparation approach can improve confidence in identifying clinically relevant pathogens, highlighting the impact of sample preparation on results quality.<br><br>CONCLUSION: In this study we describe a reproducible method that can be incorporated into a practical framework for clinical application of metagenomic sequencing in CNSI diagnostics.}, }
@article {pmid42277905, year = {2026}, author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C}, title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00950-y}, pmid = {42277905}, issn = {2050-7771}, support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.<br><br>METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n&#x2009;=&#x2009;68) and UC (n&#x2009;=&#x2009;77) patients, their healthy first-degree relatives (CD-HFDRs, n&#x2009;=&#x2009;37; UC-HFDRs, n&#x2009;=&#x2009;30), and unrelated healthy controls (HCs, n&#x2009;=&#x2009;497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.<br><br>RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.<br><br>CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.}, }
@article {pmid42278013, year = {2026}, author = {Mei, Z and Zhou, H and Du, H and Liu, K and Gao, C and Sheng, Z and Gong, Y}, title = {Heat Stress Induces Metabolic and Physiological Imbalance in Laying Hens, Accompanied by Hepatic Transcriptomic, Cecal Microbial, and Metabolomic Alterations.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, pmid = {42278013}, issn = {2076-2615}, support = {2023ZD0405203//the Biological Breeding-National Science and Technology Major Project/ ; 2023ZD0407106//the Biological Breeding-National Science and Technology Major Project/ ; HBZY2023B007//the Hubei Fund for Seed Industry High-Quality Development Project/ ; 2025HBSTX4-04//the Earmarked Fund for Hubei Agriculture Research System/ ; 2018YFE128100//the National Key Research and Development Program of China/ ; 2023BBA029//he Major Program of Hubei Province/ ; }, abstract = {Heat stress is a major constraint to productivity and physiological homeostasis in laying hens. This study investigated integrated responses to acute heat stress using a multi-omics approach, including performance traits, serum biochemical parameters, histology, hepatic transcriptomics, cecal metagenomics, and metabolomics. Acute heat stress impaired productive performance, as reflected by changes in egg production and reduced eggshell strength, and induced systemic physiological disturbances, including increased stress- and injury-related blood indicators and disrupted metabolic and electrolyte balance. Histological analysis confirmed liver and intestinal tissue damage. Hepatic transcriptomics revealed inflammatory activation and suppression of metabolic pathways, particularly those involved in lipid metabolism, energy production, and redox homeostasis. Cecal metagenomic and metabolomic analyses showed altered microbial composition and functional potential, along with disruptions in amino acid, lipid, and energy metabolism. Collectively, these findings suggest that acute heat stress is associated with coordinated inflammatory responses and metabolic reprogramming, together with liver and intestinal injury and gut microbiota-metabolite alterations. The study provides a framework for understanding early heat stress responses and highlights potential targets for nutritional and microbiota-based interventions in poultry production. Importantly, serum biochemical indicators such as D-lactic acid and aspartate aminotransferase may serve as potential early biomarkers for monitoring heat-stress-induced physiological disturbances.}, }
@article {pmid42278142, year = {2026}, author = {Yuan, Z and Xie, F and Ding, Y and Li, X and Ghonaim, AH and Jiang, C and Ren, M and Li, S}, title = {Dietary Fiber Levels Modulate Intestinal Mucosal Architecture and the Microbiome-Metabolome Axis to Support Immune Homeostasis in Brooding Wanxi White Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, pmid = {42278142}, issn = {2076-2615}, abstract = {Dietary fiber is a critical determinant of intestinal health, yet its optimal inclusion level for WWG during the critical brooding period remains undefined. This study aimed to evaluate the effects of varying dietary CF levels (approximately 3%, 5%, and 9%) on the intestinal morphology, immune function, and microbiome-metabolome axis of brooding WWG. A total of 120 one-day-old goslings were randomly assigned to the three dietary treatments for a 28-day trial. Histological analysis revealed that the 9% CF diet significantly improved gut morphology, yielding superior villus-to-crypt ratios in the jejunum and ileum. Molecular assays indicated that higher fiber levels (5-9%) upregulated the expression of nutrient transporters (SGLT1 and GLUT2). Concurrently, the 9% CF diet effectively suppressed the potent pro-inflammatory cytokine TNF-α in the jejunum while appropriately upregulating IL-6 and NF-κB, indicating enhanced mucosal immune vigilance and structural maturation. Multi-omics integration (shotgun metagenomics and LC-MS metabolomics) demonstrated that specific fiber levels significantly shifted microbial abundances, specifically enriching Bacteroidetes and Actinobacteria. These microbial shifts were strongly correlated with enriched metabolic pathways, notably lysine biosynthesis and purine metabolism, which synergistically support mucosal homeostasis. Collectively, these findings demonstrate that a 9% dietary CF inclusion is an effective nutritional strategy to optimize intestinal architecture and microbial-metabolic profiles in brooding WWG.}, }
@article {pmid42278211, year = {2026}, author = {Shematorova, EK and Shpakovski, GV}, title = {Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278211}, issn = {1422-0067}, support = {thematic plan 1&#x444;.4.1//National Research Center "Kurchatov Institute"/ ; }, mesh = {*DNA-Directed RNA Polymerases/genetics/chemistry/metabolism ; *Evolution, Molecular ; *Archaea/genetics/enzymology ; Protein Subunits/genetics/chemistry ; *Archaeal Proteins/genetics/chemistry/metabolism ; Phylogeny ; Amino Acid Sequence ; Protein Domains ; }, abstract = {The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10-12 subunits. Perhaps the only exception that seems to confirm this rule is the Rpo8 subunit (homologue of the eukaryotic Rpb8), which only some classes of archaea have. The development of metagenomic sequencing has led to a significant revision of the classification system of prokaryotes, in particular to the identification of a number of new Archaea evolutionary lineages. This makes it possible to analyze the subunit composition and structure of RNA polymerase of all currently isolated archaeal phyla. Our analysis shows that the Rpo8 subunit is present only in the RNA polymerase of Archaea species from the Thermoproteota of the Thermoproteati superphylum and from the whole superphylum Promethearchaeati, formerly known as the Asgard. After analyzing the changes in the small Rpo6 subunit (homologue of eukaryotic Rpb6), functionally interacting with Rpo8, we noticed that the largest number of changes in the primary and domain structures of this small subunit occurred in archaeal phyla that lack Rpo8. Shortened forms of Rpo6 without N- or C-terminal regions were observed only in representatives of archaea with an RNA polymerase that does not contain the Rpo8 subunit. Our analysis shows that the changes in Rpo6 are an adaptation of a multisubunit transcription complex to the disappearance of Rpo8. Most likely, the Rpo8 subunit was present in the RNA polymerase of the Last Common Ancestor of Archaea (LCAA) and, in the course of evolution, disappeared in the superphyla Euryarchaeota and Nanobdellati and two divisions of the Thermoproteati superphylum: Bathyarchaeota and Thaumarchaeota.}, }
@article {pmid42278252, year = {2026}, author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B}, title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278252}, issn = {1422-0067}, support = {101079425//Centre of Biotechnologie of Sfax/ ; }, mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.}, }
@article {pmid42278256, year = {2026}, author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M}, title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278256}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital &amp; Research Centre/ ; }, mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota ; *Homeostasis ; *Breast/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.}, }
@article {pmid42278324, year = {2026}, author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y}, title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278324}, issn = {1422-0067}, support = {24-14-00059//Russian Science Foundation/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; Mice ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Chromosome Aberrations/radiation effects/drug effects ; RNA, Ribosomal, 16S/genetics ; *Radiotherapy/adverse effects ; Radiation-Protective Agents/pharmacology ; Male ; Lactobacillus ; *Minerals/pharmacology ; *Dysbiosis/etiology ; }, abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.}, }
@article {pmid42278475, year = {2026}, author = {Ermakov, VS and Falah, K and Nigam, SK}, title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278475}, issn = {1422-0067}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.}, }
@article {pmid42278495, year = {2026}, author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E}, title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278495}, issn = {1422-0067}, support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; }, abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.}, }
@article {pmid42278559, year = {2026}, author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH}, title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278559}, issn = {1422-0067}, support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; }, mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; }, abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.}, }
@article {pmid42278576, year = {2026}, author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T}, title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278576}, issn = {1422-0067}, mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; }, abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.}, }
@article {pmid42278616, year = {2026}, author = {Gajic, I and Jovicevic, M and Kekic, D and Kabic, J and Vicic, I and Lukovic, B and Tomic, A and Sovljanski, O and Skoric, M and Sikanic, I and Jankovic, M and Smitran, A and Bozic, L and Golic, B and Basic, J and Karabasil, N and Opavski, N}, title = {Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278616}, issn = {1422-0067}, support = {7042//Scientific Fund of the Republic of Serbia/ ; }, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Humans ; Animals ; *Bacterial Infections/diagnosis/microbiology ; Metagenomics/methods ; *Bacterial Typing Techniques/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.}, }
@article {pmid42279294, year = {2026}, author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG}, title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.}, journal = {Cancers}, volume = {18}, number = {11}, pages = {}, pmid = {42279294}, issn = {2072-6694}, abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.}, }
@article {pmid42279452, year = {2026}, author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z}, title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, pmid = {42279452}, issn = {2075-4418}, abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.}, }
@article {pmid42279756, year = {2026}, author = {Abaalkhail, MA and Mohamed, SHS and Aljurbua, MS and Alkhuraisi, RA and Aladhadh, M}, title = {Microbial Diversity of Spontaneously Fermented Camel Milk.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42279756}, issn = {2304-8158}, abstract = {Camel milk is widely consumed in the world's arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk's microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization.}, }
@article {pmid42280335, year = {2026}, author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E}, title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280335}, issn = {2072-6643}, support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; }, mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration &amp; dosage/isolation &amp; purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; }, abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.<br><br>METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.<br><br>RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.}, }
@article {pmid42280338, year = {2026}, author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ}, title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280338}, issn = {2072-6643}, support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; }, mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.<br><br>METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.<br><br>RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.<br><br>CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.}, }
@article {pmid42280669, year = {2026}, author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W}, title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280669}, issn = {2223-7747}, support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; }, abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.}, }
@article {pmid42280715, year = {2026}, author = {Beckett, T and Hesse, U}, title = {Transcriptome Profiling of Leaves and Roots from Rooibos (Aspalathus linearis) Using Oxford Nanopore Sequencing.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280715}, issn = {2223-7747}, support = {PMDS22062326365//National Research Foundation/ ; N/A//Rooibos Council of South Africa/ ; }, abstract = {Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low stress tolerance. Transcriptome data can serve to identify molecular markers for improved stress response, which would speed up selection and facilitate the establishment of breeding programmes. Previously, rooibos leaf transcriptomes have been sequenced using Illumina, which yields short reads, hampering correct reassembly of full-length transcripts. Here, we established Oxford Nanopore-based, long-read transcriptome analysis for leaf and root samples from rooibos. We report on potential pitfalls in data pre-processing (PolyA tail trimming and rRNA removal), and compare two assemblers (RATTLE and RNA-Bloom2) and two clustering algorithms (VSEARCH and CD-HIT). The best assembly comprising 169,122 transcripts was generated using RNA-Bloom2 with short-read polishing, followed by CD-HIT clustering. Of the 95,054 predicted proteins, only 67% were also present in the Illumina dataset. The remainder comprised substantially shorter, mostly full-length sequences from a wide range of primary and secondary biosynthesis pathways. Functional annotation indicated that this transcriptome represents a high-quality, comprehensive resource for data mining. In the leaf fraction, comparative transcriptomics identified overexpressed rooibos transcripts potentially involved in photosynthesis, photorespiration and carbon fixation. In the roots, overexpressed transcripts encoded enzymes potentially involved in regulation of root growth and secondary metabolite biosynthesis. These transcripts may represent first targets for molecular marker development.}, }
@article {pmid42281243, year = {2026}, author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE}, title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685381}, pmid = {42281243}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; }, abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.}, }
@article {pmid42281420, year = {2026}, author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG}, title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10583}, pmid = {42281420}, issn = {1520-5851}, abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.}, }
@article {pmid42282013, year = {2026}, author = {Dobbler, PT and Ravi, A and Větrovský, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Single-contig bacterial genomes recovered from cattle fecal metagenomes at farms with variable antibiotic use.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9715194/v1}, pmid = {42282013}, issn = {2693-5015}, abstract = {Cattle feces represent a complex microbial reservoir with implications for animal health and the environmental dissemination of microorganisms and antibiotic resistance genes. Metagenomic studies have shown that cattle fecal communities are dominated by Bacillota and Bacteroidota, whereas low-abundance taxa, including potential pathogens, often remain underrepresented due to methodological detection limits. Here, we present 84 single-contig, medium- to high-quality metagenome-assembled genomes (MAGs) recovered from cattle feces after enrichment for bacteria able to grow in acetate-supplemented minimal medium. The MAGs were classified within the phyla Actinomycetota (20 MAGs), Bacillota (5), Bacteroidota (21), Patescibacteriota (5), and Pseudomonadota (33), with 41 MAGs representing putative novel taxa at species to family level. Nineteen MAGs carried antibiotic resistance genes and six MAGs were assigned to opportunistic pathogenic species. This dataset thus provides a genomic resource for studies of bacterial diversity and antimicrobial resistance at the animal-environment interface within a One Health framework.}, }
@article {pmid42282041, year = {2026}, author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G}, title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9856875/v1}, pmid = {42282041}, issn = {2693-5015}, abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.}, }
@article {pmid42282268, year = {2026}, author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M}, title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2679810}, pmid = {42282268}, issn = {2993-3935}, abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.<br><br>METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90&#x2009;y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID&#x2122;), readiness-for-change (adapted URICA), at-home stool sample collection.<br><br>RESULTS: Seventeen participants completed sufficient assessments (HC n&#x2009;=&#x2009;11; MCI n&#x2009;=&#x2009;6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.<br><br>CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.}, }
@article {pmid42282663, year = {2026}, author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G}, title = {Site-specialization of human oral Porphyromonas species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729646}, pmid = {42282663}, issn = {2692-8205}, abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.}, }
@article {pmid42282812, year = {2026}, author = {Jiang, AK and Grant, MR and Arp, G and Dufault-Thompson, K and Clarke, AM and Li, Y and Lehman, D and Jarmusch, AK and Hall, B and Jiang, X}, title = {Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.01.729425}, pmid = {42282812}, issn = {2692-8205}, abstract = {Gut bacteria reduce bilirubin to urobilinogen, allowing it to be excreted through feces and urine, but studies have long noted a heterogeneous mixture of partially reduced bilirubin-derived intermediates, suggesting that multiple enzymes are involved. Here we identify bilirubin vinyl reductase (BilV), a novel Old Yellow Enzyme family reductase encoded in the genomic neighborhood of the known bilirubin reductase (bilR). Using heterologous expression and LC-MS/MS, we show that BilR acts on the methine bridges in the bilirubin reduction pathway; co-expression with BilV enables vinyl-group reduction and complete conversion to urobilinogen. In bacterial genomes, bilV co-occurs primarily with the bilR -insertion subtype and is largely absent alongside bilR -short. Analysis of 1,197 gut metagenomes across 14 vertebrate species reveals that this differential co-occurrence shapes pathway availability across hosts: carnivores and omnivores carry balanced bilR and bilV , whereas avian microbiomes, dominated by bilR -short, are depleted for bilV . These findings establish that bilirubin reduction to urobilinogen involves two enzymes with complementary regioselectivity, and that their distribution across vertebrate gut microbiomes varies in concert with host bile pigment chemistry.}, }
@article {pmid42283066, year = {2026}, author = {Zhang, J and Liang, J and Lv, F and Guo, Z}, title = {Maternal vaginal colonization screening for term singleton pregnancy: comparative evaluation of metagenomic next-generation sequencing (mNGS) versus real-time quantitative PCR (qPCR).}, journal = {Practical laboratory medicine}, volume = {50}, number = {}, pages = {e00542}, pmid = {42283066}, issn = {2352-5517}, abstract = {OBJECTIVE: To investigate the distribution characteristics of potential high-risk pathogens for early-onset neonatal infection in maternal vaginal secretions, and to perform a head-to-head comparative evaluation of detection performance for target pathogens between metagenomic next-generation sequencing (mNGS) and real-time quantitative polymerase chain reaction (qPCR), with conventional bacterial culture as the reference standard.<br><br>METHODS: A total of 294 valid maternal vaginal secretion samples were prospectively collected and tested in parallel using qPCR, mNGS, and conventional bacterial culture. The Chi-square test was used to compare the differences in pathogen detection rates among the three methods. Receiver operating characteristic (ROC) curve was plotted to calculate the area under the curve (AUC) and 95% confidence interval (CI), to systematically evaluate the detection performance of the two methods for target pathogens.<br><br>RESULTS: The spectrum of potential early-onset neonatal pathogens in maternal vaginal secretions, ranked by detection rate, was as follows: Staphylococcus aureus, Streptococcus agalactiae, Ureaplasma urealyticum, Listeria monocytogenes, and Campylobacter fetus. The detection rates of these target pathogens by qPCR, mNGS, and bacterial culture showed high consistency, with no statistically significant difference in detection rates among the three methods (all P&#x202f;>&#x202f;0.05). ROC curve analysis showed that the AUC values of both qPCR and mNGS for the above major pathogens were all above 0.90, which were significantly different from the null hypothesis of AUC&#x202f;=&#x202f;0.5 (all P&#x202f;<&#x202f;0.05), indicating good detection performance; while there was no significant difference in AUC values between qPCR and mNGS (all P&#x202f;>&#x202f;0.05). In addition, Listeria monocytogenes (3 cases) and Campylobacter fetus (1 case) were only detected by qPCR and mNGS, while not isolated by conventional culture.<br><br>CONCLUSION: This head-to-head comparative study confirms that both mNGS and targeted qPCR have high accuracy and consistency for detecting potential early-onset neonatal pathogens in maternal vaginal secretions. We propose a tiered antenatal screening strategy for maternal vaginal pathogenic colonization: qPCR is recommended as the first-line tool for routine antenatal screening due to its high cost-effectiveness and rapid turnaround time, while mNGS is reserved for high-risk pregnant women (e.g., preterm premature rupture of membranes, clinical chorioamnionitis), culture-negative suspected infection cases, or scenarios requiring comprehensive pathogen profiling, to take full advantage of its unbiased, broad-spectrum detection capability. This integrated screening strategy requires further prospective validation with paired neonatal clinical outcome data to confirm its value in the prevention and early intervention of early-onset neonatal infection.}, }
@article {pmid42283067, year = {2026}, author = {Wei, F and Wang, X and Lv, H and Xia, H and Gan, G and Chen, X and Liu, X and Chen, H and Zhao, L}, title = {Identification of a potential novel Staphylococcus species via genomic sequencing: A neonatal infection case report.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02631}, pmid = {42283067}, issn = {2214-2509}, abstract = {BACKGROUND: Coagulase-negative Staphylococci (CoNS) are common symbiotic Gram-positive bacteria colonizing human skin and mucous membranes with lower virulence than Staphylococcus aureus. As crucial pathogens of neonatal infections, they often harbor multiple drug resistance genes and can induce neonatal pneumonia, sepsis, suppurative meningitis, and other clinical manifestations.<br><br>CASE PRESENTATION: A preterm neonate at 29[+1] weeks' gestation complicated by respiratory distress syndrome and pneumonia received empirical ceftazidime and penicillin for 8 days. The condition initially improved but suddenly deteriorated on postnatal day 17 with septic shock, fever, and anemia. Routine tests suggested Staphylococcus capitis infection, and targeted anti-infective and supportive treatments relieved symptoms. Given the inconsistenty between the infection severity and that of typical Staphylococcus infections, metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were further performed, identifying a potential novel Staphylococcus species closely related to Staphylococcus warneri. Nevertheless, the origin of this potential novel species remains unclear, which needs further verification.<br><br>CONCLUSION: For neonates with sudden clinical deterioration, intractable infection or ambiguous conventional microbial results, mNGS and WGS facilitate accurate pathogen identification and treatment adjustment. This potential novel strain discovery highlights the importance of enhanced vigilance against bacterial multidrug resistance and the emergence of potential novel pathogens in neonatal care.}, }
@article {pmid42283460, year = {2026}, author = {Tothero, GK and Keffer, JL and Emerson, D and Fleming, EJ and Chan, CS}, title = {Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176825}, doi = {10.1128/msystems.01768-25}, pmid = {42283460}, issn = {2379-5077}, abstract = {The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59-3.04 Mb) than those of Groups 2 (4.55-6.06 Mb) and 3 (3.94-5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.IMPORTANCEResearchers have long noted differences in metal oxidation, morphology, and ecology among Sphaerotilus-Leptothrix, but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the Leptothrix type strain L. ochracea has never been isolated. This study provides molecular evidence that substantiates calls to reassign some Leptothrix members to the genus Sphaerotilus but adds to an emerging body of evidence that Group 1 L. ochracea and now L. toolikensis represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within Sphaerotilus-Leptothrix lineages.}, }
@article {pmid42283524, year = {2026}, author = {Hashimoto, K and Fukushima, K and Nakamura, S and Kida, H}, title = {Reply to Rojas-Ponce, "Operational considerations for implementing culture-free mycobacterial sequencing in routine laboratory settings".}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0056426}, doi = {10.1128/jcm.00564-26}, pmid = {42283524}, issn = {1098-660X}, }
@article {pmid42283633, year = {2026}, author = {Gómez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL}, title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0210625}, doi = {10.1128/aem.02106-25}, pmid = {42283633}, issn = {1098-5336}, abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.}, }
@article {pmid42283754, year = {2026}, author = {Chen, X and Fang, Z and Li, S and Wu, Q and Liu, W and Xiang, L and Liu, Q and Tan, L and Weng, Q}, title = {Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42283754}, issn = {1432-8798}, mesh = {*Genome, Viral ; *Caves/virology/microbiology ; *Pseudomonas Phages/genetics/isolation &amp; purification/classification ; Phylogeny ; China ; *Pseudomonas/virology ; DNA, Viral/genetics ; Sequence Analysis, DNA ; Genomics ; Geologic Sediments/virology ; }, abstract = {Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome places it within the genus Ghunavirus (family Autographiviridae). Notably, its genome lacks auxiliary metabolic genes (AMGs), in contrast to AMG-rich profiles reported in cave metagenomic surveys and underscoring the necessity of isolation-based approaches to complement environmental sequencing data.}, }
@article {pmid42283827, year = {2026}, author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K}, title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02807-1}, pmid = {42283827}, issn = {1432-184X}, support = {No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; }, abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.}, }
@article {pmid42284845, year = {2026}, author = {Wang, W and Sun, X and Hao, R and Li, F}, title = {Algal community composition drives lake greenhouse gas emissions via dissolved organic matter transformation and microbial processing.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130177}, doi = {10.1016/j.jenvman.2026.130177}, pmid = {42284845}, issn = {1095-8630}, mesh = {*Lakes ; *Greenhouse Gases ; *Dissolved Organic Matter ; Eutrophication ; Diatoms ; Cyanobacteria ; }, abstract = {Lakes are important sources of greenhouse gases, yet bloom-driven emissions are often assessed from total algal biomass, ignoring algal functional composition. This study examined how cyanobacteria (Microcystis aeruginosa), green algae (Chlorella vulgaris), diatoms (Cyclotella meneghiniana), and dominance-based mixtures regulate DOM transformation and CO2/N2O production under eutrophic conditions. It integrated to pure-culture experiments, water-sediment microcosms, sterilization controls, DOM fluorescence spectroscopy, gas monitoring, and metagenomics to resolve an algae-DOM-microbe-gas cascade. Cyanobacteria produced protein-like DOM and stimulated carbon mineralization, with CO2 exceeding 20 mmol L-1 by day 36; cyanobacteria-dominant mixtures followed a similar high-CO2 trajectory. Green algae generated tyrosine-like DOM and caused the strongest NO2[-] accumulation, reaching 5.21 mg L[-1] by day 21, corresponding to the highest N2O production; this pattern also occurred in green-algae-dominant mixtures. Diatom-only and diatom-dominant treatments favored humic-like DOM, organic carbon retention, and the weakest short-term CO2/N2O accumulation. Sterilization reduced inorganic carbon and greenhouse gas production, supporting microbial control. Background summer metagenomics provided functional context, showing algal-DOM turnover potential through carbon metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and the TCA cycle, while nirK and other nitrogen genes indicated capacity for substrate-driven incomplete nitrogen reduction. Functional differentiation among Candidatus_Planktophila, Limnohabitans, Rhodoferax, and Cyanobium linked DOM processing with potential gas-production pathways. These results show algal community composition, rather than biomass alone, regulates greenhouse gas production by shaping DOM quality, nutrient intermediates, and microbial C-N pathways. Incorporating algae composition into greenhouse gas assessment, this novel algae-DOM-microbe-gas framework provides mechanistic support for improving eutrophication management and lake-emission mitigation.}, }
@article {pmid42284910, year = {2026}, author = {Fu, J and Li, Z and Hu, C and Yao, L and Cao, M and Dong, Y and Wang, P and Liang, Y and Tong, L and Shi, J}, title = {Metagenomic insights into the distribution and potential influencing factors of antibiotic resistance genes in historically polluted lake sediments.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {298}, number = {}, pages = {107898}, doi = {10.1016/j.aquatox.2026.107898}, pmid = {42284910}, issn = {1879-1514}, abstract = {Lake sediments serve as time-integrated archives of the evolution and persistence of environmental antibiotic resistance genes (ARGs), providing insights into how sustained environmental pressures shape resistome structure in human-impacted lake systems. Industrially polluted lakes, as systems subjected to strong anthropogenic disturbance, are characterized by high-intensity contaminant loading in sediments; however, the accumulation patterns and environmental factors associated with ARG persistence in such environments remain poorly understood. This study investigated the horizontal and vertical distributions and potential influencing factors of ARGs along sediment depth gradients (0-40 cm, 40-80 cm, and 80-120 cm) in a lake historically polluted by industrial activities (Ya'er Lake). Results indicated that bacitracin (27.3-43.6%) and multidrug resistance genes (25.4-33.1%) dominated the resistome, with pronounced enrichment in shallow sediments near discharge outlets, reflecting the influence of legacy pollution inputs. ARGs exhibited significant vertical stratification (p < 0.05): highest abundance in shallow layers, peak diversity in middle layers, and shifts with depth of key subtypes. Host-tracking assigned ARGs to 34 major genera across four phyla, with Pseudomonadota, Actinomycetota, Bacillota, and Thermodesulfobacteriota identified as the major ARG hosts. Microbial communities and mobile genetic elements (MGEs) jointly shaped ARG persistence, with shallow sediments showing broader host-MGE coupling and deeper sediments showing stronger signatures of environmental filtering and selective MGE-mediated maintenance. Overall, ARGs shifted from surface enrichment associated with historical wastewater inputs to a more selective persistence pattern with burial depth, indicating contaminated lake sediments as long-term reservoirs and potential dissemination sources of ARGs.}, }
@article {pmid42284942, year = {2026}, author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.}, journal = {Water research}, volume = {303}, number = {}, pages = {126258}, doi = {10.1016/j.watres.2026.126258}, pmid = {42284942}, issn = {1879-2448}, abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.}, }
@article {pmid42285959, year = {2026}, author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X}, title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04161-9}, pmid = {42285959}, issn = {2158-3188}, abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.}, }
@article {pmid42286003, year = {2026}, author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M}, title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74327-y}, pmid = {42286003}, issn = {2041-1723}, support = {101007799//Innovative Medicines Initiative (IMI)/ ; }, abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.}, }
@article {pmid42286360, year = {2026}, author = {Morelli, S and Romano, S and Cosenza, G and Abate, S and Lombardi, L and Pilli, E}, title = {A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {42286360}, issn = {1618-2650}, abstract = {Species identification from highly degraded DNA remains a major challenge across ecology, conservation genetics, wildlife forensics, and museum science, where samples are often scarce, contaminated, and embedded in complex matrices. Under these conditions, standard reference-based and metagenomic classifiers are prone to false-positive assignments, particularly when ultra-fragmented DNA and conserved genomic regions are not explicitly accounted for. Here, we present a damage-aware next-generation sequencing (NGS) workflow for conservative species identification from minute quantities of highly degraded DNA, designed to minimize misclassification in low-input and damage-rich datasets. The workflow integrates micro-sampling, half-uracil-DNA-glycosylase (half-UDG) library preparation, PCR duplicate removal, multi-genome mapping against a curated reference panel, and a post-mapping read-ubiquity classifier that distinguishes species-specific reads from those shared across conserved loci. Using collagen-rich substrates as a proof-of-concept, we demonstrated accurate species attribution from samples as small as 1 mm[2], including mixtures and mineral-containing matrices. The workflow reliably identifies dominant biological sources, reduces false-positive assignments driven by conserved genomic regions, and remains robust to common physical and chemical treatments such as swelling, heating, and plaster addition. Overall, this study provides a proof-of-concept framework for conservative species identification in challenging degraded DNA contexts. The workflow may be adaptable to a broader range of degraded DNA contexts-including wildlife monitoring, regulatory enforcement, forensic investigations, and the analysis of processed biological materials-although further validation across diverse matrices will be required.}, }
@article {pmid42286394, year = {2026}, author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W}, title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {42286394}, issn = {1572-994X}, support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; }, abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.}, }
@article {pmid42286497, year = {2026}, author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H}, title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01451-5}, pmid = {42286497}, issn = {2730-6844}, support = {U54AG089334//National Institute for Health and Care Research/ ; JPMJCR20H1//JST CREST/ ; 20K10436//JSPS KAKENHI/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; }, abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.<br><br>DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 &#xd7; 150 bp paired-end reads.}, }
@article {pmid42286668, year = {2026}, author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA}, title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02447-0}, pmid = {42286668}, issn = {2049-2618}, abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.<br><br>RESULTS: ASP supplementation reduced CH&#x2084; yield by 54% (g CH&#x2084;/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH&#x2084; were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are&#xa0;critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION&#xa0;: ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.}, }
@article {pmid42286752, year = {2026}, author = {Abedini, R and Salekdeh, GH and Hashemi, M}, title = {Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42286752}, issn = {2524-4671}, abstract = {While metagenomics has transformed our view of microbial ecosystems, culture-based methods remain indispensable for accessing microbial functionality and biotechnological potential. In this study, we applied a culturomics strategy to explore the diversity, abundance, and distribution of culturable aerobic and facultative anaerobic bacteria along the gastrointestinal tract of dromedary camels (Camelus dromedarius) grazing on pristine desert flora. Using six culture media-including modified YCFA formulations-we isolated 97 bacterial species across 42 genera, 31 families, and four phyla: Firmicutes, Proteobacteria, Actinomycetota, and Bacteroidota. Strikingly, 88.6% of this diversity was recovered using YCFA-based media, and four candidate novel species were identified. The rumen harbored the most diverse and Gram-positive-dominated community, whereas the small intestine was enriched with Gram-negative taxa, many with pathogenic potential. These findings highlight the camel's unique physiological adaptation to extreme arid environments, characterized by efficient fiber degradation under nutrient- and water-limited conditions and the presence of stress-tolerant gut microbes capable of resisting acidic and osmotic challenges. Overall, this study establishes a foundational understanding of the camel gut microbiota and underscores the complementary power of culture-dependent methods to metagenomics. Future integration with anaerobic culturing and multi-omics analyses will further unveil the ecological and biotechnological potential of desert-adapted microbial life.}, }
@article {pmid42286784, year = {2026}, author = {Yu, Y and Wu, H and Ji, H and Hu, Y and Fang, Y and Lin, Y and Zhang, Y and Zhou, Y}, title = {Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00589-y}, pmid = {42286784}, issn = {2524-4671}, support = {2024-2026QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 32402702//National Natural Science Foundation of China/ ; LMS25C170002//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a threat to global public health. Swine farms are critical AMR reservoirs. Comprehensive resistome profiling and risk assessment across pig-associated niches remain limited. Metagenomic analysis of antibiotic resistance genes (ARGs) in pig nasal cavities, feces, and farm dust was performed.<br><br>RESULTS: Nasal and dust samples exhibited significantly increased ARG diversity and abundance compared with feces. We identified 78 potentially hazardous ARGs and proposed an improved risk classification framework integrating host promiscuity, mobility, and human health risks. These ARGs were classified into four risk levels: 25 Level I (current high risk), 25 Level II (potential future threats), 18 Level III (host-promiscuous but nonmobile), and 10 Level IV (host-specific). High-risk ARGs mainly confer aminoglycoside, macrolide-lincosamide-streptogramin (MLS), and tetracycline resistance. Metagenome-assembled genome (MAG) analysis revealed that bacterial taxa enriched in ARGs were predominant in nasal and dust samples. Moreover, these environments presented higher mobile genetic element (MGE) abundance and similar ARG-MGE co-occurrence patterns. Notably, 74.12% of the mobile ARGs were predicted to be plasmid-borne, and these ARGs tended to be assigned higher health risk levels than chromosomal ARGs.<br><br>CONCLUSIONS: These findings provide a practical framework for ARG risk assessment and highlight the nasal cavity and dust as underappreciated but important AMR reservoirs in pig farms.}, }
@article {pmid42286862, year = {2026}, author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M}, title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679497}, pmid = {42286862}, issn = {1949-0984}, mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; }, abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.}, }
@article {pmid42287197, year = {2026}, author = {De Visscher, J and Tytgat, B and Hodgson, DA and Wilmotte, A and Willems, A and Verleyen, E and Vyverman, W}, title = {Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {7}, pages = {}, pmid = {42287197}, issn = {1574-6941}, support = {SD/BA/03A//Belgian Science Policy Office/ ; //EU Horizon 2020 InterAct project MiBiPol/ ; SD/CA/01A//Belspo project HOLANT/ ; //Research Foundation Flanders/ ; }, mesh = {*Lakes/microbiology ; Antarctic Regions ; Arctic Regions ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; *Bacteria/genetics/classification ; }, abstract = {Benthic microbial mat communities are key drivers of ecosystem functioning in polar lakes and ponds, forming the base of aquatic food webs and contributing substantially to nutrient cycling. Although Arctic, sub-Antarctic, and Antarctic microbial mats differ in community composition, their functional genetic potential remains poorly understood. We applied shotgun metagenomic sequencing to study 17 microbial mat communities from Arctic and (sub-)Antarctic lakes differing in salinity, catchment vegetation, and climatic conditions. Stress response genes, especially cold stress, and phosphorus cycling and metabolism genes were highly abundant in all lakes. A large proportion of functional genes was shared between regions, with core functions dominated by transport mechanisms and energy production. However, clear differences in particular gene abundances were observed. Several East-Antarctic lakes and inland ponds in the Transantarctic Mountains showed a dominance of oxygenic photosynthesis and Calvin cycle genes for carbon fixation, likely reflecting the dominance of Cyanobacteriota. In Arctic and sub-Antarctic lakes with catchment vegetation and higher arthropod abundances, lignin and chitin degradation genes were more important. Our study shows that, despite distinct biogeographic patterns in community composition, the functional genetic potential of polar lake microbial mats mainly reflects climatic and local environmental conditions, emphasizing specific adaptations to extreme polar environments.}, }
@article {pmid42287489, year = {2026}, author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A}, title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287489}, issn = {1573-0972}, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.}, }
@article {pmid42287798, year = {2026}, author = {Winssy, TD and Anandham, R and Maragatham, S and Uma, D and Karthikeyan, S and Balachandar, D}, title = {Long-term nutrient management shapes soil microbial and metabolic signatures in a century-old semi-arid agroecosystem.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130209}, doi = {10.1016/j.jenvman.2026.130209}, pmid = {42287798}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Nitrogen ; Carbon ; Agroecology ; Agriculture ; Fertilizers ; Microbiota ; }, abstract = {Semi-arid tropical soils inherently contain low soil organic carbon (SOC) and limited nutrient reserves, resulting in poor productivity. Intensive cropping with synthetic fertilizers, further deteriorate soil quality and impair ecosystem functioning. In contrast, organic amendments alone or combined with synthetic fertilizers sustain soil biodiversity through microbially mediated processes. However, how long-term nutrient management shapes soil microbiomes and their functional diversity in semi-arid tropical systems remains largely unknown. To address this gap, we investigated a 116-year-old long-term nutrient management experiment using a multi-omic framework. Shotgun metagenomics characterized the total microbiome (bacteria, archaea, and eukaryota) and associated carbon- and nitrogen-cycling genes under four contrasting nutrient management practices: unfertilized control, inorganic fertilizer alone (IC), organic amendment alone (OM), and integrated nutrient management combining organic and inorganic inputs (INM). OM and INM significantly improved soil nutrient stocks, SOC, microbial biomass, and enzyme activities compared with IC and Control. These treatments also enhanced microbial diversity and shifted communities toward copiotrophic and functionally beneficial taxa, whereas IC and Control were dominated by stress-tolerant oligotrophs. Pathway analysis showed that carbon fixation dominated the C-cycling gene pool, with alternative autotrophic pathways prevailing over the Calvin cycle, particularly under OM and INM. These treatments also supported higher abundances of methanogenic and decomposition-associated genes, indicating enhanced carbon turnover. Nitrogen-cycling functions exhibited pathway-specific responses: OM enriched N-fixation and assimilatory nitrate reduction genes, whereas INM enhanced denitrification and dissimilatory nitrate reduction pathways. IC showed increased nitrification potential but the weakest biologically regulated N pathways. Volatomics profiling showed that OM and INM produced more diverse and metabolically active volatile organic compounds that were strongly associated with SOC and key biological attributes. Collectively, our study underscores the importance of carbon-rich organic inputs in rebuilding soil carbon stocks, reinforcing biological processes, and enhancing nutrient cycling for long-term sustainability of agriculture in semi-arid tropical regions.}, }
@article {pmid42287872, year = {2026}, author = {Wu, J and Wang, B and Li, Y and Zhang, X and Peng, Y and Liu, Q and Zhang, C and Lian, B and Cao, H and Li, K and Wang, H}, title = {Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in the Bohai sea.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108193}, doi = {10.1016/j.marenvres.2026.108193}, pmid = {42287872}, issn = {1879-0291}, abstract = {Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.}, }
@article {pmid42287875, year = {2026}, author = {Yang, X and Wu, P and Li, C and Zheng, Q and Shi, X and Su, H and Wang, T and Xiong, X and Liu, Y and Xiao, Y and Xu, S and Zou, J and Liu, Y}, title = {Bacterial communities and antibiotic resistance genes in seawater adjacent to inhabited and uninhabited xisha coral reef islands: Insights from 16S rRNA and metagenomic sequencing.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108197}, doi = {10.1016/j.marenvres.2026.108197}, pmid = {42287875}, issn = {1879-0291}, abstract = {The Xisha coral reefs are highly biodiverse ecosystems in the South China Sea, China. Bacterial communities drive energy flow and biogeochemical cycling in coral-reef ecosystems, and serve as indicators of reef health. Yet the composition and dynamics of both bacterial assemblages and ARGs within the Xisha coral reefs remain poorly resolved. This study used 16S rRNA amplicon and metagenomic sequencing to compare bacterial community structure across surface and bottom waters, and surface-water ARGs profiles, in Beijiao Reef (BJ; an uninhabited reef) and Qilianyu Islands (QLY; an inhabited island) of the Xisha Islands. The results revealed bacterial community composition, bacterial co-occurrence network structure, and ARGs profiles differed markedly between the two reef areas. Dominant genera-Prochlorococcus_MIT9313, Salinimonas, Synechococcus_CC9902, Vibrio, and Alteromonas-were significantly more abundant in BJ (p < 0.05), whereas QLY showed higher abundances of Planococcus, Psychrobacter, Jeotgalibacillus, Salinicoccus, and Marinococcus (p < 0.05). The QLY bacterial co-occurrence network exhibited greater complexity (higher clustering coefficients and modularity), whereas the BJ network was simpler but displayed significantly higher closeness-centrality values (p < 0.001). Surface waters of the Xisha Islands were dominated by tetracycline, aminoglycoside, and macrolide resistance genes, whereas sulfonamide and multidrug resistance genes were less abundant. In addition, ARGs concentrations in BJ were slightly higher than those in QLY, suggesting that human habitation may not be a key environmental factor influencing ARGs concentrations in the seawater of the Xisha Islands. Correlation analysis showed that high-abundance ARGs in BJ (msbA, RanA, tetB(P), tet(T)) were linked to phototrophic Prochlorococcus_MIT9313 and Synechococcus_CC9902, whereas QLY dominant ARGs (baeS, patB, MexW) correlated with Gram-negative Vibrio and Pseudomonas. These ARGs are involved in bacterial efflux mechanisms, reflecting adaptive responses to environmental stress. This study provides valuable insights for assessing water quality and evaluating the impacts of human habitation pressure on coral reef ecosystems in the Xisha Islands.}, }
@article {pmid42287910, year = {2026}, author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K}, title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142686}, doi = {10.1016/j.jhazmat.2026.142686}, pmid = {42287910}, issn = {1873-3336}, abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.}, }
@article {pmid42288243, year = {2026}, author = {Huiling, Y and Jinghui, Z and Xinxin, Y and Hang, J and Jianxiang, W and Lina, Z and Ping, XU and Chao, Z and Jianming, MO and Jing, D and Haixia, LI and Jie, LI and Ling, JI and Chang, LU}, title = {Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing in 841 Patients with Suspected Lower Respiratory Tract Infections: A Four-Year Retrospective Study from a Tertiary Hospital in Shenzhen, China.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108885}, doi = {10.1016/j.ijid.2026.108885}, pmid = {42288243}, issn = {1878-3511}, abstract = {BACKGROUND: Accurate pathogen identification is critical for managing lower respiratory tract infections (LRTIs), particularly in suspected polymicrobial infection or after empiric treatment failure. Although metagenomic next-generation sequencing (mNGS) has been increasingly used in clinical practice, its long-term diagnostic performance and clinical impact in LRTIs have not been systematically evaluated in a large single-center cohort.<br><br>METHODS: We conducted a retrospective cohort study of 841 hospitalized patients with suspected LRTIs who underwent bronchoalveolar lavage fluid (BALF) testing by both mNGS and conventional culture between December 2021 and December 2025. Positive detection rates, polymicrobial identification, pathogen distributions across age and underlying disease categories, method concordance, and clinical impact were evaluated.<br><br>RESULTS: mNGS yielded significantly higher overall and polymicrobial detection rates than culture. Pathogen profiles differed between mNGS and culture and varied across age and underlying diseases subgroups. Over half of pathogens were identified exclusively by mNGS, and over half of these mNGS-exclusive detections influenced diagnostic and antimicrobial management. Furthermore, Mycobacterium tuberculosis complex, nontuberculous mycobacteria, Cryptococcus neoformans, and Pneumocystis jirovecii retained clinical significance even at low sequencing read counts.<br><br>CONCLUSIONS: In this real-world cohort, mNGS expanded pathogen detection, improved recognition of mixed infections, and provided meaningful clinical value in LRTI.}, }
@article {pmid42288291, year = {2026}, author = {Chen, K and Zhang, X and Li, G and Luo, W and Zhou, H and Shen, Y and Nghiem, LD}, title = {Mechanistic insights into nitrogen loss during food waste composting revealed by metagenomic and qPCR analyses under varying substrate C/N ratios.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135157}, doi = {10.1016/j.biortech.2026.135157}, pmid = {42288291}, issn = {1873-2976}, abstract = {Nitrogen loss during composting can be substantial; however, it can be reduced by applying new insights to better control the substrate C/N ratio and optimise overall composting performance. This study provides mechanistic insights into how substrate C/N governs nitrogen loss during kitchen waste composting. By combining nitrogen speciation analysis, qPCR, and metagenomics analyses, this study explored the potential biochemical mechanisms of nitrogen loss. The results showed that a high substrate C/N ratio significantly reduced nitrogen loss by approximately 37 % (C/N of 25) and 47 % (C/N of 30) compared to the baseline C/N of 20. A higher substrate C/N ratio enhanced nitrogen fixation and assimilation processes while suppressing ammonification and denitrification related potential. The relative abundance of key ammonification-related genera (e.g. Thermobifida and Leuconostoc) and denitrification-related genera (e.g. Pseudomonas and Geobacillus) were decreased at a high substrate C/N ratio, resulting in synergistic mitigation of NH3 and N2O emissions. A small reduction in germination index was observed at substrate C/N ratio of 30 compared with 25. Overall, the results suggest the need to optimize substrate C/N ratio for nitrogen conservation while maintaining overall composting performance.}, }
@article {pmid42288625, year = {2026}, author = {Shin, DW and Oh, S and Hong, YJ and Park, KU}, title = {Direct microbiota profiling of apheresis-associated products for microbiological insights in cell therapy.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57771-0}, pmid = {42288625}, issn = {2045-2322}, abstract = {Cellular therapies require rigorous prevention of bacterial contamination during cell collection, manufacturing, and infusion. We characterized 16 S rRNA profiles in blood-derived specimens obtained during leukapheresis. Leukapheresis donors provided five specimen types: buffy coats (BCs), whole-blood plasma (WBP), apheresis plasma stored at room temperature for 24 h (AP24) and 72 h (AP72), and saliva. Species-level identification was performed using next-generation sequencing-based 16 S rRNA analysis and a database-weighted method. In total, 40 samples from eight donors were analyzed. Plasma specimens (WBP, AP24, and AP72) exhibited higher alpha diversity than saliva (Shannon index, p < 0.05). Beta diversity analysis identified three distinct clusters corresponding to BC, plasma specimens, and saliva (permutational multivariate analysis of variance, p = 0.001). Streptococcus oralis subsp. tigurinus was predominant across all specimens types, Bifidobacterium kashiwanohense predominated in blood-derived specimens, and Enhydrobacter aerosaccus was observed exclusively in plasma specimens. Skin swab culture performed before and after venipuncture site disinfection exhibited no bacterial growth post-disinfection, suggesting that skin-derived carryover is unlikely to fully explain the detected microbial DNA signals. This study provides microbial DNA profiles of various blood-derived specimens obtained during leukapheresis. These findings provide preliminary reference information that may assist interpretation of molecular microbial signals in cellular therapy manufacturing.}, }
@article {pmid42288650, year = {2026}, author = {Yang, Y and Guo, Y and Xu, T and Wu, Y and Cao, J and Wen, Z and Liu, S}, title = {Enrichment risk and drivers of manure-derived antibiotic resistance genes in black soldier fly larval gut.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00237-0}, pmid = {42288650}, issn = {2731-8745}, support = {ASTIP//the Agricultural Science and Technology Innovation Program/ ; 2022YFD1301800//National Key R&amp;D Program of China/ ; CARS-42-10//China Agriculture Research System of MOF and MARA/ ; 325QN438//Hainan Provincial Natural Science Foundation of Chin/ ; }, abstract = {Black soldier fly larvae (BSFL) are promising for converting animal manure into protein; however, the risk of antibiotic resistance gene (ARG) enrichment in the larval gut during this process remains unclear. Here, we employed metagenomic and metatranscriptomic analyses to investigate this risk during BSFL conversion of duck manure. Our results demonstrated that within the BSFL treatment system, ARG abundance and diversity in manure decreased significantly over time. Concurrently, total abundance and transcriptional activity of ARGs in the larval gut were significantly lower than those in manure. However, comparative sequence analysis suggested the potential for ARG exchange between bacterial communities in manure and larval gut. Klebsiella, Escherichia, Citrobacter, and Pseudomonas were identified as the primary hosts in the gut. The enrichment and dynamics of these manure-derived ARGs were jointly driven by shifts in physicochemical properties (notably organic matter and total nitrogen), mobile genetic elements, and the bacterial community. Validation experiments demonstrated that modulating these key physicochemical drivers can mitigate ARG abundance in the larval gut. Overall, this study highlights the potential enrichment risk of manure-derived ARGs in the BSFL gut, identifies key hosts and drivers, and provides actionable mitigation strategies for safer BSFL application.}, }
@article {pmid42289139, year = {2026}, author = {Kevill, JL and Knight, ME and Jain, Y and Marsden, KA and Williams, RC and Herridge, K and Courtene-Jones, W and Robins, P and Malham, SK and Jones, DL}, title = {Fate and transport of viruses, bacteria and antimicrobial resistance associated with wet wipes and microplastics through wastewater treatment to coastal waters.}, journal = {Water research}, volume = {303}, number = {}, pages = {126281}, doi = {10.1016/j.watres.2026.126281}, pmid = {42289139}, issn = {1879-2448}, abstract = {Microplastics (MPs) in wastewater are increasingly recognised as potential vectors for pathogens and antimicrobial resistance (AMR), yet their role across treatment remains poorly understood. This study tracked viral, bacterial, and AMR associations with MPs from hospital wastewater through to coastal receiving waters, including simulated combined sewer overflow (CSO) events, using quantitative real-time PCR, and shotgun metagenomics. MP concentrations found naturally in the wastewater matrix, declined from 467 to 33 particles L[-1] during WWTP passage, achieving 93% removal. Norovirus (GI and GII) and bacteria colonised beads and wet wipes throughout, with wet wipes retaining higher viral and AMR loads than plastic beads, likely due to structural complexity. Sequential sampling across treatment stages showed a reduction in norovirus and bacterial loads by ∼1 log, yet pathogens remained detectable on beads and wet wipes in final effluent. NoV GI predominated, while NoV GII concentrations and the class I integron-integrase (intI1) gene varied by treatment stage and sample type. Metagenomics showed enrichment of potentially pathogenic genera (Aeromonas, Pseudomonas, Flavobacterium) in bead and wet wipe biofilms, and network analysis identified associations between Aeromonas and clinically relevant beta-lactam resistance genes (OXA, CTX). Shifts at the activated sludge stage indicated bead and wet wipe associated communities in effluent reflect treatment microbiota rather than influent sources. Environmental MP concentrations are below those required to deliver an infectious viral dose, suggesting MP-mediated transmission is unlikely under normal conditions. However, during CSO events, beads and wet wipes retained high viral loads and may act as pathogen transport vectors. These findings highlight CSO management as a priority for reducing MP-associated pathogen risks in receiving waters.}, }
@article {pmid42289215, year = {2026}, author = {Dai, J and Tan, X and Ma, J}, title = {Artificial intelligence in clinical metagenomic pathogen detection: A critical review of pipeline integrations, challenges, and future directions.}, journal = {Journal of microbiological methods}, volume = {247}, number = {}, pages = {107592}, doi = {10.1016/j.mimet.2026.107592}, pmid = {42289215}, issn = {1872-8359}, abstract = {Metagenomic next-generation sequencing (mNGS) has expanded the scope of clinical diagnostics by enabling culture-independent detection of microorganisms in patient samples. However, mNGS clinical utility remains constrained by substantial computational demands, reference database biases, and the persistent challenge of distinguishing true pathogens from host background, commensal flora and environmental contamination. Traditional alignment and k-mer-based bioinformatics pipelines frequently struggle to balance speed, sensitivity, and the ability to detect highly divergent or novel organisms. This review critically synthesizes the current landscape of Artificial Intelligence (AI) and Machine Learning (ML) applications across the mNGS diagnostic pipeline, examining deep learning architectures-including Convolutional Neural Networks (CNNs), Long Short-Term Memory networks (LSTMs), and Transformers-as integrated into raw read processing, host sequence depletion, primary taxonomic classification, and ancillary detection of antimicrobial resistance (AMR) and virulence factors. While several AI methodologies report high classification accuracy in benchmarking studies, we note that most performance claims derive from simulated datasets or controlled mock communities rather than prospective clinical validation. Significant gaps persist, including limited AI integration in front-end signal optimization, inadequate automated clinical reporting, absence of standardized benchmarking metrics, and unresolved questions regarding data leakage, reproducibility, and generalizability. Successful clinical translation will require addressing the interpretability limitations of current explainable AI approaches, navigating complex and evolving regulatory landscapes for Software as a Medical Device (SaMD), and bridging the gap between computational feasibility and demonstrated patient-outcome benefit. The development of genomic foundation models and multi-modal clinical integration holds promise for advancing mNGS toward real-time, actionable diagnostics, though substantial evidence gaps remain between current proof-of-concept demonstrations and validated clinical deployment.}, }
@article {pmid42289247, year = {2026}, author = {Lin, Y and Nie, B and Liu, X and Zhang, Q}, title = {Mechanistic insights into superior biofilm formation with heterotrophic nitrification-aerobic denitrification bacteria under polypropylene microplastic stress.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135159}, doi = {10.1016/j.biortech.2026.135159}, pmid = {42289247}, issn = {1873-2976}, abstract = {Microplastics may disturb microbial activity and biofilm development in biological wastewater treatment systems, yet the response of three-dimensional rotating biological contactor start-up biofilms to polypropylene microplastic stress remains unclear. This study evaluated a biofilm initiation strategy using heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria (H-3D-RBCs) and compared it with activated sludge-inoculated systems (A-3D-RBCs) under polypropylene microplastic (PP-MP) exposure. H-3D-RBCs showed superior resistance to PP-MP disturbance, with total nitrogen removal decreasing by only 14 %, compared with an approximately 60 % decline in A-3D-RBCs. Respiratory activity inhibition remained below 15 % in H-3D-RBCs but exceeded 90 % in A-3D-RBCs. 16S rRNA gene sequencing showed that PP-MP reduced species richness and diversity in A-3D-RBCs and was associated with a > 90 % loss of core denitrifying genera, including Corynebacterium and Pseudoxanthomonas, whereas H-3D-RBCs maintained community stability and enriched Pseudoxanthomonas to 13.8 %. Metagenomic analysis indicated that PP-MP impaired nitrification and denitrification potential in A-3D-RBCs, as reflected by decreased genes encoding AMO and HAO, a 51.78 % decrease in nosZ abundance, and enhanced dissimilatory nitrate reduction to ammonium (DNRA), which likely intensified competition with denitrification and promoted nitrogen conversion to ammonia. In contrast, H-3D-RBCs suppressed DNRA and maintained high nosZ abundance. Untargeted metabolomics further showed that PP-MP was associated with metabolic disorders in A-3D-RBCs, especially disruptions in alanine, aspartate, and glutamate metabolism and arginine biosynthesis, whereas H-3D-RBCs preserved these key nitrogen metabolic processes. Overall, this study identifies key vulnerabilities of nitrogen-removal biofilms under PP-MP disturbance and provides multi-omics evidence to support the development of microplastic-resistant biofilm wastewater treatment systems.}, }
@article {pmid42289444, year = {2026}, author = {Masuoka, H and Miyatake, T and Park, J and Negishi, H and Kurokawa, R and Tsuchihashi, H and Makino, S and Suda, W}, title = {Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56821-x}, pmid = {42289444}, issn = {2045-2322}, support = {J24K18210//Japan Society for the Promotion of Science, Japan/ ; J24K01676//Japan Society for the Promotion of Science, Japan/ ; }, abstract = {Emerging evidence suggests that fatigue caused by accumulated stress may serve as a prodromal symptom of psychiatric disorders, and gut microbiome dysbiosis has been reported in many such conditions. However, little is known about microbial and metabolic signatures associated with fatigue in otherwise healthy individuals. This study aimed to investigate associations between fatigue, the gut microbiome, and fecal metabolites in healthy Japanese adults. We identified characteristic microbial and metabolic differences specific to fatigued healthy individuals. Taxonomic analysis revealed a reduction in potentially beneficial bacteria and an enrichment of Escherichia coli in their gut microbiome. Functional profiling demonstrated enrichment of KEGG orthologs related to oxidative stress and depletion of energy-producing pathways. Correspondingly, key energy metabolites such as citrate were decreased. Notably, some fatigue-associated bacterial alterations overlapped with findings from external datasets on psychiatric disorders and myalgic encephalomyelitis/chronic fatigue syndrome, suggesting associative overlap in gut microbial alterations. These findings suggest associations between host fatigue and gut microbiome alterations involving oxidative stress and impaired energy metabolism. The consistent overlap of fatigue-associated microbial changes with those observed in psychiatric disorders highlights the potential relevance of gut microbial signatures in fatigue-related biological states. This study provides a foundation for future studies on gut microbial and metabolic pathways.}, }
@article {pmid42289756, year = {2026}, author = {Jia, P and Dong, L and Ma, T and Bi, Y and Tu, Y and Diao, Q}, title = {Variations in methane emissions from dairy cows: associations with rumen microbial synergy and metabolic pathway divergence.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42289756}, issn = {1674-9782}, support = {2024YFD1300200//the National key Research and Development Program/ ; CAAS-ASTIP//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Methane (CH4) is a metabolic by-product of rumen microbial fermentation, contributing significantly to global warming and dietary energy loss. Elucidating the mechanisms underlying natural variation in rumen methanogenesis is essential for the development of effective CH4 mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH4 emissions among dairy cows.<br><br>RESULTS: Enteric CH4 emissions from 111 lactating dairy cows under normal feeding conditions were utilized to characterize the natural variation in rumen methanogenesis. Metagenomic analysis revealed that the comprehensive effects of bacteria involved in starch degradation, lactate metabolism, and volatile fatty acid biosynthesis provide distinct amounts of hydrogen for rumen methanogenesis in high-methane-producing (HMP) and low-methane-producing (LMP) cows. Ciliate protozoa were universally abundant in HMP cows (P&#x2009;<&#x2009;0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P&#x2009;<&#x2009;0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (P&#x2009;<&#x2009;0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH4 production.<br><br>CONCLUSIONS: This study excluded extrinsic confounders exist for rumen microbiome and CH4 emissions in dairy cows. These findings elucidated the causal microbial and metabolic mechanisms underlying rumen methanogenesis, providing actionable targets for microbiome-based strategies to mitigate CH4 emissions from livestock farming.}, }
@article {pmid42290500, year = {2026}, author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F}, title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.}, journal = {Future microbiology}, volume = {21}, number = {8}, pages = {777-794}, doi = {10.1080/17460913.2026.2684877}, pmid = {42290500}, issn = {1746-0921}, mesh = {*Synbiotics/administration &amp; dosage ; Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Liver/metabolism/microbiology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; Animals ; *Liver Diseases/therapy/microbiology ; Proteomics ; Metabolomics ; }, abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.}, }
@article {pmid42290753, year = {2026}, author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J}, title = {Correction: Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1835424}, doi = {10.3389/fped.2026.1835424}, pmid = {42290753}, issn = {2296-2360}, abstract = {[This corrects the article DOI: 10.3389/fped.2025.1632123.].}, }
@article {pmid42291119, year = {2026}, author = {Park, J and Jang, KB and Kang, MG and Kyung, J and Yoon, J and Ryu, S and Kim, Y}, title = {Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {935-953}, pmid = {42291119}, issn = {2055-0391}, abstract = {Rumen methanogenesis is a major biological contributor to methane emissions in ruminants, yet the extent to which functional markers align with taxonomic relationships and how genome content varies across habitats, remains poorly resolved. In this study, we integrated broad phylogenetic frameworks with pangenome-resolved analysis to characterize methanogenic archaea from diverse ecosystems, including seawater, freshwater, sewage, rumen, human gut, soil, and cockroach sources. By combining these insights with pangenome reconstruction and KEGG-based pathway mapping of methanogenesis, we reveal key evolutionary and functional patterns. Notably, phylogenies based on 16S rRNA and mcrA genes showed limited concordance: only two clades exhibited overlap between trees, with most clustering patterns lacking environmental specificity. This discrepancy reflects the deep conservation of 16S rRNA compared with the evolutionary plasticity of mcr genes, shaped by lateral gene transfer, gene loss, and pathway modularity. The pangenome comprised of 8,695 orthogroups across 71 genomes, with core and soft-core genes enriched in translation, amino acid metabolism, and coenzyme biosynthesis, while the shell contained many poorly annotated orthogroups, highlighting annotation gaps in archaeal genomes. KEGG analysis revealed habitat-specific signatures: rumen methanogens were notably depleted in genes of the acetyl-CoA pathway, whereas human gut methanogens lacked key cofactor biosynthesis modules, including those for coenzymes M, B, F420, and methanofuran. From rumen-derived shotgun metagenomes, we identified 53 methane-producing, 4 canonical methanogenic, 10 potential competitor, and 1 methanotrophic metagenome-assembled genomes based on functional gene content. Competitor candidates included nitrate-reducing and Wood-Ljungdahl pathway-utilizing acetogens, suggesting hydrogen redirection under high-hydrogen or inhibitor conditions. These findings support a functional marker strategy that integrates 16S rRNA with pathway-specific genes and a pangenome framework to enhance ecological interpretations of methanogens and to prioritize potential targets for methane mitigation in ruminants.}, }
@article {pmid42291259, year = {2026}, author = {Feng, S and Liu, Q and Chen, Y and Kang, D and Zou, S}, title = {Different grazing intensities affect soil nitrogen cycling by altering microbial nitrogen metabolism in alpine wetlands.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116009}, pmid = {42291259}, issn = {2589-0042}, abstract = {Grazing significantly affects soil nitrogen cycling in eastern Qinghai-Tibet Plateau alpine wetlands. Grazing did not alter soil microbial α-diversity, but shifted community composition via metagenomic analysis. Moderate and heavy grazing reduced soil total and active nitrogen contents by 53.8%-92.0% vs. light grazing, significantly decreased abundances of nitrification genes (amoA and hao) and ammonium assimilation gene (glnA), while increased dissimilatory nitrite reduction to ammonium gene (nirB) by 142.1%. A nitrification bottleneck from impaired nitrification drove active nitrogen decline, and structural equation modeling identified nitrogen cycle gene abundance as the key driver. This study reveals microbial nitrogen cycling mechanisms and provides a scientific basis for sustainable grazing management in alpine wetlands.}, }
@article {pmid42291297, year = {2026}, author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X}, title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809022}, pmid = {42291297}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; }, abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.<br><br>METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).<br><br>RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p&#xa0;<&#xa0;0.01). Candida albicans (p&#xa0;=&#xa0;0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p&#xa0;=&#xa0;0.038) and Prevotella pallens (p&#xa0;=&#xa0;0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p&#xa0;<&#xa0;0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.<br><br>CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.}, }
@article {pmid42291302, year = {2026}, author = {Wang, R and Yang, H and Zhang, C and Zi Neng, X}, title = {The complexity of invasive fungal diseases in the intensive care unit: evaluation of metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1820501}, pmid = {42291302}, issn = {2235-2988}, mesh = {Humans ; *Intensive Care Units ; *Invasive Fungal Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; Middle Aged ; Immunocompromised Host ; Male ; Aged ; *Fungi/genetics/classification/isolation &amp; purification ; Adult ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND: In the intensive care unit (ICU), a subset of adult individuals who are non-neutropenic and lack conventional host risk factors frequently develop fungal infections, which constitute a major mortality risk in this population. This patient group has received limited attention to date, and research on diagnostic approaches remains insufficient. This research looks into whether metagenomic next-generation sequencing (mNGS) could be used to diagnose this group of people.<br><br>METHODS: We performed a retrospective analysis of 106 individuals with invasive fungal infections between July 2022 and February 2025. These patients were divided into two groups: immunocompetent and immunocompromised. Demographic and clinical characteristics were analyzed and compared between the two groups. The diagnostic value of mNGS was carefully assessed, and its diagnostic performance was contrasted with that of conventional microbiological tests (CMTs). In addition, the impact of mNGS results from different specimen types on clinical management and antifungal treatment decisions was summarized.<br><br>RESULTS: Among the 106 adult patients, 66.26% were immunocompetent, but many of them had underlying comorbidities. A total of 81 pathogens were identified, of which 74 were detected by mNGS and 44 by CMTs. The predominant fungal pathogens included Candida species, Pneumocystis jirovecii, and Aspergillus fumigatus. mNGS showed a distinct superiority in identifying uncommon pathogens and mixed infections, with its total positive rate markedly exceeding that of CMTs. mNGS results led to beneficial modifications in clinical management for 75 patients (70.75%). The clinical impact varied by specimen type, including bronchoalveolar lavage fluid (BALF; 61 cases), blood (14 cases), and other sterile body fluids (31 cases), with blood specimens yielding the least clinical benefit.<br><br>CONCLUSION: In the ICU, a substantial number of invasive fungal infections occur among patients without classical host risk factors. mNGS offers substantial benefits in identifying fungal pathogens and mixed infections, hence enhancing the diagnostic efficacy of invasive fungal diseases (IFDs). The extent of clinical benefit is affected by the kind of specimen provided for testing.}, }
@article {pmid42292195, year = {2026}, author = {Borgio, JF and Sharma, HS and Almandil, NB and AbdulAzeez, S and van der Spek, PJ}, title = {Editorial: Molecular informatics in personalized medicine, volume II.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1861955}, doi = {10.3389/fmed.2026.1861955}, pmid = {42292195}, issn = {2296-858X}, }
@article {pmid42292299, year = {2022}, author = {Oliveira, C and Shakiba, E and North, D and McGraw, M and Ballard, E and Barrett-D'Amico, M and Glazko, G and Rahmatallah, Y}, title = {16S rRNA Gene-Based Metagenomic Analysis of Rhizosphere Soil Bacteria in Arkansas Rice Crop Fields.}, journal = {Agronomy (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {42292299}, issn = {2073-4395}, abstract = {The rhizomicrobiome is composed of microbes that live in association with plant roots. From nutrient cycling to carbon sequestration, soil microorganisms have provided a solid base for natural and agricultural ecosystems to function. The relationship between plant roots and soil microorganisms is especially relevant in food staples such as rice (Oryza sativa L.), as the various properties of these microbes can influence crop yield and plant health, thereby affecting a major portion of the food supply for an ever-growing world population. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the impact of crop rotation and soil cultivation methods (no-till or tillage) on rhizosphere bacterial diversity and composition in eight crop fields in Arkansas. Illumina MiSeq sequencing revealed 56 Phyla, with four major Phyla: Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes. Soil microbial communities in the samples studied were phylogenetically diverse but with a stable community structure. Crop rotation and tillage did not significantly affect bacterial diversity.}, }
@article {pmid42292361, year = {2026}, author = {Jiang, H and Lu, E and Liu, Q and Li, Z and Zhu, Y}, title = {Etiological study of pulmonary infections following solid organ transplantation using metagenomic next-generation sequencing and development of a risk prediction model: a retrospective cohort study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1734832}, pmid = {42292361}, issn = {1664-3224}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Middle Aged ; *Organ Transplantation/adverse effects ; Prognosis ; Risk Assessment ; Adult ; *Respiratory Tract Infections/etiology/diagnosis/microbiology ; Risk Factors ; }, abstract = {OBJECTIVE: To analyze the pathogenic etiology of pulmonary infection after solid organ transplantation and construct a prognostic prediction model based on metagenomic next-generation sequencing (mNGS) technology, systematically identifying key predictors to provide evidence for clinical risk stratification and individualized interventions.<br><br>METHODS: Clinical data were retrospectively collected from patients who developed pulmonary infection after liver or kidney transplantation at a single hospital between January 2020 and December 2023. All patients underwent mNGS detection of bronchoalveolar lavage fluid or sputum for pathogen identification. Collected data included demographic characteristics, transplant-related parameters, underlying diseases, laboratory test results, mNGS pathogen detection outcomes, and prognostic indicators. The dataset was randomly divided into a training set (n=262) and a test set (n=66). Within an AutoML framework, model hyperparameters were optimized using the Improved Dharma Optimization Algorithm (IDRA). Feature importance was validated bidimensionally via LASSO regression and SHAP interpretable models, with an interactive MATLAB-based decision support system developed.<br><br>RESULTS: The overall positive detection rate of pathogens by mNGS significantly exceeded that of conventional methods (84.76% vs. 61.89%, P<0.001). No statistically significant differences existed in baseline characteristics or laboratory indicators between the training and test sets (all P>0.05), confirming randomized stratified sampling validity. Both cohorts showed highly consistent proportions of poor prognosis events (training set: 27.48% vs. test set: 28.79%, &#x3c7;[2]=0.045, P&#xa0;=&#xa0;0.832). The prediction model achieved a ROC-AUC of 0.9694 and PR-AUC of 0.9690 in the training set, and ROC-AUC of 0.9206 (95% CI: 0.854-0.987) with PR-AUC of 0.9273 (95% CI: 0.867-0.988) in the test set, outperforming comparative models. Fourteen key variables were ultimately selected: mNGS bacterial detection, mNGS fungal detection, procalcitonin (PCT), C-reactive protein (CRP), mNGS viral detection, white blood cell count, creatinine, post-transplantation time, neutrophil percentage, diabetes, age, total bilirubin, alanine aminotransferase (ALT), and lymphocyte percentage. The feature overlap rate with AutoML-screened variables was 78.6% (11/14). SHAP analysis revealed descending importance ranking: mNGS bacterial detection, mNGS fungal detection, PCT, etc.<br><br>CONCLUSION: Integrating multidimensional clinical data with explainable machine learning techniques, this study confirms the central role of pathogenic etiology characteristics in prognostic prediction for post-transplant pulmonary infection and demonstrates the potential for real-time risk assessment to inform clinical decisions. However, prospective validation across diverse care settings is required to establish its efficacy as an interventional guide. This work offers innovative tools and methodological frameworks to advance precision diagnosis and management, subject to ongoing refinement through multicenter collaboration.}, }
@article {pmid42292462, year = {2026}, author = {Xing, Y and Wang, J and Li, X and Yin, X}, title = {Behind the mask of relapsing bimodal encephalitis: herpesvirus 7 and Epstein-Barr virus associated with Hashimoto's encephalopathy: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782631}, pmid = {42292462}, issn = {1664-3224}, mesh = {Adult ; Female ; Humans ; Autoantibodies/blood ; Electroencephalography ; *Encephalitis/diagnosis/virology/drug therapy ; *Encephalitis, Viral/virology/diagnosis/drug therapy ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; *Hashimoto Disease/virology/diagnosis/drug therapy ; *Herpesvirus 4, Human/physiology ; *Herpesvirus 7, Human/physiology ; Magnetic Resonance Imaging ; Recurrence ; }, abstract = {BACKGROUND AND PURPOSE: Relapsing bimodal encephalitis in adults remains poorly characterized. We describe a case of relapsing viral encephalitis followed by secondary autoimmune-mediated encephalitis and explore its potential underlying mechanisms.<br><br>CASE DESCRIPTION: A previously healthy adult female initially presented with fever and headache; brain magnetic resonance imaging (MRI) showed punctate white matter hyperintensities, and electroencephalogram revealed background slowing with intermittent &#x3b4; waves. Initial cerebrospinal fluid (CSF) analyses were suggestive of viral encephalitis. Although no pathogen was identified by CSF metagenomic next-generation sequencing (mNGS), she responded favorably to empirical antiviral therapy. 22 days after discharge, she was readmitted with decreased responsiveness, hypersomnia, and acute psychosis. Concurrent MRI revealed progressive white matter lesions. CSF analysis demonstrated oligoclonal bands restricted to the CSF, while autoimmune encephalitis antibody panels were negative. Serum autoantibodies (anti-SSA/SSB, anti-thyroglobulin, and thyroid peroxidase) were elevated. Considering probable autoimmune encephalitis, intravenous immunoglobulin and methylprednisolone were administered, leading to clinical and serological remission with radiological improvement. After 22 months, the patient relapsed with similar clinical manifestations, beginning with fever and headache, followed by decreased responsiveness, and subsequently developed an acute mental disorder. Repeat CSF mNGS detected human herpesvirus 7 (HHV-7) and Epstein-Barr virus (EBV), accompanied by new white matter lesions and recurrent thyroid autoantibodies. The patient responded favorably to the same treatment. At one-month follow-up, the patient developed hyperthyroidism.<br><br>CONCLUSION: HHV-7 and EBV with long latency are likely associated with a cascade of autoimmune encephalitis, presenting as relapsing bimodal encephalitis. Thyroid autoantibodies-rather than conventional neuronal antibodies-appear central to the autoimmune phase, consistent with Hashimoto's encephalopathy.}, }
@article {pmid42292537, year = {2026}, author = {Jung, CG and Gautam, S and Song, Y and Poorey, K and Mishra, U}, title = {Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient-Degrading Enzyme-Encoding Genes Across Continental US Ecoregions.}, journal = {Ecology and evolution}, volume = {16}, number = {6}, pages = {e73869}, pmid = {42292537}, issn = {2045-7758}, abstract = {Understanding the spatiotemporal patterns in the relative abundance of soil extracellular enzyme-encoding genes is critical for predicting microbial responses to environmental change and their potential role in nutrient cycling. Yet, integrating novel metagenomic observations with spatiotemporal environmental gradients to infer regional patterns and future trajectories has remained unclear. To address this gap, we applied a machine learning (ML) approach, integrating soil metagenomic data with environmental variables-soil properties, topography, vegetation, and climate-to predict the relative abundance of enzyme-encoding genes for soil carbon (C), nitrogen (N), and phosphorus (P) across surface soils of the continental United States. We assessed potential responses under future emission scenarios (SSP2-4.5 and SSP5-8.5) by comparing a baseline (1985-2014) to a future period (2071-2100). The ML model explained 57%-63% of baseline variation. Precipitation was identified as the most influential factor for the relative abundance of C- and N-degrading enzyme-encoding genes, while slope length, representing horizontal distance that water can travel downslope, was the primary driver for P-degrading enzyme-encoding genes abundance. Projections revealed spatially heterogeneous shifts across continental US ecoregions: the relative abundance of C- and N-degrading enzyme-encoding genes decreased in wetter ecoregions and increased in drier ecoregions under future climate, while P-degrading enzyme-encoding genes abundance decreased significantly in semiarid and Mediterranean ecoregions. This study demonstrates the utility of metagenomic data for mapping soil genetic potential and predicting its regional response to environmental change, to inform ecosystem management strategies.}, }
@article {pmid42292847, year = {2026}, author = {You, Q and Jin, M and Zhou, B and Huang, C and Lin, Z and Hu, J and Xue, J and Chen, X and Xiao, Y and Li, R and Zong, Y and Wu, M and Zhang, T and Liu, H}, title = {Gut microbiome components predict response to neoadjuvant short-course radiotherapy followed by camrelizumab and chemotherapy in locally advanced rectal cancer (UNION): a prospective study.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1829108}, pmid = {42292847}, issn = {1663-9812}, abstract = {BACKGROUND: Although the gut microbiome shapes responses to anti-tumor immunotherapy and chemotherapy, its predictive value for neoadjuvant short-course radiotherapy (SCRT) followed by camrelizumab (CAM) and CAPOX in patients with locally advanced rectal cancer (LARC) has not been defined. This exploratory study aimed to evaluate whether the gut microbiome is associated with response to neoadjuvant SCRT followed by CAM and CAPOX.<br><br>METHODS: We obtained a total of 77 fecal samples from 36 patients with LARC, including 17 assigned to the long-course chemoradiotherapy (LCRT) group and 19 to the SCRT group. Samples were collected at three time points: baseline, after radiotherapy, and after chemoimmunotherapy. DNA was extracted, followed by metagenomic sequencing to profile microbiota dynamics during neoadjuvant treatment.<br><br>RESULTS: In this pilot analysis, we observed significant differences in the gut microbiota between the SCRT and LCRT treatment cohorts. Specifically, Bifidobacterium and Dorea were significantly enriched following completion of SCRT sequential CAM and CAPOX therapy. Further analysis revealed that the relative abundances of these two genera changed significantly only before and after the SCRT regimen, with no notable changes observed in the LCRT group. Preliminary ROC analysis suggested potential utility of these taxa for predicting treatment response, though validation in larger cohorts is needed.<br><br>CONCLUSION: The gut microbiome offers potential biomarkers that may stratify response to SCRT followed by CAM and CAPOX, representing a promising exploratory finding with potential clinical relevance.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04928807.}, }
@article {pmid42293010, year = {2026}, author = {de Oliveira, SAS and Sheat, S and Margaria, P and Lima, AL and Dos Santos, JA and Rocha, HS and da Silveira, HF and Ramos de Jesus, C and Winter, S}, title = {Association of Rhizoctonia theobromae with cassava witches' broom outbreak in Brazil and genetic relatedness to Southeast Asian isolates.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1799146}, pmid = {42293010}, issn = {1664-462X}, abstract = {BACKGROUND: A new cassava disease outbreak was identified in indigenous communities in Oiapoque, Amapá, Brazil, characterized by stunting, proliferation of thin shoots, broom-like leaf formations, and apical dieback. These symptoms are consistent with Cassava Witches' Broom Disease (CWBD), previously reported in other regions of South America and Asia.<br><br>METHODS: Metagenomic profiling, molecular diagnostics, phylogenetic analyses, and multilocus genotyping were used to investigate microbial communities associated with symptomatic cassava plants.<br><br>RESULTS: Rhizoctonia (Ceratobasidium) theobromae was identified as the predominant fungal species associated with symptomatic plants. Genetic analyses indicated a close relationship between Brazilian isolates and Asian reference strains, suggesting a possible transcontinental introduction and supporting an association between R. theobromae and CWBD. This represents the first confirmed report of R. theobromae in Brazil, expanding its known geographic distribution in the Americas.<br><br>CONCLUSION: The detection of this quarantine pathogen represents a potential threat to cassava production, food security, and preservation of indigenous cassava landraces in Brazil. These findings reinforce the need for surveillance, phytosanitary measures, and further studies on emerging fungal pathogens associated with cassava diseases.}, }
@article {pmid42293020, year = {2026}, author = {Yutong, Z and Yaling, L and Wei, Y and Fengling, S}, title = {Spatiotemporal dynamics of rhizosphere microbial communities in alfalfa across saline-alkali agro-ecosystems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1792882}, pmid = {42293020}, issn = {1664-462X}, abstract = {The rhizosphere represents a highly active plant-soil interface, where microorganisms play critical roles in the growth and development of alfalfa and in regulating local ecosystem processes. However, the mechanisms by which alfalfa rhizosphere microorganisms respond to spatiotemporal variation in saline-alkali environments remain poorly understood. Here, we collected alfalfa plants from one- to eight-year-old stands across three pastoral regions differing in soil type and characterized their rhizosphere soils. Using soil physicochemical analyzes, soil enzymology, and metagenomics, we examined how rhizosphere microbial communities respond to temporal and spatial variation in saline-alkali soils. Our findings indicate that alfalfa rhizosphere microecology may maintain rhizosphere health by modulating soil physicochemical properties, reducing peroxidase activity, enhancing reductase activity, and increasing the abundance of beneficial microorganisms. These results underscore the potential value of introducing exogenous beneficial bacteria to shape indigenous rhizosphere microecology.}, }
@article {pmid42293161, year = {2026}, author = {Nunez, H and Straub, TJ and Imam, N and Goad, D and Mueller, NT and Mars, RAT and Sew Hoy, C and Paullin, T and Sukhum, KV}, title = {Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1804117}, pmid = {42293161}, issn = {2813-4338}, abstract = {INTRODUCTION: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.<br><br>METHODS: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).<br><br>RESULTS: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.<br><br>DISCUSSION: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.}, }
@article {pmid42293411, year = {2025}, author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z}, title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719445}, pmid = {42293411}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; }, abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.}, }
@article {pmid42293516, year = {2026}, author = {Zou, Y and Liu, L and Chen, H and Luo, Z and Zhu, Z and Li, Z and Lin, B and Zhuang, Z and Li, W and Yang, Q and Yang, X and Zhou, H and Luo, M and Dai, D}, title = {Study protocol for a randomized controlled trial of fecal microbiota transplantation via different routes in children with moderate-to-severe autism spectrum disorder.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829532}, pmid = {42293516}, issn = {1664-302X}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) shows promise for autism spectrum disorder (ASD) by modulating the gut-brain axis, but the optimal delivery route remains unknown. Our previous single-arm study suggested efficacy of nasojejunal FMT in children with moderate-to-severe ASD, yet could not exclude placebo effects or compare routes. This randomized controlled trial aims to determine the most effective and tolerable FMT administration route.<br><br>METHODS: This single-center, randomized, triple-blind, double-dummy, placebo-controlled, three-arm parallel-group trial will enroll 75 children (aged 3-16 years) with moderate-to-severe ASD [Childhood Autism Rating Scale, Second Edition (CARS-2) &#x2265;36]. Participants are randomized 1:1:1 to: (1) FMT via nasojejunal tube + sham colonoscopy (FMT-NJT); (2) active FMT via colonoscopy with transendoscopic enteral tube placement (first session) + two subsequent infusions via the indwelling tube + sham nasojejunal intubation (FMT-C); (3) placebo via both routes (sham procedures). Three FMT/placebo sessions (5 mL/kg, max 100 mL) are administered over 5 days. Primary outcome is change in CARS-2 score from baseline to Week 24. Secondary outcomes include changes in Social Responsiveness Scale, Autism Behavior Checklist, Gastrointestinal Symptom Rating Scale, Short Sensory Profile, Children's Sleep Habits Questionnaire, gut metagenomic profiles (baseline, Weeks 2,6,12,24,48), and adverse events.<br><br>RESULTS: This is a study protocol; no results are available.<br><br>CONCLUSIONS: This first head-to-head comparison of FMT routes in pediatric ASD will provide high-level evidence to guide treatment standardization, directly addressing the translational gap identified in our preliminary work.}, }
@article {pmid42293521, year = {2026}, author = {Liu, Z and Xiahou, Y and Li, J and Wu, F and Fan, Y and Liu, R and Zhou, M and Ding, Z and Zhang, Y and Chen, C and Huang, L and Ai, H}, title = {Metagenomic analysis of the DNA virome communities in swine lungs.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798033}, pmid = {42293521}, issn = {1664-302X}, abstract = {Viruses play critical roles in shaping microbial communities and regulating host metabolism. Investigating the lung virome of pigs can inform swine health management and provide a comparative resource for studies of the human lower respiratory virome. However, viral communities in the porcine lower respiratory tract remain poorly characterized. In this study, lung-associated viral communities were investigated using virus-like particle (VLP) enrichment and DNA metagenomic sequencing of 49 lung-derived samples collected from 17 domestic pigs and 20 wild boars. A total of 18,412 viral operational taxonomic units (vOTUs) were identified. Among the 2,559 vOTUs with genome completeness ≥50%, nearly 95% did not cluster with sequences in current viral reference databases at the species-level threshold (ANI ≥ 95% and AF ≥ 85%), suggesting putative viral novelty in the porcine lung while also reflecting incomplete reference database coverage. Meanwhile, 10,819 vOTUs (accounting for 58.8% of the total 18,412 identified vOTUs) were assigned to known viral taxa, spanning 29 viral orders and 65 viral families. The most prevalent viral families were Microviridae, Circoviridae, Smacoviridae, Adintoviridae, and Autographiviridae. Host prediction linked a subset of vOTUs to putative bacterial hosts, mainly from Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. In addition, we identified 191 vOTUs carrying 40 auxiliary metabolic genes (AMGs) mapped to 31 metabolic pathways. These AMGs were mainly associated with sulfur metabolism, cysteine and methionine metabolism, folate biosynthesis, and one-carbon pool by folate pathways. Comparative analysis under this study design showed that domestic pigs harbored higher viral diversity with a greater number of unique vOTUs (n = 12,611) than wild boars (n = 3,072). Domestic pigs viromes were enriched in Circoviridae and Microviridae, whereas wild boars showed higher relative abundances of Adintoviridae and Genomoviridae. Putative AMGs related to coenzyme synthesis and DNA methylation were more frequently detected in domestic pigs, whereas AMGs associated with nucleotide biosynthesis and cofactor metabolism were enriched in wild boars. These findings characterize the composition and functional potential of lung-associated DNA viral communities in pigs and provide a resource for future respiratory virome studies.}, }
@article {pmid42293528, year = {2026}, author = {Seth, N and Bansal, M and Mazumdar, S and Mazumdar-Leighton, S and Lakhanpaul, S and Vats, S and Arafat, Y and Babu, CR}, title = {Functional diversity in bacterial communities of an integrated constructed wetland used for in situ bioremediation of sewage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1803785}, pmid = {42293528}, issn = {1664-302X}, abstract = {Constructed wetlands (CWs) offer effective, economical, environment-friendly and energy-efficient solution to growing challenges of increasing sewage and wastewater loads in urban areas. Although microbial communities form an integral component of constructed wetlands for sewage treatment, functional processes and their dynamics during sewage bioremediation in constructed wetlands remain largely uncharacterized. Moreover, the association of specific bacterial taxa with remediation of different sewage and water quality parameters remains largely unclear. This study explored the functional diversity likely associated with microbial communities of a constructed wetland system used for in situ remediation of 1 MLD (Million Liters per Day) sewage without external energy input since 2014. Different bacterial functional groups in the sludge from a stabilization pond and from rhizospheric sediments of the integrated constructed wetland were predicted using a 16S rRNA gene metagenomic sequencing dataset. Correlation analysis, multivariate statistics and a co-occurrence network were used to assess the bacterial groups associated with changes in water quality as it flows through different components of the integrated CW and highlight association patterns predicting major exchanges which might be operating in the microbial communities. While stabilization pond microbiome was dominated by bacterial groups such as Firmicutes, Desulfobacterota and Methylomirabilota known to be involved in carbon fermentation, sulphate reduction and methanogenesis, the rhizospheric sediments showed prevalence of bacteria associated with nitrogen reduction including Nitrospirota and Planctomycetota contributing to improved sewage quality parameters. Such results indicated complex microbial interactions involving bacteria from diverse functional groups sustaining bioremediation in the CW. The identification of primary bacterial taxa along with their putative functions can help in designing strategies to improve sustainable, nature-based wastewater treatment by CW systems.}, }
@article {pmid42293535, year = {2026}, author = {González-Reguero, D and Robas-Mora, M and García Ordiales, E and Fernández-Pastrana, VM and Penalba-Iglesias, D and Probanza Lobo, A and Jiménez Gómez, PA}, title = {Recovery of organic waste from a wastewater treatment plant, improved with plant growth promoting bacteria: model of Quercus suber L.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1754063}, pmid = {42293535}, issn = {1664-302X}, abstract = {Cork oaks (Quercus suber L.) are key tree species in Mediterranean ecosystems, playing a crucial role in fire mitigation due to their thick, fire‑resistant bark, while also contributing to biodiversity conservation and soil stability. Integrating waste valorization strategies with biofertilizers based on plant growth‑promoting bacteria (PGPB) may enhance reforestation efficiency. This study evaluated different irrigation regimes under controlled phytotron conditions, including water, organic fertilizer derived from a wastewater treatment plant (WWTP), and sterilized WWTP fertilizer, combined with Bacillus pretiosus CECT30673[T] and Pseudomonas agronomica CECT30673[T]. Microbial functional diversity (Shannon index), antibiotic resistance profiles, and rhizosphere community structure were assessed using 16S rRNA‑based metagenomic analyses, including taxonomic composition, beta diversity, and genus‑level relative abundances. Plant performance was evaluated through biomass production, stem length, and nutritional parameters, including protein composition, sugar content, and fatty acid profile. The application of PGPBs together with WWTP‑derived fertilizers resulted in a significant increase in plant biomass and stem length compared to traditional water irrigation. Nutritional quality was also significantly improved, with higher protein, sugar, and fatty acid contents. Additionally, the combined treatments reduced minimum inhibitory concentrations (MICs) within the rhizosphere microbial community while maintaining its functional and structural stability. These results demonstrate that combining PGPBs with WWTP‑derived matrices enhances cork oak growth and nutritional quality without disrupting native soil microbiomes, supporting their potential as sustainable tools for Mediterranean reforestation.}, }
@article {pmid42293540, year = {2026}, author = {Velaz Martín, M and Rießland, H and Rabe, KS and Niemeyer, CM}, title = {Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838890}, pmid = {42293540}, issn = {1664-302X}, abstract = {Microbial communities play central roles in ecosystem functioning across natural and engineered environments, yet their accurate characterization remains challenging due to methodological biases in amplicon sequencing. Primer choice can strongly influence taxonomic resolution, diversity estimates, and ecological interpretation. Here, we systematically compared primer performance across multiple ribosomal marker genes (16S, 18S, 28S rRNA, and ITS) and contrasting habitats, including soil, wastewater, and a photobioreactor-derived suspension. Amplicon-based profiles were benchmarked against shotgun metagenomic data. Primer choice significantly affected community composition, diversity metrics, and concordance with metagenomic profiles across all habitats and markers. Although 16S rRNA gene primers targeting the V3 region showed the highest agreement, no primer set fully reconstructed community structure. Applying the best-performing primer to a structured soil enrichment system using MESIF chips revealed rapid divergence from native soil and convergence toward less diverse communities, consistently favoring copiotrophic, surface-associated taxa while characteristic soil taxa declined. Across the 21-day incubation period, MESIF-associated communities diverged strongly from native soil, whereas medium-specific differences were comparatively smaller. This suggests that early enrichment was dominated by colonization of the structured matrix, while longer incubations and functional analyses will be needed to resolve substrate-specific selection. Overall, our findings highlight primer selection as a critical factor in microbial community analysis and show that combining optimized amplicon sequencing with structured cultivation enables reproducible enrichment, improved community monitoring, and targeted recovery of functionally relevant microorganisms. These insights are relevant for environmental monitoring, wastewater treatment, biotechnology, and controlled environment agriculture.}, }
@article {pmid42293542, year = {2026}, author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S}, title = {Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798330}, pmid = {42293542}, issn = {1664-302X}, abstract = {INTRODUCTION: Alterations in the gut microbiome are closely associated with the progression of multiple myeloma (MM). Previous research has predominantly focused on the bacterial components of the microbiota; however, the virome, a significant component of the microbiota, also plays a critical role, with bacteriophages influencing bacterial community composition and evolution.<br><br>METHODS: This study utilized shotgun metagenomic sequencing of fecal samples to explore the interaction between the gut microbiota and MM development. Fecal samples from 28 MM patients and 20 healthy controls were analyzed to evaluate microbial diversity. Taxonomic profiling of both bacterial and viral communities was performed using the Kraken2 classifier.<br><br>RESULTS: Our analysis confirmed microbial dysbiosis in MM patients and revealed concomitant changes in both bacterial and viral communities. At the phylum level, this study identified a significant increase in the relative abundance of Pseudomonadota (from 1.63 to 8.88%, p&#x202f;<&#x202f;0.001) and a decrease in Bacillota in MM patients compared to controls. Furthermore, several viral taxa were notably enriched in the MM cohort, including the phylum Heunggongvirae (linear discriminant analysis [LDA] = 4.74, p&#x202f;= 0.00003), phylum Uroviricota, and genus Punavirus (specifically Punavirus RCS47). Functional analysis demonstrated shifts in microbial metabolic pathways associated with MM, including a reduced capacity for amino acid and secondary bile acid biosynthesis and an enrichment of pathways associated with biofilm formation and cationic antimicrobial peptide (CAMP) resistance.<br><br>DISCUSSION: This multi-kingdom metagenomic analysis reveals distinct bacterial and viral signatures associated with MM, enhancing our understanding of gut microbial dysbiosis in the disease. These findings lay the groundwork for future mechanistic investigations and highlight the importance of validating these results in larger, independent cohorts.}, }
@article {pmid42293553, year = {2026}, author = {Ali, M and Srivastava, A and Arora, PK}, title = {Probiotics: multifunctional microorganisms for human health and biotechnological applications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1847515}, pmid = {42293553}, issn = {1664-302X}, abstract = {Probiotics are live microorganisms that, when ingested in sufficient amounts, can have a beneficial impact on health. As crucial agents in maintaining gut homeostasis, enhancing immunity, and preventing of numerous diseases, they are fundamentally important. Probiotic function is based on pathogen inhibition, the release of antimicrobial substances, immune modulation, and the enhancement of the intestinal barrier integrity. Technological advances in the area, including molecular identification, microencapsulation methods, and metagenomics, have also been discussed. In addition, research methodologies for several subclasses of probiotics including Lactobacillus and Bifidobacterium continually being investigated. The role of probiotics in health of human, along with existing challenges related to probiotic viability and strain specificity, has also been discussed. This review highlights the growing understanding of probiotics and underscores their potential for optimizing human health and therapeutic applications.}, }
@article {pmid42293554, year = {2026}, author = {Behera, BK and Ren, W and Kumar, A}, title = {Editorial: Biodegradation of agricultural pesticides.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1874629}, pmid = {42293554}, issn = {1664-302X}, }
@article {pmid42293560, year = {2026}, author = {Tenea, GN and Jarrín-V, P and Reyes, P}, title = {Metagenomic insights into postbiotic-mediated modulation of strawberry surface microbiome and metabolic activity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1841388}, pmid = {42293560}, issn = {1664-302X}, abstract = {INTRODUCTION: The increasing demand for sustainable alternatives to chemical disinfectants in postharvest fruit handling has incentivized exploration into microbiome-based interventions. We evaluated the impact of lactic acid bacteria (LAB)-derived postbiotic formulations (FF1, FF2, FF3) and a commercial disinfectant (CD) on the microbial community structure of the strawberry fruit surface.<br><br>METHODS: Taxonomic and functional changes in the microbial communities were evaluated using shotgun metagenomic sequencing, enabling comprehensive profiling of microbial composition and functional potential through gene family abundance, EggNOG functional categories, KEGG pathways, and MetaCyc metabolic reconstruction. The tested formulations consisted of a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O (FF2), used as the antimicrobial agent, and an exopolysaccharide (EPS) from W. confusa UTNCys2-2 (FF3), serving as a biopolymer carrier, applied in combination (FF1: PPGt21O + EPSCys2-2) or individually.<br><br>RESULTS: Our integrated analysis revealed that the highly suppressive formulation, FF1, outperformed the CD by fundamentally restructuring the microbial landscape. Taxonomically, FF1 notably reduced the abundance of key opportunistic spoilage or hazardous organisms. Rather than acting as an indiscriminate biocide, FF1 functioned as a targeted ecological disruptor. Functional profiling (eggNOG, KEGG, and MetaCyc) suggested potential shifts in functional capacity, including a reduced relative abundance of genes associated with translation machinery, cellular membrane expansion (stearate biosynthesis), and host lipid degradation (fatty acid &#x3b2;-oxidation). In parallel, the FF1-treated microbiome showed a higher relative abundance of genes linked to stress-response functions, including heat shock proteins and cell wall-related processes such as peptidoglycan maturation. In contrast, less restrictive formulations (FF2 and FF3) permitted the proliferation of opportunists such as Pseudomonas spp. and Xanthomonas fragariae, accompanied by active energy-consuming and tissue-degrading metabolic signatures.<br><br>CONCLUSION: These findings suggest possible underlying mechanisms of LAB-derived postbiotics, demonstrating that FF1 forces the surface microbiome into a metabolically restricted, non-degradative survival state, potentially contributing to the preservation of postharvest strawberry quality.}, }
@article {pmid42293865, year = {2026}, author = {Zhang, H and Zhang, W and Yao, D and Li, X and Ali, HSM and Xi, J and Liang, Y and Zhao, F and Yu, S and Yu, K}, title = {Scion varieties and nitrogen levels affect carbon and nitrogen assimilation in apple via modulating rhizosphere microbial structure and function.}, journal = {Horticulture research}, volume = {13}, number = {3}, pages = {uhaf334}, pmid = {42293865}, issn = {2662-6810}, abstract = {The efficiency of carbon and nitrogen uptake in apple trees is co-regulated by plant genotype and rhizosphere microbial communities. However, the mechanisms by which different scion varieties modulate microbial structure and function under varying nitrogen levels remain poorly understood. In this study, Malus sieversii was used as the rootstock, onto which three scion cultivars (M. sieversii, Malus domestica cv. Hanfu, and Malus domestica cv. Red Fuji) were grafted under two nitrogen regimes. A combination of [13]C/[15]N isotope labeling, Illumina MiSeq amplicon sequencing, and metagenomic analysis was employed to elucidate how scion-rootstock interactions and nitrogen availability affect carbon and nitrogen acquisition. Under nitrogen-deficient conditions, Red Fuji exhibited stronger root activity and larger root surface area, indicating enhanced nutrient foraging capacity. Conversely, under nitrogen application, Hanfu showed significantly greater [13]C and [15]N uptake, with 5.7-fold and 1.6-fold higher [13]C accumulation in roots and stems, respectively, and markedly higher [15]N utilization efficiency in roots and leaves compared with M. sieversii. In parallel, Hanfu under nitrogen input showed enrichment of beneficial microbial taxa and more complex microbial co-occurrence networks. Metagenomic analysis and random forest analyses revealed that the relative abundance of specific functional genes related to carbon and nitrogen transformation (rbcL, abfA, napB/C, nasA) was significantly higher under specific scion-nitrogen combinations, contributing to enhanced microbial carbon fixation and nitrogen reduction. Collectively, these results demonstrate that scion genotype modulates rhizosphere microbial structure, physiological root traits, and carbon-nitrogen distribution patterns, thereby improving nutrient uptake efficiency under different nitrogen inputs.}, }
@article {pmid42293986, year = {2026}, author = {Lou, L and Li, X and Zhang, P and Wu, H and Chen, H and Ma, J and Zhang, K}, title = {Eravacycline-Cefiderocol Combination Therapy for Carbapenem-Resistant Acinetobacter baumannii Infective Endocarditis: A Case Report and Brief Review of the Literature.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {615678}, pmid = {42293986}, issn = {1178-6973}, abstract = {BACKGROUND: Infective endocarditis (IE) caused by carbapenem-resistant Acinetobacter baumannii (CRAB) is rare and associated with limited treatment options because of extensive antimicrobial resistance.<br><br>CASE PRESENTATION: We hereby present a case of prosthetic valve endocarditis (PVE) caused by CRAB, presenting with fever, persistent bloodstream infection, cerebellar hemorrhage, and aortic valve vegetation. The application of a novel combination therapy comprising eravacycline and cefiderocol effectively eliminated the bloodstream infection. Concomitantly, the monitoring of adverse reactions and the subsequent adjustment of medication and dosage ensured the favorable safety. Although bloodstream infection and valve vegetation were controlled, progressive perivalvular leakage indicated the need for timely surgical intervention when clinically feasible.<br><br>CONCLUSION: This case indicates that eravacycline combined with cefiderocol may represent a novel and effective treatment option for refractory IE caused by carbapenem-resistant Gram-negative pathogens, including PVE caused by CRAB.}, }
@article {pmid42294186, year = {2026}, author = {Saenko, EV and Kuznetsova, MV and Nesterova, LY and Valtsifer, IV and Levin, LY and Zaitsev, AV and Karipova, MO and Strelnikov, VN and Valtsifer, VA}, title = {Analysis of Microbial Tolerance and Physicochemical Properties of HFA‑E Hydraulic Fluids Used in Mechanized Mine Roof Supports.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {31925-31939}, pmid = {42294186}, issn = {2470-1343}, abstract = {This study presents a comparative analysis of microbial tolerance and physicochemical properties of HFA-E (fire-resistant hydraulic fluid, aqueous-based, emulsion type) hydraulic fluids based on commercial "Hydrotol-ITCh HFAE" and "Fimitol P87 AF" concentrates used in mining hydraulic roof support systems. Metagenomic analysis revealed distinct microbial community structures in the two fluids. The Hydrotol-ITCh HFAE-based fluid microbiota consisted predominantly of Bacteria (99.77%), especially Proteobacteria, while the Fimitol P87 AF-based fluid exhibited a more complex and taxonomically diverse community, including a significant proportion of Archaea (47.09%) and Bacteria (52.92%) from groups such as methanogens (Methanobacteriaceae) and sulfate-reducing bacteria (Desulfovibrionaceae), respectively. In vitro tests confirmed the inherent antimicrobial activity of the fluids, which significantly reduced planktonic microbial viability and eradicated the majority of bacteria. The physicochemical properties of the fluids remained stable even under high initial bacterial load, confirming their reliability during microbial contamination. However, under industrial conditions, the Hydrotol-ITCh HFAE-based fluid demonstrated lower contamination and higher emulsion stability (pH reduced to 8.5 after one year of operation versus 6.5 for "Fimitol P87 AF"), which reduced the risk of biocorrosion and the need for additional treatments. This study emphasizes the importance of comprehensive monitoring of microbial diversity and physicochemical parameters for predicting the service life of hydraulic systems, developing effective biocides, and minimizing risks to equipment and personnel. The obtained data can be used to optimize hydraulic fluid compositions and their operational strategies.}, }
@article {pmid42294227, year = {2026}, author = {Tan, AJ and Li, TR and Yang, JJ and Li, XL and Li, WQ and Yu, JW}, title = {Liraglutide and Dapagliflozin Synergistically Reshape Gut Microbiota and Metabolic Profiles to Ameliorate Type‑2 Diabetes in Mice.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {32363-32379}, pmid = {42294227}, issn = {2470-1343}, abstract = {Background: Type-2 diabetes mellitus (T2DM) poses a formidable global health challenge, characterized by persistent hyperglycemia resulting from insulin resistance and progressive β-cell dysfunction. Liraglutide (LIRA), a GLP-1 receptor agonist, and dapagliflozin (DAPA), an SGLT2 inhibitor, are established therapies with complementary mechanisms. However, the potential synergy of their combination, particularly through modulation of the gut microbiota and host metabolism, remains incompletely understood. To elucidate the gut microbiota-metabolite axis underlying the therapeutic effects of combination therapy in T2DM, we explored the interplay between β-cell function, fecal microbiota composition, and microbial metabolites. Methods: A T2DM mouse model was induced by a high-fat diet and streptozotocin. Mice were treated for 4 weeks with LIRA, DAPA, or their combination (COM). We assessed glycemic control, insulin sensitivity, pancreatic islet morphology, serum biochemistry, gut microbiota (shotgun metagenomic sequencing), and plasma metabolome (nontargeted metabolomics). Integrated multiomics analysis was performed to elucidate microbiota-metabolite interactions. Results: Combination treatment demonstrated superior efficacy compared to monotherapies, resulting in significantly greater improvements in body weight, glucose tolerance, insulin sensitivity, lipid profiles, and liver function. Histologically, COM most effectively restored pancreatic islet architecture, increased β-cell mass, and normalized α/β-cell ratio. Metagenomic analysis revealed that COM induced a unique and restorative remodeling of the gut microbiota, distinct from monotherapies. This was characterized by suppression of pathobionts (e.g., Klebsiella and Enterorhabdus) and enrichment of beneficial taxa (e.g., Akkermansia, Lactobacillus, and Faecalibaculum). Metabolomics profiling showed that COM extensively normalized the diabetic plasma metabolome. Key altered pathways included tryptophan metabolism, sphingolipid metabolism, and branched-chain amino acid degradation. Integrated correlation analysis unveiled significant associations between specific microbial genera and host metabolites, suggesting a functional gut microbiota-metabolite axis underpinning the synergistic benefits. Conclusions: The combination of liraglutide and dapagliflozin exerts synergistic antidiabetic effects that extend beyond glycemic control to encompass pancreatic protection and systemic metabolic improvement. This synergy is mechanistically linked to collaborative remodeling of the gut ecosystem and consequent normalization of host metabolic pathways. Our findings provide a novel rationale for this combination therapy and highlight the gut microbiota as a pivotal target for T2DM management.}, }
@article {pmid42294679, year = {2026}, author = {Henkel, JV and Røy, H and Jørgensen, BB and Rotaru, A-E and Jovicic, D and Marshall, IPG and Jiang, C and Nielsen, PH and Singleton, CM and Arz, HW and Plewe, S and Kjeldsen, KU}, title = {Desulfatiglans-related bacteria associated with conductive mineral particles in marine subsurface sediments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0083826}, doi = {10.1128/mbio.00838-26}, pmid = {42294679}, issn = {2150-7511}, abstract = {UNLABELLED: Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Recent observations suggest that acetate is oxidized syntrophically in the methanic zone of marine sediments, and that electrically conductive mineral particles could provide niches for electroactive microbial communities that perform this process. We combined radiotracer measurements, a novel procedure for ferromagnetic mineral particle extraction, and metagenomic analyses to examine this process in Baltic Sea sediments. Our results confirm that acetate is oxidized syntrophically across and below the sulfate-methane transition zones of the sediments, where the transfer of reducing equivalents from acetate oxidation to CO2 fuels methanogenesis. Ferromagnetic particles consistently occurred throughout the geochemical zones and mainly consisted of the electrically conductive minerals magnetite and pyrite-greigite. The microbial communities associated with ferromagnetic particles were dominated by members phylogenetically affiliated with the bacterial genus Desulfatiglans. Known Desulfatiglans species are dissimilatory sulfate reducers; however, metagenome-assembled genomes indicate that Desulfatiglandales populations associated with ferromagnetic particles lack genetic potential to respire sulfate. Instead, they may grow by acetate oxidation coupled with extracellular electron transfer, consistent with a conductive mineral-associated lifestyle. We hypothesize that Desulfatiglans relatives are acetate-oxidizing partners in a syntrophic process facilitated by interspecies electron transfer via conductive particles. We identified cytochrome-rich ANME-1 archaea as the predominant methane-cycling microorganisms associated with ferromagnetic particles; however, their potential role as methanogenic syntrophic partners remains uncertain. Overall, our study reveals that distinct microbial communities are associated with ferromagnetic particles and shows conductive minerals as a niche for electroactive microorganisms in marine sediments.<br><br>IMPORTANCE: Acetate is a central intermediate in the anaerobic breakdown of organic matter. In Baltic Sea sediments at and below the sulfate-methane transition zone, we observed acetate oxidation to carbon dioxide at rates similar to methane formation from carbon dioxide reduction, a pattern indicative of syntrophic acetate oxidation. Previous enrichment studies suggest that electrically conductive mineral surfaces can facilitate this process. Motivated by this observation, we extracted ferromagnetic conductive particles from sediments and compared particle-attached microbial communities with bulk sediment. Particle-attached communities were distinct and enriched in the bacterial genus Desulfatiglans. Their genomes lacked genes for sulfate respiration, yet encoded traits consistent with acetate oxidation and extracellular electron transfer. Our findings suggest conductive minerals as distinct microbial niches and highlight Desulfatiglans-related bacteria as a potential key organism in particle-associated acetate oxidation.}, }
@article {pmid42294682, year = {2026}, author = {Ai, C and Tang, X and Han, H and He, Y and Zhang, H and Liu, C and Liao, H and Zhou, S}, title = {Active prophages as key drivers of microbial adaptation in global soil ecosystems.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069326}, doi = {10.1128/mbio.00693-26}, pmid = {42294682}, issn = {2150-7511}, abstract = {Soils harbor the most complex microbial diversity on Earth, in which bacteria are ubiquitously infected by temperate phages. While integrated prophages often enhance host fitness, active (inducible) prophages are traditionally perceived as "molecular time bombs" due to their intrinsic lysis threat. This dual nature has raised fundamental questions about the true contribution of temperate phages to microbial adaptation and ecosystem stability. To address this gap, we conducted a global-scale integrative analysis by synthesizing 123,207 high-quality bacterial genomes, 183 soil-specific viromic data sets, and 3,749 metagenomes. We established the Global Soil Active Prophage Database (GSAPD), comprising 21,397 high-confidence active prophages, which we found to represent 34.3% of the total soil viral population within our analytical framework. Our comparative genomic analysis reveals that active prophages possess significantly larger genomes and greater genetic complexity compared with their dormant counterparts. Crucially, by mapping phage-encoded auxiliary metabolic genes (AMGs) across diverse biomes, we found that active prophages are disproportionately enriched in key pathways for carbon, nitrogen, and sulfur cycling, as well as specialized resistance mechanisms against heavy metal toxicity. These findings suggest that active prophages act as dynamic reservoirs of functional diversity. We demonstrate that their lytic potential is not merely a survival risk, but a sophisticated mechanism underpinning host environmental adaptation and niche expansion. Ultimately, this study provides a comprehensive global catalog of soil viral pathways and redefines the role of temperate phages as pivotal drivers of microbial evolution and biogeochemical cycling in terrestrial ecosystems.IMPORTANCESoils contain immense microbial diversity, yet the ecological role of temperate phages-especially their active (inducible) forms-remains poorly understood. This study provides the first global-scale assessment of active prophages in soils, revealing that they are widespread and functionally distinct from dormant forms. By building a comprehensive database and integrating multi-omics data, we show that active prophages are enriched in genes linked to key biogeochemical processes and stress resistance. These findings challenge the traditional view of active prophages as purely harmful agents and instead highlight their role as dynamic contributors to microbial function and adaptation. Our work offers new insights into how viruses shape ecosystem processes and provides a valuable resource for future studies on soil microbial ecology and nutrient cycling.}, }
@article {pmid42294703, year = {2026}, author = {Kady, MR and Britton, RA}, title = {Revised complete genome sequences of Limosilactobacillus reuteri DSM 20016[T] and ATCC PTA-6475 and confirmation of an intragenic macrosatellite in adhesin gene cmbA.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0400525}, doi = {10.1128/spectrum.04005-25}, pmid = {42294703}, issn = {2165-0497}, abstract = {UNLABELLED: Cell and mucus binding protein A (CmbA) is a cell-wall-anchored adhesin common to human isolates of Limosilactobacillus reuteri, which governs mucosal adhesion in vitro. Recent attempts to sequence cmbA in different L. reuteri strains revealed significant genomic inconsistencies with the publicly available closed genome sequences, especially with that of the L. reuteri type strain, DSM 20016[T]. We report here a revised closed genome sequence for DSM 20016[T] and a closed genome sequence for the closely related L. reuteri ATCC PTA-6475 (MM4-1A). Hybrid long- and short-read sequencing demonstrated that two genomic regions totaling 40 kbp, previously thought to be absent in DSM 20016[T], were in fact intact. The cmbA gene, present in one of these regions, is the longest predicted gene in both genomes and was confirmed to contain an intragenic tandem repeat region. In DSM 20016[T], the region consists of 11 identical ~290 bp tandem direct repeats totaling 3.2 kbp, while ATCC PTA-6475 has 8 repeats totaling 2.3 kbp. This macrosatellite posed a challenge to PCR-based approaches to confirm the length of the gene. Polyacrylamide gel electrophoresis of cell wall extracts from ATCC PTA-6475 showed a ~160 kDa band, which was absent from a cmbA-knockout strain, consistent with the expected size based on whole-genome sequencing and confirmed by mass spectrometry to be CmbA. Overall, we present refined publicly available genome sequences for two frequently studied L. reuteri strains and validate the length of a large gene with a conspicuously high number of identical tandem repeats.<br><br>IMPORTANCE: Studies comparing bacterial genomes and routine cloning work often implicitly assume that the closed genome sequences available from public databases are accurate. However, as technologies improve and we gain new data, inconsistencies can arise which prompt the resequencing of strains, sometimes with surprising results. We show here that a significant sequencing assembly artifact led to a large gap in the publicly available closed genome of the Limosilactobacillus reuteri type strain which has remained uncorrected for nearly two decades, despite a vast body of L. reuteri work over that time. Another region contained a large stretch of repetitive intragenic DNA that still posed a challenge to modern PCR techniques. Therefore, in addition to being useful to L. reuteri biologists, this work serves as an important reminder of the intrinsically experimental nature of sequencing data; it usually pays to resequence early and often.}, }
@article {pmid42294704, year = {2026}, author = {He, Y and Wang, X and Li, S and Zhang, C and Xu, M and Zhou, Y and Sanford, RA and Liang, R and Zhu, Y and Yang, D and Dan, L and Mao, X and Zhang, L and Sun, W and Jiang, Y and Hu, Y and Jiang, Z and Li, Y and Song, W and Hu, N and Zhao, L and Dong, Y and Shi, L}, title = {Ecological plasticity of Halanaerobium microorganisms across terrestrial saline to hypersaline subsurface environments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0138126}, doi = {10.1128/spectrum.01381-26}, pmid = {42294704}, issn = {2165-0497}, abstract = {UNLABELLED: Members of the genus Halanaerobium are widely distributed in hypersaline environments, including oil and gas reservoirs, and saline lake sediment. However, a comprehensive understanding of their physiological traits, metabolic capacities, adaptive strategies, and biogeography remains limited. In this study, a strictly anaerobic and halophilic strain, H. saccharolyticum_B KY39 was isolated from produced water in the Zhongyuan Oilfield, China. Strain KY39 grew at 20-45°C, 2-30% salinity, pH 5.3-9.0, and up to 50 MPa hydrostatic pressure. It could ferment various carbohydrates (e.g., glucose, xylose, sucrose, and maltose) or use mannitol and pyruvate as electron donors under Fe(III)-reducing conditions. Comparative genomic analyses of 31 high-quality Halanaerobium strains revealed an open pangenome. Genes involved in osmotic and pressure stress responses, including those related to osmoprotectant biosynthesis and ion transport, were highly conserved. The thiosulfate sulfurtransferase (TST) gene, responsible for converting thiosulfate to sulfite, was universally present. Notably, compared to the strains from saline lakes, those from oil and gas reservoirs possessed larger genomes and harbored a broader repertoire of genes related to peptidoglycan biosynthesis, nitrogen fixation, sulfur metabolism, biofilm formation, and carbohydrate uptake, suggesting enhanced metabolic flexibility and environmental adaptation. Moreover, a survey of the available metagenomes revealed that Halanaerobium species were globally distributed across diverse environments exhibiting a broader salinity range. In addition to oil and gas reservoirs and saline lakes, they also widely reside in soils, fermented foods, and marine ecosystems. Collectively, these findings advance the systematic understanding of ecological plasticity and metabolic versatility of Halanaerobium, shedding light on their ecological roles and potential industrial impacts.<br><br>IMPORTANCE: Members of the genus Halanaerobium are prominent inhabitants of surface and deep subsurface hypersaline environments, yet their ecological roles and adaptive strategies remain poorly understood. Here, through the isolation of a novel strain from the production fluid of an oil field combined with comparative genomic analyses across the genus, we revealed the metabolic versatility, stress tolerance, and global distribution of Halanaerobium. Our findings underscore the ecological plasticity, functional diversity, and niche differentiation within this genus, providing fundamental insights into its potential industrial and environmental applications.}, }
@article {pmid42294714, year = {2026}, author = {Sajib, MSI and Oravcova, K and Brunker, K and Everest, P and Fuentes, M and Wilson, C and Murphy, ME and Forde, T}, title = {Rapid and modular workflows for same-day sequencing-based detection of bloodstream infections and antimicrobial resistance determinants using culture-enriched samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0324025}, doi = {10.1128/spectrum.03240-25}, pmid = {42294714}, issn = {2165-0497}, abstract = {UNLABELLED: Bloodstream infections (BSI) are a major global health concern, and existing diagnostic methods are too slow to guide targeted antibiotic therapy for critically ill patients. Rapid metagenomic next-generation sequencing (mNGS) can facilitate swift microbiological diagnosis, but identification is challenged by significant host versus bacterial DNA in blood and blood culture media. To accelerate reporting time, we developed M-15, a rapid mNGS-based host DNA depletion workflow optimized for culture-enriched samples, validated with suspected BSI blood culture samples and rapid culture-enriched spiked blood. M-15 was benchmarked with five commercial/published protocols, combined with rapid mNGS, and tested on blood culture samples (n = 33) from suspected BSI cases identified on BACT/ALERT-VIRTUO. To determine whether it is possible to utilize M-15 mNGS prior to blood culture flagging positive, a rapid enrichment method was tested starting with 1-10 colony-forming units of the top 15 bacterial species causing BSI spiked into BACT/ALERT medium enriched with 10 mL sheep blood. All six chemical depletion protocols reduced host DNA by 2.5 × 10[0]- to 4.1 × 10[6]-fold, with the in-house M-15 protocol performing best. With BACT/ALERT specimens, M-15 mNGS identified 28/28 mono-bacterial and 2/4 multi-bacterial species. With rapid culture enrichment and M-15 mNGS, <18% DNA was classified as host, and all bacterial species tested (n = 10) were correctly identified. M-15 mNGS accurately predicted phenotypic AMR/susceptibility for 90.3% (232/257) of drug/bacteria combinations from BACT/ALERT-positive samples. This study demonstrates that M-15 mNGS can facilitate species and AMR gene detection within 5-7 hours of BACT/ALERT positivity and possibly 13-15 hours of sample collection. Further clinical validation is required to assess its performance and the potential to improve patient outcomes in BSI.<br><br>IMPORTANCE: Bloodstream infections (BSI) are among the leading global health challenges, and traditional culture-based diagnostic methods are too slow (often taking >48 hours) to guide critical clinical interventions. This study demonstrates the development and utility of M-15 metagenomic next-generation sequencing (mNGS), a modular Oxford Nanopore-based chemical host DNA depletion and metagenomic sequencing workflow applied to enriched blood culture media for the same-day detection of bacterial etiologies and their antimicrobial resistance (AMR) genes. The selective chemical host DNA depletion method (M-15) described in this study can remove approximately 4.1 &#xd7; 10[6]-fold unwanted host DNA from whole blood, providing high-resolution genomic information from the bacteria at a fraction of the sequencing time/cost (approximately &#xa3;120-&#xa3;160/sample). We have tested this workflow on culture-positive clinical and rapid enriched spiked blood samples and demonstrated its ability to identify bacterial species and AMR genes between 5 and 7 hours post blood culture positivity. Based on our in vitro experiments using rapid enrichment, we believe similar results could be achieved within 13-15 hours from blood sample collection. Although further clinical validation is required, especially to fully assess the rapid version of the protocol, M-15 mNGS offers a promising advancement in BSI diagnosis. This workflow is modular and can be expanded in the future to adapt for other infections, which makes it a versatile tool to improve patient outcomes in sepsis.}, }
@article {pmid42294728, year = {2026}, author = {Mao, Z and Jiang, M and Zhao, Z and Xu, S and Wang, H and Chen, K and Duan, J and Chen, Z and He, D and Xing, P and Wu, QL}, title = {Biofilm-forming traits enrich the plasmid diversity and functional potential in particle-attached bacteria in coastal ecosystems.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0046026}, doi = {10.1128/spectrum.00460-26}, pmid = {42294728}, issn = {2165-0497}, abstract = {UNLABELLED: Planktonic microorganisms play a central role in aquatic biogeochemical processes and are commonly divided into particle-attached (PA) and free-living (FL) fractions. Although these two lifestyles differ in ecological strategy, the contribution of plasmids to their niche differentiation remains poorly resolved. Here, we conducted a plasmid-centric metagenomic analysis of two anthropogenically impacted coastal ecosystems in South China, the Pearl River Estuary (PRE), and Daya Bay (DYB), to determine the environmental and biological drivers of plasmid diversity, and their functional potenitial. We found that plasmid diversity was jointly shaped by different fractions and environmental stressors. The PA fraction contained significantly higher plasmid abundance and richness than the FL fraction, and was enriched in multifunctional and conjugative plasmids. These plasmids were associated with genes adapting to the PA lifestyle or microenvironments, suggesting linkage between particle attachment and plasmid maintenance. Structural equation modeling indicated that different fractions shaped plasmid diversity primarily through biofilm-forming genes. Along an anthropogenic gradient from DYB to PRE, increasing pollution levels were accompanied by higher plasmid diversity and greater abundances of antibiotic and metal resistance genes. Plasmid diversity was strongly correlated with resistance gene abundance. The enrichment of transferable plasmids in the PA fraction, where cell densities are high and intercellular distances are close, suggested that particle-associated habitats favor genetic exchange and the persistence of resistance traits. Together, these results demonstrate that particle-associated microbial communities represent key reservoirs of plasmid diversity and resistance potential in coastal ecosystems and highlight the combined influence of lifestyles and anthropogenic stress on plasmid-mediated microbial adaptation.<br><br>IMPORTANCE: Plasmids play an important role in microbial adaptation by mediating horizontal gene transfer, yet the ecological contexts that favor their persistence and diversification in natural environments remain poorly understood. This study showed that particle-attached microbial communities in coastal waters harbored substantially higher plasmid diversity and resistance potential than free-living communities, and that this enrichment is strongly linked to biofilm-associated traits. By demonstrating how particulate habitats and pollution gradients jointly shape plasmid diversity and resistance gene abundance, our findings identify particle-associated microenvironments as critical reservoirs for plasmid-mediated functions in coastal ecosystems. These results advance understanding of how microbial lifestyle and human activities influence microbial evolution and the environmental dissemination of resistance traits.}, }
@article {pmid42294989, year = {2026}, author = {Thomas, PW}, title = {Hidden Fungal DNA Structures May Shape Sequencing Outcomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {48}, number = {6}, pages = {e70153}, pmid = {42294989}, issn = {1521-1878}, mesh = {*DNA, Fungal/chemistry/genetics ; Genome, Fungal ; *Fungi/genetics ; Nucleic Acid Conformation ; *Sequence Analysis, DNA/methods ; }, abstract = {Fungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in rapid pore clogging and unusual translocation dynamics, possibly due to intrinsic, yet undescribed, structural complexities. Exploring these signals could reveal novel fungal genome architectures, enhance sequencing accuracy, and drive advances in fungal biology.}, }
@article {pmid42295167, year = {2026}, author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P}, title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0054225}, doi = {10.1128/iai.00542-25}, pmid = {42295167}, issn = {1098-5522}, abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.}, }
@article {pmid42295179, year = {2026}, author = {Guitart-Matas, J and Ramayo-Caldas, Y and González-Rodríguez, O and Giler-Baquerizo, N and Migura-Garcia, L and Ballester, M}, title = {Implementation of a high-throughput microfluidic platform for antimicrobial resistance surveillance in swine production systems.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42295179}, issn = {2057-5858}, mesh = {Animals ; Swine/microbiology ; Metagenomics/methods ; Feces/microbiology ; *Microfluidics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Shotgun Sequencing ; }, abstract = {Antimicrobial resistance poses a serious threat to public health worldwide and demands interventions with a One Health perspective. A key challenge is determining the collection of antimicrobial resistance genes of a specific environment, also known as the resistome. Surveillance and monitoring of the resistome are essential for tracking the emergence and dissemination of resistance mechanisms. In this study, we took advantage of shotgun metagenomics and metatranscriptomics sequencing data of piglets treated with different post-weaning diarrhoea treatments to generate an antimicrobial resistance gene catalogue of the pig gut microbiome during pre-weaning and post-weaning stages. The selected catalogue, comprising a total of 102 genes and representing the majority of antibiotic classes, has been implemented in the microfluidic Biomark[™] X9 System and validated using total DNA and RNA extracted from piglets' faecal samples. Additionally, this platform has been verified by demonstrating a strong and statistically significant correlation with resistome quantification data from both metagenomic and metatranscriptomic sequencing. Overall, the microfluidic qPCR platform implemented here demonstrated enhanced detection of low-abundance targets, successfully identifying genes and transcripts that remained below the stochastic detection threshold of shotgun sequencing. This approach enables high-throughput monitoring and surveillance of antimicrobial resistance, providing a critical tool to support the reduction of antimicrobial use in farms.}, }
@article {pmid42295208, year = {2026}, author = {Chaudhary, A and Lin, X and Vitaterna, MH and Auch, B and Liachko, I and Green, SJ}, title = {Metagenome-assembled genome sequence of an uncultured Roseburia sp. generated from mouse fecal DNA from the International Space Station.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0104725}, doi = {10.1128/mra.01047-25}, pmid = {42295208}, issn = {2576-098X}, abstract = {The effects of spaceflight stressors, such as microgravity, cosmic radiation, and confinement, on the host physiology and gut microbiome remain unclear. Here, we report the metagenome-assembled genome (MAG) sequence of an uncultured Roseburia sp. strain that showed a significant gravity dose response in the gut microbiome of mice during spaceflight.}, }
@article {pmid42295273, year = {2026}, author = {Mawire, P and Gregori, MNJ and Makumbi, JP and Bezuidt, OK and Makhalanyane, TP}, title = {High-quality metagenome-assembled genomes of carbon-degrading, sulfate-reducing, and sulfur-oxidizing Acidobacteriota from Sub-Antarctic Marion Island soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0034226}, doi = {10.1128/mra.00342-26}, pmid = {42295273}, issn = {2576-098X}, abstract = {Here, we present high-quality Acidobacteriota metagenome-assembled genomes (n = 20) belonging to understudied lineages (UBA7541 [n = 13] and SbA1 [n = 7]) from sub-Antarctic soils. Nutrient cycling genes were prevalent in these MAGs, which provide a resource for understanding the ecological role of Acidobacteriota in extreme environments.}, }
@article {pmid42295521, year = {2026}, author = {Ferdous, J and Islam, SMR and Chakma, K and Hasan, MM and Tanni, AA and Ahmed, R and Sikder, U and Biswas, S and Siddiki, AZ and Crandall, KA and Rahnavard, A and Hussain, MH and Sharifuzzaman, SM and Chowdhury, MSN and Mannan, A}, title = {Antimicrobial resistance and gut microbiome profiles in wild and cultured shrimp (Penaeus monodon) from the coast of the northern Bay of Bengal, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42295521}, issn = {1573-2959}, mesh = {Animals ; *Penaeidae/microbiology ; Aquaculture ; Bangladesh ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Bays ; Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; }, abstract = {The coastal waters of Bangladesh support rich aquatic biodiversity, including the commercially important shrimp Penaeus monodon. However, antimicrobial resistance (AMR) poses a growing threat to aquaculture, ecosystem stability, and human health. In this study, we investigated bacterial AMR profiles and characterized the gut microbiomes of wild (Natural) and cultured P. monodon from the northern Bay of Bengal, Bangladesh. Culture-based and biochemical methods were used to identify bacterial pathogens of shrimp shells, and antimicrobial susceptibility was assessed using the disc diffusion method. Shotgun metagenomic sequencing was used to characterize gut microbial diversity and identify antibiotic resistance genes (ARGs). All Klebsiella isolates were resistant to ampicillin (100%) and showed high resistance to azithromycin (83%) and nitrofurantoin (73%). Pseudomonas isolates were 93.10% resistant to ampicillin, whereas Vibrio isolates had notable resistance to azithromycin (71.05%) and colistin (63.16%). Metagenomic analysis revealed comparable alpha diversity between wild and cultured shrimp, with Vibrio being predominant in both groups and V. parahaemolyticus as the most abundant species. Cultured shrimp harbored greater microbial diversity, including additional genera such as Shewanella, Lactococcus, and Enterobacter. A total of 30 ARGs were detected, primarily associated with β-lactams and tetracycline resistance. Cultured shrimp exhibited a broader ARG spectrum, reflecting potential anthropogenic impacts on aquaculture practices. These findings suggest that cultured shrimp environments can serve as reservoirs of resistant bacteria and ARGs. Therefore, improved antimicrobial stewardship and regular monitoring are essential to curb the spread of AMRs in marine ecosystems.}, }
@article {pmid42295988, year = {2026}, author = {Soge, OO and Fifer, H and Alexander, S and Buss, SN}, title = {Diagnostics and novel laboratory approaches to combat Neisseria gonorrhoeae antimicrobial resistance.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2026.2689689}, pmid = {42295988}, issn = {1744-8352}, abstract = {INTRODUCTION: Neisseria gonorrhoeae (gonococcus, GC) has developed resistance to all antimicrobials recommended for gonorrhea treatment, owing to its genetic plasticity and capacity to acquire antimicrobial resistance (AMR). This review examines the crucial role of diagnostics and novel laboratory approaches in mitigating the spread of GC-AMR and in preserving the long-term effectiveness of current and future antimicrobials for gonorrhea.<br><br>AREAS COVERED: Recent advances in diagnostics and novel laboratory approaches for detection of GC-AMR, enhancing GC-AMR surveillance and clinical management of gonorrhea.<br><br>EXPERT OPINION: The rapid emergence and global dissemination of multidrug-resistant GC including ceftriaxone-resistant strains poses a grave challenge to current gonorrhea control and prevention strategies. The implementation of rapid diagnostics and novel laboratory approaches can, when used appropriately, support the rapid detection of GC-AMR, ensure timely treatment, reduce transmission, and preserve last-line antibiotics by enabling resistance-guided therapy. These diagnostics and novel laboratory approaches are also crucial for the early detection of emerging resistance to antimicrobials recently approved by the FDA, and other antimicrobials currently under development and anticipated for future clinical use. Integrating culture-based GC-AMR surveillance with rapid molecular assays targeting genetic determinants of AMR offers a comprehensive approach for robust monitoring and timely response to the ever-evolving GC-AMR.}, }
@article {pmid42296170, year = {2026}, author = {Diale-Makhongela, MO and Mpai, T and Bopape, FL and Mtsweni, P and Salawu-Rotimi, A and Shargie, NG and Gerrano, AS and Morey, L and Kubheka, B and Hassen, AI}, title = {16S rRNA-based metagenomics insights into the microbial diversity and functional attributes of soils from the rhizosphere of selected C4 crops of farms in Mpumalanga and Limpopo provinces, South Africa.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0347776}, pmid = {42296170}, issn = {1932-6203}, mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; South Africa ; *Soil Microbiology ; *Metagenomics/methods ; *Crops, Agricultural/microbiology ; Pennisetum/microbiology/growth &amp; development ; Sorghum/microbiology/growth &amp; development ; Soil/chemistry ; Bacteria/genetics/classification ; Phylogeny ; Farms ; Biodiversity ; Carbon/metabolism ; }, abstract = {The rhizosphere serves as a hub for a variety of microorganisms that are highly beneficial to crop production and improvement of soil health. However, intensive farming practices including utilization of agrochemicals can cause a decline in microbial diversity that could severely compromise soil health and crop productivity. Here we investigated the taxonomic abundance and functional diversity of the microbial communities of sorghum and pearl millet rhizosphere soil samples from sixteen farms in Mpumalanga and Limpopo Provinces of South Africa. Soil samples were collected at the rhizosphere of sorghum and pearl millet crops and pooled into 34 samples. The soil samples were used for 16S rRNA amplicon sequencing analysis, soil physicochemical properties, and community-level physiological profiles. The results indicated that carbon utilization was highest in the majority of soil samples from Jane Furse, which also demonstrated greater microbial richness. The 16S rRNA amplicon sequencing analysis provides insight into the relative abundance of soil microbial communities, where at phylum level Planctomycetes, Proteobacteria, and Actinobacteria were the most predominant in all farms, but their relative abundances varied. Our results revealed that physicochemical properties could affect microbial abundance and diversity. The distance-based redundancy analysis (dbRDA) explained 46.8% of the variation in the soil bacterial community structure, with Mn, Fe, NO3[-]-N, and Ca identified as the key soil physicochemical variables shaping community composition. Thus, this study may contribute to advancing sustainable agricultural practices by providing baseline data that may inform future bioinoculant development.}, }
@article {pmid42296229, year = {2026}, author = {Yu, Q and Liu, F and Xu, R and Jie, J and Tang, M and Li, D and Gu, Y and Song, L}, title = {Bronchoscopic Cytology and Metagenomic Sequencing to Differentiate Cancer Treatment-related and Infectious Lung Injury.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/70725}, pmid = {42296229}, issn = {1940-087X}, mesh = {Humans ; *Bronchoscopy/methods ; Bronchoalveolar Lavage Fluid/cytology/microbiology ; *Metagenomics/methods ; *Lung Injury/diagnosis/microbiology/etiology/pathology/genetics ; *High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Patients with cancer treatment-related lung injury (CTLI) frequently present with non-specific respiratory symptoms and radiological changes that closely mimic infectious pneumonia or tumor progression, presenting a significant challenge for a definitive diagnosis. Traditional diagnostic processes, mainly evaluated through blood biomarkers and standard microbial cultures, usually cannot make a clear diagnosis and take too much time. Here, we present a comprehensive protocol to diagnose CTLI by combining bronchoalveolar lavage fluid (BALF) cytological analysis with metagenomic next-generation sequencing (mNGS). The procedural workflow consists of three primary stages. First, standardized bronchoscopy is performed to obtain high-quality BALF samples. Second, conducting cytological analysis of the obtained BALF samples provides a snapshot of the lung microenvironment. This allows identification of inflammatory features and screening for malignant cells to exclude tumor progression. Finally, mNGS is utilized to identify or exclude active infectious etiologies. This advanced genomic technique achieves rapid, highly sensitive, and unbiased pathogen detection, successfully overcoming the limitations of traditional cultures. Representative results using this method demonstrate that this approach can effectively distinguish immune-related pneumonitis from active pulmonary infections or tumor progression. Compared with traditional diagnostic methods, this protocol has the advantage of quickly and accurately distinguishing CTLI from infectious etiologies and occult malignancies. Ultimately, this standardized workflow clarifies clinical diagnoses, guides critical treatment decisions, and improves patient outcomes.}, }
@article {pmid42296622, year = {2026}, author = {Pravara, R and Praveen, R and Seema, B}, title = {Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {60}, number = {}, pages = {101902}, doi = {10.1016/j.cbd.2026.101902}, pmid = {42296622}, issn = {1878-0407}, abstract = {BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus.<br><br>RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism.<br><br>CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.}, }
@article {pmid42296787, year = {2026}, author = {Lu, HB and Kong, LY and Chen, L and Chen, GJ}, title = {Janthinobacterium foliorum sp. nov., isolated from the decayed leaves of wild alpine rhododendron.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126736}, doi = {10.1016/j.syapm.2026.126736}, pmid = {42296787}, issn = {1618-0984}, abstract = {Janthinobacterium strains, which belong to the family Oxalobacteraceae, have attracted considerable attention due to their ability to synthesize violacein and degrade polyphenols. Wild alpine rhododendrons dominate the mountainous vegetation in southwestern China, and their leaf litter decomposition contributes to humification in alpine lakes. The Janthinobacterium strains may play a key role in the decomposition of these leaf litters. In 2025, metagenomic approaches combined with isolation and cultivation methods were applied to investigate microbial resources in stacked decayed leaves from these alpine lakes. The predominant phyla are Pseudomonadota and Actinomycetota with the relative abundances of 47.9% and 39.9%, respectively. The relative abundance of genus Janthinobacterium is only 0.1% in the community, but 11 Janthinobacterium strains were isolated. Based on the ANI and phylogenomic analyses, strains Du111 and Du118 should represent a novel species, for which the name Janthinobacterium foliorum sp. nov. is proposed. The ANI and AAI values between Janthinobacterium aestuarii and Janthinobacterium violaceum are 95.5% and 97.1%, respectively, implying that the recent proposed J. violaceum is the synonym of J. aestuarii. Comparative genomic analyses further reveal that not each of Janthinobacterium strains could produce violacein and prodigiosin, but most Janthinobacterium strains have the potential for participating in the decomposition of lignin and cellulose. This study clarifies the novel role of Janthinobacterium strains, showing that the isolated strains do not represent a novel taxonomic species but have adapted to the alpine microenvironment associated with Rhododendron leaf litter.}, }
@article {pmid42297107, year = {2026}, author = {Cr, P and Krishna, V and Sethuraman, N and Nambi P, S and Ramasubramanian, V and Balaguru, P and Gopalakrishnan, R}, title = {Diagnostic utility of 16S rRNA meta genomic next-generation sequencing in clinical Infectious Diseases practice: a retrospective study from South India.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {101166}, doi = {10.1016/j.ijmmb.2026.101166}, pmid = {42297107}, issn = {1998-3646}, abstract = {OBJECTIVES: 16S rRNA sequencing is an emerging diagnostic tool for bacterial syndromes caused by fastidious pathogens and in culture negative infections. However, it can pose significant challenges from pre-analytic to post-analytic phase due to sampling issues, lack of an approved platform and test characteristics. We aimed to evaluate the diagnostic performance of 16S rRNA sequencing in sterile site samples compared to conventional microbiological techniques [CMT] and a composite reference standard [CRS] METHODS: We conducted a retrospective study at a tertiary hospital from January 2022 to July 2024. We included clinical data of patients with sterile site samples processed for both CMT and 16S rRNA sequencing. Sequencing used the Credence Genomics pipeline.<br><br>RESULTS: 166 samples met the inclusion criteria: 97 tissue, 35 pus, and 34 fluid samples. Pathogen detection rate was 42.8% [71/166] by CMT and 58.4% [97/166] by 16S rRNA. Concordance between methods was 50.6%. Sensitivity and specificity of 16S rRNA against CMT was 60.6% and 43.2%; and 69.4% and 66.7% against CRS respectively. CMT showed 54% sensitivity and 92.9% specificity against CRS. Combined testing improved sensitivity to 84.7% and accuracy was 78.9%.<br><br>CONCLUSION: 16S rRNA sequencing provides incremental diagnostic sensitivity over conventional microbiological techniques but at the cost of reduced specificity. Its routine frontline use as a standalone diagnostic tool is not supported by our findings. Instead, it may be best reserved for selected culture-negative cases with high clinical suspicion, where results can be interpreted in conjunction with clinical, radiological, and microbiological data by experienced clinicians.}, }
@article {pmid42297247, year = {2026}, author = {Yang, S and Xing, KY and Tao, YF and Wang, JY and Liu, KH and Zhang, M and Xu, XR and Zhu, L and Wei, W}, title = {Metagenomics-guided targeted isolation and mechanistic elucidation of haloalkaliphilic bisphenol A-degrading microorganisms.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135172}, doi = {10.1016/j.biortech.2026.135172}, pmid = {42297247}, issn = {1873-2976}, abstract = {Bisphenol A (BPA), a typical endocrine-disrupting compound, poses significant environmental risks. Efficient bioremediation in high-salinity and alkaline environments, such as saline-alkaline industrial wastewater and landfill leachate, remains challenging due to the lack of microorganisms capable of maintaining activity under extreme conditions. Here, this study developed a strategy integrating metagenomic functional prediction with targeted enrichment and isolation. Soil microcosm experiments combined with metagenomic analyses identified soda saline-alkaline soils with high BPA degradation potential, and predicted microbial degradation predominantly via hydroxylation, with archaeal involvement also suggested. Guided by these predictions, 14 saline-alkaline-tolerant BPA-degrading bacterial strains (13 genera) and 20 haloalkaliphilic archaeal strains (16 genera) were successfully isolated. The proportion of BPA-degrading archaea (95.24%) was higher than bacteria (58.33%), challenging the view that this function is restricted to bacteria and fungi. Genomic analyses revealed bacterium Pseudomonas reidholzensis SAS-B12 and archaeon Natronomonas gomsonensis SR-A11 degrade BPA via hydroxylation, with differing downstream ring-cleavage pathways. SR-A11 also exhibited high laccase activity, suggesting multi-enzyme synergistic degradation. Response surface methodology optimization showed SAS-B12 achieved ∼50% BPA degradation under simulated saline-alkaline wastewater (pH 8.3, salinity 2.3%), and SR-A11 achieved similar efficiency under extreme conditions (pH 9.8, salinity 23.6%). This study expands the phylogenetic diversity of BPA-degrading microorganisms and provides microbial resources, enzymatic insights, and methodological support for targeted bioremediation in saline-alkaline wastewater.}, }
@article {pmid42297252, year = {2026}, author = {Li, Q and Zhang, Q and Huang, D and Chen, S and Zhang, B}, title = {Electrically enhanced, Nature-Driven microbial attenuation of chromate and dichloromethane in groundwater.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135175}, doi = {10.1016/j.biortech.2026.135175}, pmid = {42297252}, issn = {1873-2976}, abstract = {Natural attenuation is a nature-based approach that relies on intrinsic biogeochemical and microbial processes to mitigate mixed heavy metals and organic pollutants in aquifer, yet its efficiency is limited by electron donor scarcity and suppressed microbial activity. Here, a low-energy bioelectrochemical strategy that uses a mild electric field (0.6 V) was introduced to sustainably stimulate the attenuation of chromate [Cr(VI)] and dichloromethane (DCM) co-contamination in groundwater. With minimal electrical input, Cr(VI) and DCM removal reached 95.0 ± 2.6% and 95.2 ± 0.5%, substantially outperforming the no-voltage and single-pollutant systems. The electric field alleviated electron-donor limitations and metabolic inhibition, enabling efficient and energy-conserving bioremediation. Mineralogical and spectroscopic analyses (SEM-EDS, XPS, XRD) confirmed the reduction of Cr(VI) to Cr(III) precipitates (e.g., Cr2O3) and the progressive dechlorination and mineralization of DCM. Integrated metagenomic and metatranscriptomic profiling revealed active functional guilds (e.g., Sphingopyxis, Pseudomonas, Hyphomicrobium) expressing key genes for chromate reduction (yieF, chrA), dehalogenation (dhlA, dcmA), and electron-shuttling metabolism (ribE). This work demonstrates an applicable remediation technology that can be powered by renewable electricity and integrated into secure groundwater management systems. It offers a pathway for environmentally safe pollutant mitigation by harnessing nature-based microbial processes, supporting the transition toward enhanced natural attenuation.}, }
@article {pmid42297258, year = {2026}, author = {Wei, S and Wang, L and Li, Y and Wang, B and Wang, T and Li, J}, title = {Cometabolic degradation of ofloxacin by aerobic methane oxidation coupled with denitrification: Identification of degraders, helper bacteria, and metabolic networks.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135168}, doi = {10.1016/j.biortech.2026.135168}, pmid = {42297258}, issn = {1873-2976}, abstract = {The aerobic methane oxidation coupled with denitrification (AME-D) system enables simultaneous nitrogen removal and antibiotics cometabolic degradation, yet the underlying microbial ecological mechanisms remain poorly understood. This work took ofloxacin (OFL) as a typical antibiotic pollutant and established long-term stable sequencing-batch AME-D reactors to explore their nitrogen removal efficiency and OFL degradation sustainability under antibiotic stress. A multi-omics approach combining metagenomics, metaproteomics, and metabolomics was adopted to identify the core degraders and functional helper bacteria, and unravel the synergistic metabolic interactions sustaining the system's performance. Results indicate that the AME-D cometabolic system maintains high-efficiency nitrogen removal capacity and achieves effective OFL degradation under OFL stress. The piperazine ring is the primary reactive site of OFL, undergoing ring cleavage to form intermediate products. Multi-omics results demonstrate that microbial community structure is significantly reshaped by OFL pressure. Aerobic methane-oxidizing bacteria (MOB) are identified as core degraders, which mediate OFL cometabolism via methane monooxygenase (pMMO/sMMO) and supply available electron donors. Denitrifiers and stress-tolerant auxiliary bacteria form synergistic networks by optimizing nitrogen metabolism, activating efflux pumps and regulating antioxidant defenses, which maintains system functional stability under high OFL stress. Fluorescence in situ hybridization (FISH) verification confirms that MOB, nitrifiers and denitrifiers form compact spatial interaction structures in sludge, which provide favorable conditions for interspecific substance exchange and electron transfer. This study clarifies the multi-scale functional maintenance mechanism of AME-D cometabolic system, offering theoretical support for the treatment of antibiotic-laden wastewater and ecological risk control of antibiotic resistance.}, }
@article {pmid42297276, year = {2026}, author = {Maas, MAM and Rutjes, SA and Bossers, A and Stege, PB and van der Plaats, RQJ and Kuiper, I and van der Ark, KCH and de Roda Husman, AM}, title = {Use of metagenomics for the detection of pathogens in the environment: A scoping review.}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {125050}, doi = {10.1016/j.envres.2026.125050}, pmid = {42297276}, issn = {1096-0953}, abstract = {Pathogens in the environment may pose a threat to our ecosystem and public health by causing infectious disease outbreaks. Early detection and identification are crucial for effective surveillance, outbreak prevention, and source attribution. However, analyzing environmental samples (e.g., air, soil, water, biowaste) is challenging due to their complex composition. Testing for each pathogen, known and undiscovered ones, is not possible yet. Metagenomic shotgun sequencing offers a promising approach for pathogen-agnostic DNA detection in these matrices. This review provides guidance and recommendations for experimental design, DNA extraction, library preparation, sequencing, and bioinformatics, and underscores the need for standardized protocols and inter-laboratory studies. This scoping review addresses metagenomic methodologies for pathogen detection in environmental matrices by highlighting current practices, challenges and limitations, and provides guidance for researchers and practitioners. Following the PRISMA guidelines, we identified 81 relevant studies from 6034 initial records. Most studies utilized Illumina short-read sequencing, with fewer using long-read platforms like Oxford Nanopore Technologies or Pacific Biosciences. DNA extraction protocols varied, with a trade-off between DNA yield and preserving community structure. Few studies reported inter-laboratory comparisons or standardized workflows. Selection of bioinformatics tools and reference databases significantly influenced taxonomic classification, yet reporting of analytical parameters was often incomplete. This review highlights the need for appropriate controls and increased transparency in reporting applied methods and settings. Methodological diversity and unreported gaps hinder reproducibility and comparability, while a systematic approach in environmental metagenomics holds great promise for pathogen and ecosystem monitoring.}, }
@article {pmid42297323, year = {2026}, author = {Li, Y and Hu, Y and Cheng, S and Fang, H and Guo, Y}, title = {Compound-specific effects of phthalate esters on nitrogen cycling and N2O emissions in paddy soils under contrasting moisture regimes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128593}, doi = {10.1016/j.envpol.2026.128593}, pmid = {42297323}, issn = {1873-6424}, abstract = {Phthalates (PAEs) are commonly used as plasticizers and agrochemical additives, easily released and accumulated in soils. As emerging organic pollutants, how PAEs affect soil nitrogen (N) cycling remains unclear. Here, a 91-day microcosm experiment was conducted to investigate the response of functional microorganisms and nitrous oxide (N2O) emissions to dimethyl phthalate (DMP) and di(2-ethylhexyl) phthalate (DEHP) enrichment under different moisture regimes. Metagenomic analysis showed that PAE type, rather than concentration, predominantly shaped microbial community structure and N-cycling functional profiles. Under unflooded conditions, DEHP increased cumulative N2O emissions by 42%, accompanied by enhanced nitrification potential, higher abundances of amoA and hao, and enrichment of Nitrosospira. Conversely, DMP and co-exposure treatments reduced cumulative N2O emissions by 49.24-67.86%, together with suppressed autotrophic nitrification and increased denitrification module abundance. Under flooded conditions, DMP and co-exposure increased nosZ abundance and enriched Telmatospirillum, indicating a greater potential for N2O reduction. In addition, PAE exposure increased the complexity of microbial co-occurrence networks and strengthened associations between functional taxa and N-cycling genes. Structural equation modelling showed that PAE-induced shifts in soil pH, dissolved organic carbon, and inorganic N pools jointly regulated nitrification and denitrification pathways, thereby determining N2O emission patterns. These findings highlight the potential for plasticizer contamination to reshape nitrogen transformation and nitrogen loss pathways in paddy soils under contrasting moisture regimes.}, }
@article {pmid42297331, year = {2026}, author = {Fan, S and Li, Y and Zhang, L and Xie, S}, title = {Experimental evidence for the role of phages in mitigating antibiotic resistance genes in mangrove sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128589}, doi = {10.1016/j.envpol.2026.128589}, pmid = {42297331}, issn = {1873-6424}, abstract = {The ecological role of bacteriophages (phages) in mitigating or proliferating antibiotic resistance genes (ARGs) in mangroves remains elusive due to the lack of direct experimental validation. Climate change-driven seawater encroachment introduces non-native phages into mangrove ecosystems, yet the potential impacts of this process on ARG spread have not been elucidated. Here, we established flooded microcosms inoculated with phage suspensions derived from native and non-native mangrove sediments, thus simulating phage input disturbance caused by climate change. Our results revealed distinct phage-host interaction patterns: non-native phages exerted short-term disturbances on bacterial communities, but neither phage source altered the bacterial or resistome structure. Nevertheless, phages specifically influenced the composition and dynamics of ARGs, with non-native phages showing stronger regulatory effects. Furthermore, 77 ± 2.1% of viral operational taxonomic units (vOTUs) were lytic, and 154 out of 185 phage-antibiotic-resistant bacteria (ARB) links were lytic, indicating that lytic phages played a dominant role in controlling ARB abundance and promoting ARG mitigation, whereas 0.68 ± 0.46% of host-infecting lysogenic phages carried ARGs, contributing little to ARG proliferation. Moreover, only 3.2 ± 0.56% vOTUs carried ARGs, resulting in negligible phage-mediated transduction for ARG dissemination. This study provides the first direct experimental evidence for the impacts of phages from different sources on the fate of ARGs in mangrove ecosystems, and offers novel insights into the ecological mechanisms underlying the spread of ARGs in the context of global climate change.}, }
@article {pmid42297767, year = {2026}, author = {Song, YC and Shi, C and Stratton, KG and Ayala-Ortiz, C and Stohel, I and Freire-Zapata, V and Tfaily, MM and Eloe-Fadrosh, E and Graham, EB}, title = {Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42297767}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/chemistry ; *Metagenome ; *Bacteria/metabolism/genetics/classification ; Archaea/metabolism/genetics/classification ; *Organic Chemicals/metabolism/chemistry ; }, abstract = {Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon-atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.}, }
@article {pmid42298252, year = {2026}, author = {Biter, R and Regney, M and Schmidt, AE and Swanson, N and Elrod, M and Lescroël, A and Burnham, C and Jongsomjit, D and Winquist, S and Pennycook, J and Ainley, DG and Dugger, KM and Ballard, G and Kraberger, S and Varsani, A}, title = {Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42298252}, issn = {1432-8798}, support = {1935870//National Science Foundation/ ; }, mesh = {Animals ; Antarctic Regions ; Phylogeny ; Genome, Viral ; *Papillomaviridae/genetics/isolation &amp; purification/classification ; *Papillomavirus Infections/veterinary/virology ; *Charadriiformes/virology ; *Bird Diseases/virology ; DNA, Viral/genetics ; }, abstract = {Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua (Stercorarius maccormicki) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake (Rissa tridactyla), Larus smithsonianus papillomavirus 1 from American herring gull (Larus smithsonianus) and Fratercula arctica papillomavirus 1 from Atlantic puffin (Fratercula arctica), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp. and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins (Pygoscelis adeliae), Weddell seals (Leptonychotes weddellii), Antarctic fur seals (Arctocephalus gazella), leopard seals (Hydrurga leptonyx) and emerald notothen (Trematomus bernacchii).}, }
@article {pmid42298353, year = {2026}, author = {Strokach, A and Zakharevich, N and Aginova, V and Grigoryevskaya, Z and Petukhova, I and Bagirova, N and Romanov, M and Dyachkova, M and Morozov, M and Veselovsky, V and Kanaeva, V and Kalinin, D and Larin, A and Shitikov, E and Klimina, K}, title = {Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681788}, pmid = {42298353}, issn = {1949-0984}, mesh = {Humans ; *Immunotherapy ; *Melanoma/therapy/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome ; Female ; Cohort Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Russia ; Metagenomics ; Metagenome ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; Treatment Outcome ; Adult ; }, abstract = {Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.}, }
@article {pmid42298382, year = {2026}, author = {Raj, K and Sharma, P and Riyaz, M and Shouche, YS and Multani, K and Sharma, M and Dhaliwal, M}, title = {Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05248-5}, pmid = {42298382}, issn = {1471-2180}, support = {S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; }, abstract = {BACKGROUND: The human gut microbiome consists of a complex and diverse community of commensal microorganisms and has been under extensive research consideration in the past few decades. Although several recent studies have targeted the determination of bacterial composition of the ecosystem, the knowledge about the mycobiome, virome, and functional attributes of the same remains scarce. The aim of the present study was to investigate the functional and resistome profile of the gut microbiome in the Pangwala tribal community of India using a combined Whole Metagenome Shotgun (WMS) sequencing and bioinformatics approach.<br><br>RESULTS: The findings revealed a remarkable diversity of microorganisms inhabiting the gut of both groups, with similar level of diversity among the dominant genera like Prevotella, Bifidobacterium and Succinivibrionaceae. The mycobiome was dominated by the subkingdom Dikarya (74%), while Fungi incertae sedis accounted for 23% of the total fungal species in both groups. The virome analysis showed the dominance of the Caudoviricetes class, with bacteriophages being the most dominant. Moreover, functional analysis identified the prominent metabolic pathways and the key gene families involved in the pathways, highlighting Prevotella copri as the major contributor. Additionally, the study identified the resistome and showed that there were more than 100 potential antibiotic-resistant genes (ARGs) and high levels of resistance to vancomycin in both groups.<br><br>CONCLUSION: This study presents a comprehensive overview of the gut microbiome in the Pangi population, detailing both in its taxonomic structure and functional traits. The results show that, despite the high degree of diversity in the gut microbiome, there seems to be evident functional redundancy, which underlines a core stable microbiome. The resistome profile offers complete exploratory picture of the resistome and establishes a valuable baseline for future studies. Furthermore, we anticipate that these findings will add valuable insights to understand the Antimicrobial resistance (AMR) stewardship in the light of one health aspect.}, }
@article {pmid42298622, year = {2026}, author = {Wang, F and Sang, Y and Guo, J and Fu, Y and Yang, M and Shan, F and Chen, Y and Zhang, S and Li, X and Li, J and Zhang, L}, title = {Dietary glycyrrhizic acid improves growth performance and modulates upper respiratory microbiota in weaned piglets.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05622-5}, pmid = {42298622}, issn = {1746-6148}, support = {231111111600//Henan Province Key Research and Development Plan Project/ ; 251111113300//Henan Province Key Research and Development Plan Project/ ; CARS-35//the National Pig Industry Technology System/ ; }, abstract = {BACKGROUND: Natural products with dual immunomodulatory and antimicrobial functions offer promising strategies to reduce antibiotic use in livestock. Glycyrrhizic acid (GA), the principal bioactive component of licorice, has demonstrated anti-inflammatory and antiviral properties, yet its translational potential in swine health remains underexplored. This study evaluated the efficacy of GA in weaned piglets under commercial nursery conditions as an antibiotic alternative. A total of 225 weaned piglets were assigned to five groups: negative control (CON, basal diet), farm routine (FA, conventional antibiotics), and three GA-supplemented groups (GLL, 0.65 g/kg; GLM, 1.3 g/kg; GLH, 2.6 g/kg).<br><br>RESULTS: The result showed that dietary GA supplementation (2.6 g/kg) numerically improved growth performance and reduced cough scores, although not statistically significant. GA significantly decreased the diarrhea index and improved skin scores. GA also significantly increased serum IgG and IgM levels in piglets and showed a trend toward higher IgA levels. Furthermore, GA exhibited a trend toward lowering serum IL&#x2011;1&#x3b2; levels while upregulating IFN&#x2011;&#x3b3; and IL&#x2011;10 levels. Regarding antioxidant parameters, GA significantly upregulated T&#x2011;SOD, GSH&#x2011;PX, and CAT activities and downregulated LDH activity. Metagenomic analysis revealed that high&#x2011;dose glycyrrhizic acid (GA) significantly increased the abundance of Alloprevotella, while decreasing the abundances of Moraxella pluranimalium and 11 other pathogenic species associated with respiratory diseases and lung injury, including Glaesserella parasuis, Mesomycoplasma hyorhinis, Mesomycoplasma hyopneumoniae, Streptococcus suis, among others, thereby reshaping the upper respiratory tract microbiota of pigs.<br><br>CONCLUSIONS: Collectively, these findings support GA as a viable non-antibiotic strategy for improving immune function, antioxidant capacity, and respiratory health in weaned piglets.}, }
@article {pmid42298631, year = {2026}, author = {Yan, Q and Li, M and Wang, G and Zhang, A and Li, Y and Guo, R and Zhang, Y and Yang, W and Zhang, Y and Liu, X and Li, X and Zheng, N and Wang, L and Fan, S and Ma, R and Lu, T and Zhou, S and Guan, T and Xing, G and Li, S and Wang, L and Li, Y}, title = {Cross-kingdom microbial associations characterize responsiveness to fecal microbiota transplantation in patients with irritable bowel syndrome.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08269-w}, pmid = {42298631}, issn = {1479-5876}, abstract = {BACKGROUND: Precise outcome prediction for fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) remains a clinical challenge. The roles of the gut virome and its interplay with bacteria in FMT efficacy are particularly underexplored. This secondary analysis aimed to conduct an exploratory, hypothesis-generating investigation into these cross-kingdom dynamics.<br><br>METHODS: We conducted a secondary, integrative analysis of a published cohort, performing longitudinal, cross-kingdom metagenomic profiling on 83 samples from 22 IBS patients and healthy donors. We integrative approach combined microbial diversity, species-specific biomarker identification, bacterial-viral associated networks, and exploratory random forest modeling to identify microbial features associated with FMT outcomes.<br><br>RESULTS: IBS patients showed higher bacterial and viral alpha diversity than donors. Cross-kingdom profiling identified 223 bacterial and 724 viral biomarkers. Donor-enriched biomarkers were predominantly health-associated Bacteroidetes (e.g., B. ovatus, B. faecis), whereas pre-FMT-enriched biomarkers were largely Firmicutes (e.g., B. obeum) with potential pathobiont roles. The Effect and No effect groups displayed different microbial trajectories. Although both groups shifted toward a donor-like composition initially, only responders maintained a stable donor-like ecology throughout the 12-month follow-up, supported by more resilient bacterial-viral association networks. Exploratory random forest modeling highlighted microbial features, such as R. pickettii, with high relative importance for outcome discrimination. However, permutation testing (p&#x2009;=&#x2009;0.548-0.616) confirmed that model performance on this small cohort did not exceed chance level, underscoring the risk of overfitting and the exploratory nature of these computational findings.<br><br>CONCLUSIONS: This integrative re-analysis provides preliminary evidence that cross-kingdom gut microbiome profiles are strongly associated with FMT outcomes in IBS. Successful outcomes appear linked to sustained donor-like remodeling and stable bacterial-viral networks. Our findings are primarily hypothesis-generating and offer a framework of candidate biomarkers for future validation in larger cohorts. This work underscores the necessity of external validation to develop robust, microbiome-based tools for personalized FMT therapy.}, }
@article {pmid42298685, year = {2026}, author = {Yanagawa, Y and Yoshida, N and Makiuchi, T and Kawashima, A and Uemura, H and Aoki, T and Mizushima, D and Gatanaga, H and Watanabe, K}, title = {Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00845-1}, pmid = {42298685}, issn = {1757-4749}, support = {IN-JP-380-5724//Gilead Sciences/ ; JP26K10011//Japan Society for the Promotion of Science/ ; JP23fk0108680h0001//Japan Agency for Medical Research and Development/ ; }, abstract = {Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem-particularly microbiota-derived metabolites such as secondary bile acids-supports persistent colonization remains unclear. We investigated whether gut microbiome-metabolite features are associated with Eh carriage and could influence parasite phenotypes METHODS: We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh-, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro RESULTS: Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid-driven adaptive program consistent with intestinal persistence CONCLUSIONS: Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome-bile acid-parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy.}, }
@article {pmid42298736, year = {2026}, author = {Amat, S and Holman, DB and Luecke, SM and Gzyl, KE and Anas, M and Stokka, G}, title = {The bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00587-0}, pmid = {42298736}, issn = {2524-4671}, support = {20-21-2022; 22-14-0231; 24-30-0265//North Dakota State Board of Agricultural Research and Education/ ; }, abstract = {BACKGROUND: Despite widespread use of antimicrobials and vaccines, the incidence of infectious bovine keratoconjunctivitis (IBK), or pinkeye, continues to increase in North American beef cow-calf operations. Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit Moraxella spp. in vitro. Ocular swabs (n = 143) were collected from IBK-affected (n = 102) and healthy cattle (n = 41) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including Moraxella bovoculi, Moraxella bovis, and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of Moraxella spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.<br><br>RESULTS: The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to Bacillus (25.9%), Streptococcus (11.1%), Staphylococcus (10.1%), and Moraxella (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R&#xb2; = 0.05; P&#x2009;=&#x2009;0.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included Cutibacterium acnes, Mannheimia pernigra, Mesomycoplasma bovoculi, Moraxella bovis, and Moraxella bovoculi. Eight bacterial species, including Bifidobacterium globosum and Bacillus licheniformis, were more abundant in healthy cattle, while Arthrobacter luteus was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as Mesomycoplasma bovoculi. Moraxella spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited Moraxella, with Weizmannia coagulans, Lentilactobacillus buchneri, and Paenibacillus polymyxa showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.<br><br>CONCLUSION: The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.}, }
@article {pmid42298774, year = {2026}, author = {Chen, X and Ding, S and Tang, H and Yang, Q and Yuan, L and Zhang, A and Li, Y and Wang, Q and Yan, X and Wang, Z and Wang, M and Zheng, Z}, title = {Monochromatic light reprograms transcription, metabolism, and rhizosphere microbial communities in Salvia miltiorrhiza.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2686334}, pmid = {42298774}, issn = {1559-2324}, mesh = {*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics ; *Rhizosphere ; *Light ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Transcription, Genetic/radiation effects ; }, abstract = {Salvia miltiorrhiza is a valuable medicinal plant with diverse pharmacological applications and high market demand. Light quality is a critical environmental factor regulating plant growth, secondary metabolism, and interactions with rhizosphere microorganisms. However, the effects of short-term, pure monochromatic light exposure on S. miltiorrhiza remain largely unexplored. In this study, we employed integrated transcriptomic, metabolomic, and rhizosphere metagenomic analyzes to investigate the responses of S. miltiorrhiza under different monochromatic light conditions: ultraviolet (UV), blue (B), red (R), and far-red (FR), with white light (WL) as the control. GO enrichment analysis indicated that all monochromatic light treatments activated defense responses, while specific pathways related to light stimulus, wounding, and reactive oxygen species were uniquely enriched under B, R, and FR light. Metabolomic analysis showed a general decrease in metabolite abundance under monochromatic light compared to WL, with the R treatment inducing the highest number of significantly upregulated metabolites. Integrated KEGG pathway analysis of differential transcripts and metabolites highlighted the enrichment of secondary metabolic pathways, including diterpenoid, monoterpenoid, and phenylpropanoid biosynthesis. Notably, quantitative HPLC analysis confirmed that UV, R, and FR light significantly promoted the accumulation of dihydrotanshinone I and tanshinone IIA, while decreasing salvianolic acid A content. Metagenomic analysis revealed that monochromatic light, especially B light, reduced rhizosphere microbial alpha diversity and altered the abundance of specific bacterial families and species. Functional gene annotation also showed treatment-specific shifts in microbial metabolic potential and virulence factors. In conclusion, short-term monochromatic light culture, particularly R and FR, effectively modulates the transcriptome and metabolome of S. miltiorrhiza, enhancing the accumulation of key bioactive tanshinones, while simultaneously reshaping its rhizosphere microbial community. These findings offer a potential light-based strategy for improving the quality of S. miltiorrhiza.}, }
@article {pmid42299582, year = {2026}, author = {Yu, Y and Wang, C and Pan, X and Ding, C and Chen, J}, title = {Metagenomic profiling of biliary microbiota reveals distinct microbial and functional features in cholelithiasis and cholecystic polyps.}, journal = {Medicine}, volume = {105}, number = {24}, pages = {e49251}, pmid = {42299582}, issn = {1536-5964}, support = {2022YFC2804205//National key research and development program of China/ ; }, mesh = {Humans ; *Cholelithiasis/microbiology ; *Metagenomics/methods ; *Polyps/microbiology ; *Microbiota/genetics ; Female ; *Bile/microbiology ; Male ; *Metagenome ; Middle Aged ; Aged ; }, abstract = {Cholelithiasis and cholecystic polyps are common gastrointestinal conditions, and recent studies suggest that biliary microbiota dysbiosis may be closely associated with their pathogenesis. In this small cohort (n = 11), bile samples were aseptically collected during surgery from 6 patients with cholelithiasis and 5 patients with cholecystic polyps. Metagenomic sequencing was performed to investigate differences in the microbial composition and functional profiles between the 2 groups. The results revealed that the microbial α diversity of bile from patients with cholelithiasis was significantly greater than that of the polyp group, with significant differences in the Richness, Chao1, ACE, and Shannon indices (P < .05). β-diversity analysis further revealed distinct differences in microbial community composition across the groups. Linear discriminant analysis effect size analysis revealed Pseudomonadota as the only phylum enriched in the polyp group, whereas the cholelithiasis group was enriched with multiple phyla, such as Campylobacterota, Bacillota, and Fusobacteriota, and 35 genera, such as Bacteroides, Mucilaginibacter, and Pedobacter. Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis indicated that the microbial community in the cholelithiasis group was significantly associated with neurodegenerative disease-related pathways, while the microbial community in the polyp group was enriched in pathways related to ribosomes and fluid shear stress. This study highlights the potential role of biliary microecological imbalances in the development of biliary diseases and provides a theoretical basis for exploring pathogenesis and microbiota-based therapeutic strategies.}, }
@article {pmid42299645, year = {2026}, author = {Paulsen, J and Sharrett, ST and Mumey, D and Larsen, EM and Nguyen, NK and Lendemer, J and Calabria, LM and Hoffman, JR and Magori, K and Allen, JL}, title = {Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkag153}, pmid = {42299645}, issn = {2160-1836}, abstract = {Transposable elements (TEs) have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e., dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of TEs using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradicts previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of TEs in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater TE activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving TE proliferation in rare species' genomes, and if TE content is predictive of increased extinction risk.}, }
@article {pmid42299860, year = {2026}, author = {Barandouzi, ZA and Eng, T and Khanna, N and Shelton, J and Scott, I and Patel, P and Remick, J and Jin, R and Meador, R and Bruner, DW}, title = {Gut Microbiome Associations With Depressive Symptoms in Women With Gynecologic Cancer: A Longitudinal Study.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004261461549}, doi = {10.1177/10998004261461549}, pmid = {42299860}, issn = {1552-4175}, abstract = {About one-quarter of women diagnosed with gynecologic cancer experience depressive symptoms. While the precise mechanism remains unclear, little is known about the association between gut microbiota and depressive symptoms in gynecologic cancer. Thus, this study aimed to evaluate the associations between gut microbiota and depressive symptoms in women with gynecologic cancer over cancer treatment. Thirty-seven women with cervical or endometrial cancer were followed at pre-treatment (T0), 6-8 weeks (T1), and 6 months post-radiation (T2). Depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Rectal swabs were collected at each visit and sequenced for the V4 region of the 16S rRNA gene. MaAsLin2 models evaluated cross-sectional associations between gut microbial taxa and depressive symptoms at each time point, whereas GEE models assessed longitudinal associations over the course of cancer treatment. The patients had an average age of 60 years, and 43% were Black. At baseline (T0), 24% of patients exhibited depressive symptoms, which decreased to 21% at T1 and further to 13% at T2. GEE models showed that lower α-diversity (Shannon index, p = 0.05), dissimilar β-diversity (Bray-Curtis distance, p = 0.02), and reduced abundance of the genus Ruminococcus (p = 0.02) were predictive factors associated with depressive symptoms throughout cancer treatment. Higher depressive symptoms were longitudinally associated with lower gut microbial Shannon diversity, dissimilar microbial community composition, and lower abundance of the genus Ruminococcus. Larger longitudinal studies using shotgun metagenomic sequencing are needed to validate these findings and further elucidate the microbial mechanisms underlying depressive symptoms in women with gynecologic cancers.}, }
@article {pmid42300105, year = {2026}, author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG}, title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00158k}, pmid = {42300105}, issn = {2042-650X}, abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.}, }
@article {pmid42300247, year = {2026}, author = {Götze, S and Beemelmanns, C}, title = {Advances in the discovery and functional analysis of Anti-infective and immunomodulatory natural products from host-associated microbiomes.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6np00003g}, pmid = {42300247}, issn = {1460-4752}, abstract = {Covering: 2018 to 2025Over recent years, metagenomic-driven studies have revealed an enormous encoded repertoire for the biosynthesis of secondary metabolite scaffolds within host-associated microbiota, yet only a small fraction of these chemical scaffolds has been characterized. This review focuses on recent discoveries of natural products with anti-infective and immunomodulatory properties derived from diverse host-associated microbiomes, covering the period from 2018 to 2025. The selected examples span a wide range of anti-infective and immunomodulatory activities, underscoring the deep integration of microbial secondary metabolism with host physiology, while also highlighting the need for more targeted and efficient combined approaches to fully exploit the predicted biosynthetic capacity of microbiomes for anti-infective research and beyond.}, }
@article {pmid42300737, year = {2026}, author = {Bueno de Mesquita, CP and Stallard-Olivera, E and Fierer, N}, title = {Predicting oxygen levels in microbial habitats using a metagenome-based approach.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0054526}, doi = {10.1128/msystems.00545-26}, pmid = {42300737}, issn = {2379-5077}, abstract = {Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats.IMPORTANCEOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.}, }
@article {pmid42300757, year = {2026}, author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y}, title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo01565d}, pmid = {42300757}, issn = {2042-650X}, abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.}, }
@article {pmid42300775, year = {2026}, author = {Hawkes, CG and Carroll, BO and Moylan, AD and Stiker, MEJ and Wang, T and Serrano, MG and Ridlon, JM and Miller, DP}, title = {Genomic and phenotypic insights into the novel species Selenomonas lamontii type strain ATCC 33150, currently described as Selenomonas sputigena.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0034126}, doi = {10.1128/spectrum.00341-26}, pmid = {42300775}, issn = {2165-0497}, abstract = {Selenomonas sputigena is an anaerobic, gram-negative bacterium found in the human mouth and upper respiratory tract. This organism is emerging as an important contributor to human health and disease. In the oral cavity, S. sputigena contributes to periodontitis and is associated with early childhood caries. Much of our current understanding of the genus Selenomonas and its relation to human health derives from studies of a single species, S. sputigena, and is further limited to the type strain, ATCC 35185. As S. sputigena is emerging as a significant contributor to human health, we sought to characterize the S. sputigena ATCC 33150 strain. Genomic analyses revealed that ATCC 33150, previously described as S. sputigena, is a novel Selenomonas sp., and we propose the name Selenomonas lamontii. Phenotypic comparison to S. sputigena reveals that S. lamontii grows more slowly and to a lower density in vitro. S. lamontii is more motile than S. sputigena and does not form surface-attached biofilms. Re-analysis of existing metagenomic data revealed the consistent presence of ATCC 33150 across all samples, with significantly elevated relative abundance in periodontitis-associated saliva compared to healthy donor controls. Collectively, we have identified ATCC 33150 as a new Selenomonas sp. and conducted one of the first direct comparative studies of traits relevant to colonization and persistence among Selenomonas spp.IMPORTANCERecognizing that strain ATCC 33150, historically described as Selenomonas sputigena, is a previously undescribed species has important implications for microbial systematics, physiology, and pathogenesis. Accurate taxonomic assignment underpins all downstream biological interpretation (e.g., comparative genomics, microbiome composition studies, virulence studies, and metabolic modeling). The identification of a novel species, therefore, refines the phylogenetic framework of the genus Selenomonas, enables more precise genotype-phenotype correlations, and may uncover previously unrecognized adaptations relevant to oral biofilm ecology and host interactions. Beyond taxonomy, this discovery strengthens the foundation and rigor of future mechanistic studies and provides context for discrepancies in previous studies involving this strain and ATCC 35185.}, }
@article {pmid42300931, year = {2026}, author = {Medouni-Haroune, L and Medouni-Adrar, S and Messaoudene, L and Negrichi, S and Bouiche, C and Sahraoui-Remini, Y and Allam, A and Meghlaoui, Z and Mouhoubi, K and Abbou, A and Brahimi, N and Mellal, MK and Sari, Z and Madani, K}, title = {Animal-based diets and the human gut microbiota: an integrative review combining metagenomic profiling and graphical synthesis of diet-microbiota associations.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00371k}, pmid = {42300931}, issn = {2042-650X}, abstract = {This review examines the relationships between animal-based diets, gut microbiota architecture, and human health by integrating insights from metagenomic studies and literature-based graphical representations. The gut microbiota is a complex microbial ecosystem, whose organization is closely linked to intestinal homeostasis and host health. Drawing on published metagenomic datasets, the review synthesizes patterns of dominant microbial groups and their organization within the gut, providing a framework for interpreting diet-related microbial variations across different geographic and cultural contexts. Evidence from the literature on animal-derived foods is integrated through graphical visualization to illustrate associations between specific foods and gut microbial taxa. These visualizations highlight distinct association patterns and microbial responses to various animal-based dietary components. The review discusses these patterns in relation to intestinal health, disease susceptibility, and potential dietary interventions. Overall, this work provides a structured, integrative perspective on the impact of animal-based diets on gut microbiota architecture, emphasizing the relevance of combining metagenomic insights with literature-based synthesis to inform nutritional science and public health strategies.}, }
@article {pmid42301021, year = {2026}, author = {Echeverry-Pérez, JS and Castelli, M and Muñoz-Leal, S and Nava, S and Sassera, D and Sánchez-Vialas, A and Olmeda, AS and Valcárcel, F and Uribe, JE}, title = {Genomic evolution of Francisella: metabolic innovation, endosymbiotic transitions to ticks, and biogeographic history.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag135}, pmid = {42301021}, issn = {1759-6653}, abstract = {Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provide essential B vitamins lacking in their blood-based diet. The most extensively studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. The genus Francisella encompasses endosymbionts (FE), pathogens (FP), opportunistic pathogens (FO) and free-living environmental strains (FL), making it a powerful system for evolutionary and comparative genomic analyses. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to generate new FE genomes. Seven deeply sequenced public metagenomes were also assembled, yielding 71 Francisella and three Allofrancisella strains. This dataset supported phylogenomic reconstruction and comparison of genomic features, including vitamin biosynthesis and virulence pathways, with a focus on transitions to tick endosymbiosis. A densely sampled MLST phylogeny was constructed to explore biogeographic patterns. Our results show that, except for FE, no ecological trait is monophyletic, supporting an origin of Francisella diversity from free-living ancestors. Biogeography suggests Palearctic and Afrotropical FE strains are derived and may involve horizontal transfers. Francisella comparative genomics reveals two contrasting profiles: environmental generalists and host-restricted specialists. These findings reinforce the role of tick FEs as nutritional mutualists, retaining key pathways such as riboflavin, shikimate, and biotin biosynthesis. In contrast, virulence is not ancestrally conserved but an innovation in pathogenic lineages, largely degraded in tick FEs. These results advance understanding of endosymbiont evolution and provide genomic insights with potential for disease control.}, }
@article {pmid42301089, year = {2026}, author = {Wang, H and Liang, Y and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {12}, pages = {e72059}, doi = {10.1096/fj.202601343R}, pmid = {42301089}, issn = {1530-6860}, support = {2025M780240//China Postdoctoral Science Foundation/ ; 2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, mesh = {Animals ; *Glutamates/pharmacology/administration &amp; dosage ; Female ; *Lactobacillus/drug effects/metabolism ; Signal Transduction/drug effects ; Swine ; *Proto-Oncogene Proteins c-akt/metabolism ; *Reproduction/drug effects ; *Dietary Fiber/pharmacology/administration &amp; dosage ; *Phosphatidylinositol 3-Kinases/metabolism ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; }, abstract = {The aim of this study was to investigate the combined effects of a high-fiber diet supplemented with N-carbamylglutamate (NCG) (H + N) on the gut microbiota, metabolites, and transcriptome in Landrace × Yorkshire sows using a multi-omics approach. Sows were allocated to four groups in a 2 × 2 design: Low-fiber or high-fiber diets, each with or without 0.05% NCG supplementation. The H + N treatment significantly increased litter weight at weaning. Metagenomic analysis revealed H + N significantly altered gut microbiota composition and function, particularly enriching Lactobacillus at multiple taxonomic levels from order to species (including Lactobacillus sp. 910 589 175). Plasma metabolomics identified two key lipid mediators, L-α-glycerylphosphorylcholine and taurocholic acid, whose abundances were significantly elevated by H + N and positively correlated with the enriched Lactobacillus. Transcriptomic profiling showed activation of the PI3K-Akt signaling pathway in response to H + N, which was associated with observed improvement in litter weight at weaning. Collectively, the multi-omics study uncovered a novel synergistic axis wherein H + N modulated the gut microbiome (specifically Lactobacillus enrichment), which in turn shaped the lipid metabolome to activate the PI3K-Akt pathway, ultimately enhancing sow reproductive efficiency.}, }
@article {pmid42301310, year = {2026}, author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R}, title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02805-3}, pmid = {42301310}, issn = {1432-184X}, abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.}, }
@article {pmid42301501, year = {2026}, author = {Öz, M and Üstüner, E}, title = {Omics technologies in aquafeed: unlocking the black box towards systems biology.}, journal = {Functional &amp; integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42301501}, issn = {1438-7948}, mesh = {Animals ; *Systems Biology/methods ; *Aquaculture/methods ; Multiomics ; Metabolomics ; *Fishes/genetics/metabolism/growth &amp; development ; Animal Feed ; Proteomics/methods ; Nutrigenomics ; }, abstract = {The aquaculture industry is undergoing a critical transition from marine-based to plant-based and novel protein sources. However, the physiological impacts of these dietary shifts remain largely obscured when evaluated solely by traditional performance metrics such as Feed Conversion Ratio (FCR) and Specific Growth Rate (SGR). This 'Black Box' approach fails to detect sub-clinical metabolic disorders, gut dysbiosis, and molecular stress responses until phenotypic losses occur. This review provides a comprehensive synthesis of how omics technologies - nutrigenomics, proteomics, metabolomics, and metagenomics - are elucidating the molecular mechanisms underlying fish nutrition. We examine the capacity of transcriptomics to identify early markers of soybean meal-induced enteritis and the role of proteomics in assessing muscle quality beyond mere gene expression. Furthermore, we highlight the integration of these layers into a 'Systems Biology' approach, utilizing multi-omics and bioinformatics to unravel the complex diet-microbiota-host axis. Finally, the review discusses the transition towards 'Precision Aquafeed.' It identifies the current challenges in cost, data standardization, and bioinformatics that must be overcome to implement these high-throughput tools in commercial feed formulation.}, }
@article {pmid42301503, year = {2026}, author = {Bao, W and Li, X and Pan, H and Gao, Y and Zhao, L and Liu, J and Wang, S and Zhang, Y}, title = {Detoxification mechanisms of black soldier fly larvae against microcystin-LR.}, journal = {Functional &amp; integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42301503}, issn = {1438-7948}, mesh = {Animals ; *Microcystins/toxicity/metabolism ; Marine Toxins ; Larva/microbiology/metabolism/growth &amp; development/drug effects/genetics ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; Inactivation, Metabolic ; *Simuliidae/microbiology/metabolism/genetics/growth &amp; development/drug effects ; }, abstract = {This study aimed to elucidate the detoxification mechanisms of black soldier fly larvae (BSFL) against microcystin-LR (MC-LR). Using concentration-gradient exposure (0 - 400 µg/L) and integrated metagenomic and transcriptomic analyses, we investigated the growth responses, gut microbiota alterations, and synergistic detoxification mechanisms of BSFL. The results revealed that the growth performance of BSFL was not significantly affected even at high MC-LR concentrations (400 µg/L). However, significant alterations occurred in the gut microbial composition, with increased relative abundances of Actinobacteria and Firmicutes, along with increased species richness and diversity, which correlated with increasing exposure concentrations. Functional analysis revealed that functions related to carbohydrate metabolism, energy metabolism, and substrate transport were significantly enriched in the exposed groups. Transcriptomic data further indicated that MC-LR induced intestinal oxidative stress, with significant upregulation of antioxidant-related genes (superoxide dismutase, isocitrate dehydrogenase, and peroxiredoxin 6) as well as key xenobiotic metabolism genes (carboxylesterase, glutathione S-transferase, and UDP-glucuronosyltransferase). Additionally, heat shock proteins and the Toll signaling pathway were activated. We speculate that BSFL maintains gut microbial homeostasis against MC-LR toxicity through the coordinated regulation of gut microbial communities, host antioxidant systems, xenobiotic metabolism pathways, and immune responses, providing a theoretical foundation for safe resource utilization of cyanobacteria.}, }
@article {pmid42301563, year = {2026}, author = {Xiao, Q and Chen, B and Xu, Z and Cui, Z}, title = {Endophthalmitis caused by Shinella species: the first case report.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00610-0}, pmid = {42301563}, issn = {1869-5760}, abstract = {BACKGROUND: Endophthalmitis is a severe intraocular infection associated with potentially devastating visual outcomes. Shinella, a Gram-negative bacillus commonly found in water and soil, has never been reported as a cause of human disease.<br><br>CASE PRESENTATION: A 49-year-old female farmer presented with a 7-day history of vision loss, ocular irritation, and ophthalmalgia in her right eye. She had been previously misdiagnosed and treated with high-dose systemic corticosteroids at another institution. She underwent emergent pars plana vitrectomy. Vitreous samples were analyzed using conventional culture and metagenomic next-generation sequencing (mNGS), which identified Shinella species as the predominant pathogen. Intravitreal amikacin and systemic ceftazidime were initiated on postoperative day 3 after culture confirmed Gram-negative bacilli. Two weeks of targeted antibiotic therapy resulted in complete resolution of intraocular inflammation and near-full visual recovery.<br><br>CONCLUSION: To our knowledge, this is the first reported case of intraocular infection caused by Shinella species. This case highlights Shinella as a potential ocular pathogen and demonstrates the utility of pars plana vitrectomy combined with mNGS for diagnosing atypical intraocular infections.}, }
@article {pmid42302013, year = {2026}, author = {Nayak, AR and Shukla, J and Kulkarni, S and Biswas, R and Kurkure, N and Kaore, M and Chaudhari, S and Bajpai, U and Kannan, K and Sivanesan, S and Sontakke, SD and Husain, A and Kulurkar, PM and Bafna, A and Kashyap, RS}, title = {Study protocol on antimicrobial resistance burden, transmission dynamics, and therapeutic bacteriophages in livestock and exposed farming populations in Nagpur, India: An integrated One Health approach.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350919}, pmid = {42302013}, issn = {1932-6203}, mesh = {Animals ; India/epidemiology ; Humans ; *Bacteriophages/isolation &amp; purification/physiology ; *One Health ; *Livestock/microbiology/virology ; Anti-Bacterial Agents/pharmacology ; Longitudinal Studies ; Prospective Studies ; Drug Resistance, Multiple, Bacterial ; *Drug Resistance, Bacterial ; }, abstract = {The rise in antimicrobial resistance (AMR) is a severe public health threat worldwide. India bears a disproportionately heavy burden of this problem due to ample antimicrobial usage in both humans and animals and scarce integrated surveillance. Since humans, animals, and environmental reservoirs which can harbour resistant microorganisms interact very closely on farms livestock, these are considered critical hotspots for the emergence and dissemination of antimicrobial-resistant bacteria and resistance genes. This work presents a 36-month prospective longitudinal observational study protocol aimed at quantifying the burden and characterizing the transmission dynamics of a selected set of key bacteria, that are clinically significant and hence, pathogenic-Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa-alongside their AMRprofiles in livestock, farm-exposed human populations, and environmental reservoirs in Nagpur, India, within the framework of One Health. Seasonal sampling of milk, animal faeces, human stool, soil, wastewater, drinking water, and animal feed will be carried out on dairy farms located in urban, peri-urban, and rural areas. Pathogens will be isolated using standard microbiological techniques and characterized based on antimicrobial susceptibility by employing VITEK®2 and disc diffusion methods. At the same time, bacteriophages against multidrug-resistant isolates will be isolated, purified, and characterized through plaque assays, host-range analysis, electron microscopy, and whole-genome sequencing for their therapeutic potential evaluation. Additionally, metagenomic next-generation sequencing will be utilized on a select number of samples to comprehensively characterize the resistomes and diversity of phages. The research will provide detailed longitudinal data on the frequency and spread of AMR among human, animal, and environmental compartments, create a biobank of AMR isolates and lytic bacteriophages, and offer genomic clues to delineate phage-based treatments and well-informed mitigation strategies of AMR within the framework of One Health in India. The results will be made public through peer-reviewed articles, presentations at scientific meetings, and deposition of sequence data in open-access databases.}, }
@article {pmid42302279, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Rachid, D}, title = {From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42302279}, issn = {1477-4054}, support = {//University Mohammed VI Polytechnic (UM6P), Morocco/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Biomarkers ; *Colorectal Neoplasms/microbiology/genetics ; Machine Learning ; *Precision Medicine ; Causality ; Mendelian Randomization Analysis ; Metagenomics ; }, abstract = {Human gut microbiome research has generated many disease associations, yet few translate into clinical applications. A central obstacle is not a lack of data, but the limited integration of causal reasoning, as most studies report correlations without establishing directionality, confounding control, or mechanistic evidence. We propose a unified causal inference framework that integrates directed acyclic graphs, Mendelian randomization, double machine learning, mediation analysis, and tests of causal reversibility into a single decision-aware workflow. Unlike prior applications of these tools in isolation, our framework explicitly separates assumption mapping, causal identification, effect estimation, and mechanistic interpretation, introducing "assumption guardrails" that constrain interpretation at each stage and prevent overinterpretation of observational findings. Using a colorectal cancer case study with public metagenomic data, we demonstrate how the framework operates under real-world constraints, transforming observational associations into testable, mechanism-based hypotheses. The contribution is architectural in that it organizes existing tools into a disciplined, integrated pipeline that clarifies the strength of evidence at each stage. This operational blueprint provides a reproducible path from correlation to causation in microbiome research and toward precision interventions.}, }
@article {pmid42302398, year = {2026}, author = {Xie, S and Ding, L and Liu, L and Ong, YS and Li, J and Zhu, Z}, title = {NanoSimFormer: an end-to-end Transformer-based nanopore signal simulator with basecaller guidance.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag402}, pmid = {42302398}, issn = {1367-4811}, abstract = {MOTIVATION: High-fidelity simulation of nanopore sequencing signals is critical for rigorous benchmarking and validation of the nanopore signal processing pipeline. However, existing signal simulators often fail to capture the non-linear dynamics of nanopore current signals, relying on static pore models or lacking optimization objectives tied to basecalling, resulting in synthetic signals with low basecalling accuracy and fidelity.<br><br>RESULTS: We introduce NanoSimFormer, an end-to-end Transformer-based signal simulator that integrates basecaller guidance during training to generate high-fidelity nanopore signals. NanoSimFormer achieves a median basecalling accuracy exceeding 99% and Q-scores above 22.8 for Oxford Nanopore Technologies' latest DNA R10.4.1 and direct RNA sequencing, closely mirroring real experimental baselines. It faithfully recapitulates experimental variant calling performance across the five human samples, achieving F1-scores of 0.9953-0.9973 and 0.7862-0.8612 for single-nucleotide polymorphisms and small indels detections, respectively. Compared with previous simulators, NanoSimFormer also substantially reduces false positives in homopolymer and short tandem repeat regions. NanoSimFormer-derived reads enable high-quality de novo bacterial assembly with consensus error rates below one mismatch per 100 kbp and maintain high correlations with experimental abundance in metagenomic and transcriptomic datasets.<br><br>NanoSimFormer is freely available on GitHub at: https://github.com/BioinfoSZU/NanoSimFormer.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42302503, year = {2026}, author = {Chen, Y and Yoo, S and Ahn, S and Imran, HZB and Reyes, YA and Nguyen, DV and Soltani, T and Wu, D}, title = {Mesospace-domain biochar regulates electron transfer to enhance elemental sulfur-driven autotrophic denitrification for low-carbon mariculture wastewater treatment.}, journal = {Water research}, volume = {303}, number = {}, pages = {126268}, doi = {10.1016/j.watres.2026.126268}, pmid = {42302503}, issn = {1879-2448}, abstract = {Elemental sulfur-driven autotrophic denitrification (S[0]AD) offers a promising approach for nitrate removal from recirculating aquaculture system (RAS) wastewater. However, it is constrained by the low bioavailability and restricted electron-donating kinetics of elemental sulfur (S[0]). This study developed an enhanced S[0]AD system based on mesospace-domain biochar-embedded hydrogel scaffolds (S[0]AD-BCgel) that modulated electron transfer to promote denitrification and enabled sulfur recovery. Biochar (pyrolyzed at 800 °C; charBC800) increased denitrification efficiency and kinetics by 1.5-fold and 18.1-fold, respectively, compared to the biochar-free control. The improved S[0]AD was attributed to its three synergistic roles in regulating electron transfer: (i) a biopseudocapacitor with abundant quinone functionalities and high electron exchange capacity that facilitated electron relaying; (ii) a bioconductor with graphite-like structures that stimulated interfacial electron transfer; and (iii) a biomodulator that stimulated intracellular electron transfer and promoted extracellular electron transfer in extracellular polymeric substances by enriching cytochrome c and flavin-like compounds. These coordinated properties optimized S[0] utilization and interspecific microbial interactions. Metagenome-assembled genomes (MAGs) further unveiled a shift in the denitrifying microbiota toward modularized consortia characterized by robust metabolic cross-feeding, underpinning improved S[0]AD stability. Moreover, spent hydrogels after S° consumption enable in-situ and ex-situ recovery of biogenic sulfur, supporting material reusability. These findings shed light on the mechanisms by which immobilized biochar regulated electron transfer and microbial interactions during S[0]AD within hydrogel matrices, providing valuable references for sustainable mariculture wastewater treatment and resource recovery.}, }
@article {pmid42302690, year = {2026}, author = {Li, X and Wen, S and Yu, C and Zhang, J and Xu, W and Yue, Z and Zhang, J}, title = {Dynamic evolution of the antibiotic resistome and mobilome on the microplastics of hospital wastewater.}, journal = {Journal of environmental management}, volume = {412}, number = {}, pages = {130243}, doi = {10.1016/j.jenvman.2026.130243}, pmid = {42302690}, issn = {1095-8630}, abstract = {Antimicrobial resistance is a major global health threat. Hospital wastewater serves as a significant reservoir for both microplastics (MPs) and antibiotic resistance genes (ARGs). MPs have recently been recognized not only as persistent pollutants but also as novel ecological niches for microbial colonization. However, the underlying mechanisms and key biological carriers driving MPs - mediated antimicrobial resistance transmission in hospital wastewater remain unclear. Here, we quantified the occurrence and characteristics of MPs in hospital wastewater and combined an incubation experiment with metagenomic sequencing to resolve the temporal dynamics of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) on MPs surfaces. MPs reached an abundance of 9.5 particles/L, with polyethylene (PE) dominating. Across the 28-day colonization period, with samples collected at 7, 14, 21, and 28 days, 68 ARGs, 443 MGEs and 414 VFs were detected, along with 129 prophage, highlighting the potential for enhanced horizontal gene transfer (HGT) in the plastisphere. We further reconstructed 360 metagenome-assembled genome (MAGs) spanning 16 phyla, and identified Pseudomonadota and Bacteroidota as core hosts of ARGs on MPs. Variance partitioning analysis revealed that MGEs were the major drivers of ARGs variation, independently explaining 44.4% of the dynamics. Our findings provide new insights into the ecological processes of antibiotic resistome of the MPs in the hospital wastewater.}, }
@article {pmid42302785, year = {2026}, author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X}, title = {Power and sample-size estimation in human microbiome research.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {101174}, doi = {10.1016/j.medj.2026.101174}, pmid = {42302785}, issn = {2666-6340}, abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.}, }
@article {pmid42302870, year = {2026}, author = {Zhao, J and Wang, J and Li, S and Lu, Q and Zhang, P and Qi, Y and Xu, X and Fan, J and Chen, C and Zhang, W}, title = {Chlorella pyrenoidosa reduces fecal heavy metal concentrations and antibiotic resistance gene abundance in lambs by modulating the gastrointestinal microbiota.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135186}, doi = {10.1016/j.biortech.2026.135186}, pmid = {42302870}, issn = {1873-2976}, abstract = {Using feed additives and their residues leads to the accumulation of heavy metals and antibiotics in the feces of fattening sheep, thereby posing a threat to the surrounding soil and ecological cycle. Chlorella, a novel feed raw material or additive widely applied in aquaculture, has the potential to mitigate such ecological risks. In this study, we investigated the potential of Chlorella pyrenoidosa as a dietary supplement for fattening lambs to mitigate multi-pollutant emissions from manure via gastrointestinal microbiome modulation. The results demonstrated that dietary supplementation with 3% Chlorella pyrenoidosa (W3) markedly reduced fecal concentrations of several heavy metals (Fe, Cu, Zn, Cr, As, Pb) and total phosphorus, while shifting phosphorus speciation toward more stable forms. Metagenomic analysis revealed that W3 reshaped the metabolic functional profile of the gastrointestinal microbiota and drove the succession of key microbial taxa, particularly promoting the proliferation of Clostridium and other genera in feces. Furthermore, Chlorella pyrenoidosa reduced the abundance of high-risk antibiotic resistance genes (ARGs, e.g., macB). It simplified the ARG-metal resistance gene co-occurrence network and was associated with an attenuated potential for vertical transmission of resistance genes along the digestive tract. Structural equation modeling further confirmed that pollutant reduction was closely associated with the functional remodeling of the microbiome. Thus, this study suggests that Chlorella pyrenoidosa may mitigate the environmental risks associated with heavy metals, bioavailable phosphorus, and ARGs in manure by regulating the gastrointestinal microbial ecosystem. This provides a novel strategy and theoretical basis for reducing source pollution in animal husbandry.}, }
@article {pmid42302872, year = {2026}, author = {Wang, Y and Kang, Y and Dong, J and Cheng, C and Wu, H and Guo, Z and Zhang, J}, title = {Iron-based anodes facilitate concurrent mercury removal and bioenergy generation in constructed wetland-microbial fuel cells.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135193}, doi = {10.1016/j.biortech.2026.135193}, pmid = {42302872}, issn = {1873-2976}, abstract = {Constructed wetland-microbial fuel cell (CW-MFC) is a promising technology for wastewater treatment with concurrent resource and energy recovery. However, its power generation capacity and mercury (Hg) removal efficiency are significantly limited by the insufficient electron transfer of anode materials. In this study, CW-MFCs were developed using zero-valent iron and siderite as anode materials. The incorporation of iron-based substrates significantly enhanced Hg removal, with total Hg removal efficiencies increasing by 22.9 % and 18.4 %, respectively, compared to conventional CW-MFCs. The integration of iron-based materials increased the availability of organic/inorganic electron donors by 9.1-350.0 %, thereby enhancing power generation performance by 17.9-34.9 %. This enhancement promoted the reduction of Hg(II) and inhibited the formation of methylmercury. Additionally, the electricity generated by the MFC facilitated Fe(III)/ Fe(II) redox cycling, which supported continuous corrosion and electron release from the iron anode. Metagenomic and electrochemical analyses demonstrated that the use of iron-based materials in CW-MFCs improved both extracellular and intracellular electron transfer efficiencies, and strengthened the synergistic interaction between the iron-based anode and electroactive bacteria. The genes that related to Hg(II) reduction, including merA, were also improved. Generally, this study highlights the potential of iron-based anodes to enhance Hg removal and power generation in CW-MFCs, providing a sustainable and energy-recovering strategy for wastewater treatment.}, }
@article {pmid42304204, year = {2026}, author = {Ai, X and Ren, Z and Liu, C and Zhang, C and Li, H and Ding, H and Yu, Y and Luo, W and Bi, Y}, title = {Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05306-y}, pmid = {42304204}, issn = {1471-2180}, support = {2022YFC2807605//National Key Research and Development Program of China/ ; KP202101//the Key Laboratory of Polar Science, MNR, Polar Research Institute of China/ ; MEEST-2022-03//the MNR Key Laboratory of Marine Eco-Environmental Science and Technology, China/ ; 91851201//National Natural Science Foundation of China/ ; 31971477//National Natural Science Foundation of China/ ; }, abstract = {Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. β-Diversity differed significantly between RS and GS across these three domains (P < 0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P < 0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.}, }
@article {pmid42304206, year = {2026}, author = {Pfeifer, D and Graf, M and Rurik, C}, title = {Genestrip: exact and efficient read classification for selected groups of organisms.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {42304206}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; Databases, Genetic ; *Software ; }, abstract = {BACKGROUND: The consumption of main memory resources is a significant burden in k-mer-based metagenomic analysis when creating related databases but also when performing (unique) k-mer-counting and read classification. Genestrip addresses this issue by focusing on small but freely configurable groups of organisms. Regarding the selected organisms, Genestrip produces k-mer databases and results comparable to those of KrakenUniq but at a fraction of its required memory resources. Our tool ensures that during database generation, the most suitable lowest common ancestor taxon is assigned for each stored k-mer by also considering genomes of organisms whose k-mers are not included in the database. This enables read analysis with high precision and recall for the organisms of interest.<br><br>RESULTS: We assess the correctness, usefulness and performance of Genestrip in different contexts and show that it indeed ascertains high quality read classifications for organisms whose genomes are included in a corresponding database. Our example databases comprise millions to a few billions of k-mers covering a dozen to a few thousands of species and lend themselves to usage in tick surveillance, medical diagnostics or agriculture. All databases were generated on a regular PC within hours, and related analysis performance was competitive to highly favorable. The deliberate focus on a particular set of genera or species allows for more genomes to be included from related organisms while the resulting databases remain small. Since k-mer compression becomes unnecessary, false positives emerging from related information loss are entirely avoided. We exemplify that such small but deep databases tend to improve recall during read classification while sustaining high precision.<br><br>CONCLUSIONS: Due to Genestrip's particular way of updating the k-mers' lowest common ancestor taxa, both database creation and fastq file analysis can be realized with little memory and with favorable runtimes as well as high classification quality. So both, database creation and read classification may be performed even on regular PCs. Genestrip's qualities empower users to flexibly design, build and use small k-mer databases for their own needs with potentially deep genomic coverage.}, }
@article {pmid42304260, year = {2026}, author = {Yang, X and Jing, S and Li, S and Zhang, Y and Dong, L and Zou, T}, title = {Chronic non-bacterial osteomyelitis presenting as fever of unknown origin in a child: a diagnostic pitfall.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-07002-2}, pmid = {42304260}, issn = {1471-2431}, abstract = {BACKGROUND: Chronic non-bacterial osteomyelitis (CNO), also referred to as chronic recurrent multifocal osteomyelitis (CRMO), is a rare autoinflammatory bone disorder in children and adolescents. Bone pain is the most common presenting symptom, whereas prolonged recurrent fever of unknown origin is uncommon and may mimic infection or malignancy, leading to extensive diagnostic evaluations, including invasive procedures.<br><br>CASE PRESENTATION: We report a 12-year-old girl who presented with recurrent fever as the predominant symptom, accompanied by delayed and intermittent musculoskeletal pain. Extensive infectious, rheumatologic, and oncologic investigations, including repeated cultures, metagenomic next-generation sequencing, and bone marrow examination, were unrevealing. Magnetic resonance imaging demonstrated multifocal bone marrow edema, and positron emission tomography-computed tomography showed multifocal FDG-avid skeletal lesions, with a maximum SUV of 6.85 among the focal skeletal lesions, raising concern for malignancy. Histopathological examination of a femoral bone biopsy revealed lymphoplasmacytic infiltration with focal fibrosis and no evidence of infection, granulomatous inflammation, necrosis, or malignancy. Based on the clinical course, imaging findings, exclusion of infection and malignancy, and histopathological findings, a diagnosis of CNO/CRMO was established. The patient improved after stepwise treatment with naproxen, methotrexate, and prednisone.<br><br>CONCLUSION: This case illustrates an uncommon fever-dominant presentation of pediatric CNO/CRMO with multifocal skeletal lesions mimicking malignancy. CNO/CRMO should be considered in children with fever of unknown origin accompanied by delayed musculoskeletal symptoms or multifocal bone marrow lesions. In typical cases, biopsy may be avoided when clinical and imaging findings are characteristic; however, in atypical presentations with systemic symptoms and malignancy-like imaging findings, bone biopsy may remain necessary to exclude infection and neoplastic disease.}, }
@article {pmid42304541, year = {2026}, author = {Dutta, R and Obayomi, O and Yosef, AF and Ghazaryan, L and Chalifa-Caspi, V and Lapidot, M and Gillor, O}, title = {A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00917-4}, pmid = {42304541}, issn = {2524-6372}, support = {16-38-0038//Ministry of Agriculture and Rural Development/ ; }, abstract = {BACKGROUND: Cobalamin (vitamin B12) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome.<br><br>RESULTS: Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche.<br><br>CONCLUSIONS: Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.}, }
@article {pmid42305251, year = {2026}, author = {Zicos, MH and Barnes, I and Frantz, L and Brace, S}, title = {Megaherbivore coprolite DNA: yields and comparison of three ancient DNA extraction protocols on coprolites of giant ground sloth Mylodon darwinii.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21009}, pmid = {42305251}, issn = {2167-8359}, mesh = {Animals ; *DNA, Ancient/isolation &amp; purification/analysis ; *Sloths/genetics ; }, abstract = {Coprolites offer rich potential for palaeodietary studies as snapshots of past dietary behaviour and environment. They require adapted laboratory methods to retrieve the DNA of the depositor, its microbiome, diet and environmental taxa. Here we compare the performance of three common ancient DNA (aDNA) extraction methods to recover metagenomes from coprolites of Darwin's ground sloth Mylodon darwinii from Cueva del Milodón (Chile). The Qiagen PowerSoil Kit outperformed the other two methods in terms of DNA recovery and library complexity, but the communities inferred from the DNA extracted by the three methods were similar. We were able to recover signatures of local Patagonian flora, as well as sloth mitochondrial genomes, confirming the taxonomic identity of the coprolite depositors.}, }
@article {pmid42305671, year = {2026}, author = {Wu, C and Lou, Y and Wang, L and Wang, F and Wang, X and Liu, Y and Uwaremwe, C and Li, Z and Zhang, Z and Zhu, Y and Su, X and Tian, Y}, title = {Biocontrol mechanisms of two Paenibacillus strains against Astragalus membranaceus root rot and their effects on soil microecological structure.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827299}, pmid = {42305671}, issn = {1664-302X}, abstract = {Astragalus membranaceus is an important medicinal herb in China, yet its yield and quality are severely constrained by root rot disease. In this study, two efficient antagonistic strains, HQ-1 and HQT-2, were isolated and identified as Paenibacillus polymyxa and Paenibacillus terrae, respectively. Both strains exhibited multiple plant growth-promoting traits and strong inhibitory activity against Fusarium solani (syn. Neocosmospora solani) GF-3. In vitro assays confirmed that their sterile fermentation filtrates effectively inhibited pathogen growth and damaged fungal hyphae. GFP labeling further verified their colonization potential on plant roots, while greenhouse experiments indicated preventive efficacies of 86.046% for HQ-1 and 80.619% for HQT-2. In addition, they significantly promoted the growth of A. membranaceus. Metagenomic analysis showed that biocontrol bacterium-treated soils had significantly increased relative abundance of beneficial microorganisms, alongside a reduction in phytopathogenic taxa. Notably, despite the scarcity of biocontrol reports for P. terrae, our study introduces strains HQ-1 and HQT-2 as highly effective, multifunctional resources for sustainable control of A. membranaceus root rot. This study provides much-needed systematic evidence on the efficacy of P. terrae in biocontrol, thereby addressing a notable lack of comprehensive data in the current literature.}, }
@article {pmid42306533, year = {2026}, author = {Zhang, S and Li, L and Niu, Z and Liu, M and Mao, J and Min, J and Xu, S and Li, R and Zhang, H and Yin, J and Wu, X}, title = {A large-scale retrospective analysis reveals the fungal pathogen spectrum across diverse clinical specimens using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779223}, pmid = {42306533}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation &amp; purification/pathogenicity ; Aged ; Adult ; Child ; Adolescent ; Young Adult ; *Mycoses/microbiology/diagnosis ; *Invasive Fungal Infections/microbiology/diagnosis ; Child, Preschool ; Aged, 80 and over ; Infant ; }, abstract = {INTRODUCTION: Early diagnosis of invasive fungal diseases (IFD) remains a major clinical challenge due to pathogen diversity and nonspecific symptoms. This study used metagenomic next-generation sequencing (mNGS) technology to comprehensively characterize fungal profiles across various clinical specimens and the demographic characteristics (sex and age) of the patient population. The results provide laboratory evidence to support the diagnosis and treatment of fungal infections.<br><br>METHODS: A total of 11,161 mNGS reports from clinical specimens collected at the Renmin Hospital of Wuhan University between March 2022 to August 2024 were retrospectively analyzed. Fungal spectra and patient demographics were comprehensively profiled and compared across different specimen types.<br><br>RESULTS: The highest fungal detection rate was observed in bronchoalveolar lavage fluid (36.85%, 1,985/5,387), followed by urine (22.76%, 264/1,160), blood (13.38%, 380/2,840), pleural and peritoneal fluid (12.91%, 174/1,348), cerebrospinal fluid (CSF) (13.82%, 17/123), and wound exudates (12.87%, 39/303). Candida species were the most frequently detected fungi across all specimen types except CSF, wherein Aspergillus predominated. Overall fungal detection rates were significantly higher in male patients than in female patients (26.76% vs. 23.84%, P&#xa0;<&#xa0;0.01) and in individuals aged > 60 years compared with those aged &#x2264; 60 years (33.04% vs. 20.02%, P&#xa0;<&#xa0;0.001), although this trend varied by specimen type. Multivariate logistic regression analysis confirmed that male sex (adjusted odds ratio [aOR]=0.893,95% confidence interval: 0.824-0.967, P&#xa0;=&#xa0;0.006) and advanced age (&#x2265;80 years: aOR=14.77,95% confidence interval: 12.08-18.06, compared with minors) were independent risk factors for fungal detection. Among fungal-positive specimens, 68.28% (1,952/2,859) were co-detected with bacteria, and 15.63% (447/2,859) showed polyfungal detection (&#x2265; 2 fungal species).<br><br>CONCLUSION: In conclusion, our findings highlight the predominance of Candida and Aspergillus, identify elderly male patients as a high-risk population, and underscore the high frequency of bacterial-fungal co-detection. Overall, Clinicians should combine mNGS results with imaging, conventional fungal tests (G/GM assays, culture), and clinical presentation for a more accurate diagnosis of IFD.}, }
@article {pmid42306745, year = {2026}, author = {Hang, M and Liu, Y and Shen, X and Zhao, Y and Xu, Y and Gong, X and Xu, L and Li, N and Dong, L}, title = {The clinical and translational perspectives on the lung microbiome in interstitial lung diseases: a bibliometric review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {5}, pages = {478}, pmid = {42306745}, issn = {2072-1439}, abstract = {BACKGROUND: Increasing evidence suggests that microbiota plays important roles in the pathogenesis and progression of interstitial lung diseases (ILDs). However, the global research landscape and emerging trends in this field remain insufficiently characterized. This study aimed to systematically characterize the research landscape, evolving hotspots, and future trends in the field of host microbiota and ILDs using bibliometric and visualization approaches, and to further explore the progress of related clinical studies.<br><br>METHODS: Publications up to November 8, 2025 were retrieved from the Web of Science Core Collection. Concurrently, clinical trials within the same timeframe were extracted from PubMed to assess advancements in the field. Bibliometric and visual analyses were conducted using VOSviewer, CiteSpace, SCImago Graphica, and Microsoft Excel.<br><br>RESULTS: A total of 295 publications were included, showing a marked increase in research output since 2012. China and the United States were the leading contributors, with the United States demonstrating higher academic impact and stronger international collaboration. Core institutions and authors were mainly concentrated in North America and Europe. Keyword analysis revealed a clear evolution of research focus, shifting from early exposure-related studies and hypersensitivity pneumonitis to lung microbiome dysbiosis, the gut-lung axis, and metagenomic approaches. Recent hotspots emphasize microbiome-based clinical applications, with increasing attention to host-microbiome interactions and immune regulatory mechanisms.<br><br>CONCLUSIONS: Research on microbiota and ILDs has expanded rapidly and shows increasing interdisciplinary integration. Future studies should enhance international collaboration, clarify underlying mechanisms, and promote clinical translation of microbiome-based biomarkers and personalized therapeutic strategies.}, }
@article {pmid42306944, year = {2026}, author = {Abaeva, IS and Pestova, TV and Hellen, CUT}, title = {Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites.}, journal = {Nucleic acids research}, volume = {54}, number = {11}, pages = {}, pmid = {42306944}, issn = {1362-4962}, support = {R01 GM097014/NH/NIH HHS/United States ; R21 AI188505/NH/NIH HHS/United States ; R35 GM122602/NH/NIH HHS/United States ; }, mesh = {*Internal Ribosome Entry Sites ; *RNA, Viral/chemistry/metabolism ; Nucleic Acid Conformation ; Ribosomes/metabolism ; *Dicistroviridae/genetics ; Genome, Viral ; Base Sequence ; *Peptide Chain Initiation, Translational ; }, abstract = {Viral internal ribosomal entry sites (IRESs) are highly structured cis-acting RNAs that mediate end-independent initiation of translation. Their origin remains obscure. The simplest IRESs (type 6) occur in the intergenic region of Dicistroviridae genomes (order Picornavirales), consist of two pseudoknots, and initiate translation by factor-independent binding to ribosomes. Larger variants contain a third pseudoknot that modifies the mechanism of IRES function by engaging with the ribosomal head and promoting binding to the ribosomal aminoacyl site. Metagenomic analyses undertaken to identify structurally distinct type 6 IRESs identified subsets ranging from ∼120-260 nt in length. They differ by the cumulative addition of structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication, and form additional subdomains. Biochemical analysis showed that these novel classes of type 6 IRES all bound directly to the ribosomal peptidyl site. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of type 6 IRESs at the 5'-end of dicistrovirus-like genomes and in families other than Dicistroviridae, including Marnaviridae (order Picornavirales) and Tombusviridae (order Tolivirales).}, }
@article {pmid42306954, year = {2026}, author = {Lee, D and Norton, NJ and Dale, AP}, title = {Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {42306954}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Conventional microbiological tests have limitations in the microbial diagnosis of immunocompromised patients. Next-generation sequencing (NGS) technologies have the potential to overcome some of these challenges by enabling rapid, comprehensive, and hypothesis-free pathogen detection, potentially improving the speed and accuracy of microbial diagnosis and subsequent clinical outcomes. This review summarizes current evidence for the use of NGS technologies in immunocompromised populations, highlights areas of demonstrated clinical impact, and identifies key priorities for broader clinical integration.<br><br>RECENT FINDINGS: Case reports and series have demonstrated the utility of NGS in diagnosing unusual or atypical infections amongst immunocompromised patients that were initially missed by conventional methods. Retrospective observational studies indicate that NGS can achieve higher sensitivity and greater pathogen detection rates than conventional diagnostics, although performance may be limited for certain pathogens, such as Aspergillus and Mycobacterial species. The clinical impact of NGS-guided interventions varies, reflecting both differences in study design and challenges in interpreting metagenomic data.<br><br>SUMMARY: NGS technologies have the potential to enhance microbial diagnosis in immunocompromised patients, particularly in complex, polymicrobial, or atypical infections where conventional methods fail. However, widespread clinical adoption is limited by high costs, complex workflows, and the need for advanced bioinformatics infrastructure and expertise. Further research is required to define clinical impact, cost-effectiveness, and to standardize workflows and guide optimal time for implementation, in order to inform evidence-based integration of NGS into routine clinical practice.}, }
@article {pmid42307633, year = {2026}, author = {Carasso, S and Kasher-Dvora, M and Gefen, T and Geva-Zatorsky, N}, title = {Phase variation-mediated bacterial functional plasticity as a lens for understanding microbe‒host interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687913}, doi = {10.1080/19490976.2026.2687913}, pmid = {42307633}, issn = {1949-0984}, mesh = {Humans ; *Host Microbial Interactions ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/physiology ; *Bacterial Physiological Phenomena ; Animals ; }, abstract = {The human gut microbiome represents a dynamic microbial ecosystem profoundly influencing host physiology, immune development, and disease susceptibility. While metagenomic approaches have advanced our understanding of microbial composition and functional potential, they remain insufficient to capture the real-time molecular events governing host‒microbe interactions. Taxonomic abundance and genomic content alone do not reflect active gene expression or phenotypic output, and functional roles cannot be reliably inferred from phylogenetic identity, given the substantial heterogeneity observed even within species. Central to bridging this gap is the concept of bacterial functional plasticity, with a focus on phase-mediated functional plasticity, the intrinsic capacity of microbes to rapidly remodel their activity and phenotype in response to environmental and host-derived cues. This review highlights phase variation as a prominent and evolutionarily conserved mechanism underlying plasticity, encompassing DNA inversions, short-sequence repeat modifications, and broader structural genomic variation. Emerging evidence demonstrates not only the prevalence of phase-variable mechanisms across diverse gut taxa but also their significant regulatory, ecological, and immunological consequences. These findings reframe the microbiome from a static consortium of species to a functionally dynamic system capable of rapid rewiring in response to environmental pressures. By integrating genomic, ecological, and host-response data, this review lays the groundwork for mechanistic frameworks that could explain how flexible microbial strategies influence bacterial behavior and host outcomes. Moving beyond cataloging microbial composition toward deciphering the logic of functional adaptation will be essential for translating microbiome research into predictive, diagnostic, and therapeutic applications.}, }
@article {pmid42307846, year = {2026}, author = {Gomes, RF and García, GJY and Cardoso, MS and Dutra, JDCF and de Abreu Waldow, V and Akamine, RN and de Sousa, MP and Groposo, C and Brenig, B and Figueiredo, H and de Carvalho Azevedo, VA and Góes-Neto, A}, title = {Metagenomics and metatranscriptomics of prokaryotic and fungal microbiomes in produced water associated with petroleum degradation and pipeline corrosion from an oil terminal in Brazil.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42307846}, issn = {1573-0972}, mesh = {*Fungi/genetics/classification/metabolism/isolation &amp; purification ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Petroleum/metabolism/microbiology ; *Metagenomics ; Biodegradation, Environmental ; Corrosion ; Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Water Microbiology ; Hydrocarbons/metabolism ; Phylogeny ; }, abstract = {The prokaryotic microbial communities involved in hydrocarbon degradation and associated with oil pipeline corrosion have been extensively studied. Nonetheless, fungi can perform significant metabolic activities in these environments. Studies evaluating metabolically active microbial communities in oil reservoirs are limited. Our study investigated the total/DNA and active/RNA communities of Archaea, Bacteria, and Fungi in produced water samples from an onshore terminal in Brazil. DNA and RNA were sequenced using the Illumina HiSeq 2500 platform, and the meta-omics sequences were analyzed. Shannon alpha diversity (taxonomic and functional) revealed that total communities were more diverse than metabolically active ones, with Bacteria showing higher diversity than Archaea and Fungi. The bacterial genera Syntrophotalea (sulfur reducer) and Pseudodesulfovibrio (sulfate reducer) were most prominent in total communities, while Halanaerobium (acid producing) dominated active communities. These results confirm the presence of Microbially Influenced Corrosion (MIC); however, the aprAB and dsrABC genes showed very low expression. Methanogenic Archaea Methanocalculus, Methanoplanus, and Methanothrix were frequent in both total and active communities, and mcrABDG genes were significantly expressed in metatranscriptomic sequences. Fungal genera Absidia, Penicillium, and Rhizopus were dominant in DNA samples, whereas Saccharomycodes, Pichia, Coemansia, and Schizosaccharomyces dominated RNA samples. These fungi can remediate environments contaminated with recalcitrant hydrocarbons. Despite the limited information obtained from fungal functional profile, an in-depth investigation of their activities and interrelation with Archaea and Bacteria in oil reservoirs is crucial for monitoring and mitigating oil biodegradation and pipeline biocorrosion processes.}, }
@article {pmid42307995, year = {2026}, author = {Laiton, L and Acevedo, FE}, title = {Gut microbiome of the grape berry moth, Paralobesia viteana (Lepidoptera: Tortricidae) larvae through the grape ripening process revealed by high-throughput 16S and 18S rRNA sequencing.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42307995}, issn = {2057-5858}, mesh = {Animals ; *Vitis/parasitology/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; *Moths/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {The grape berry moth (GBM) Paralobesia viteana (Lepidoptera: Tortricidae) is an important pest of grapes in eastern North America. The larvae damage grape clusters by direct feeding and by increasing susceptibility to fungal and bacterial pathogens. In this study, we sequenced the V3-V4 region of the 16S rRNA gene and the V4 region of the 18S rRNA gene to characterize the composition and diversity of GBM larval gut bacterial and fungal communities when fed on immature and mature 'Concord' grapes. The data were analysed with QIIME 2, and downstream analyses included taxonomic composition, differential abundance, phylogenetic, functional and alpha/beta diversity analyses. While overall bacterial community diversity did not differ significantly between treatments, differential abundance analysis identified specific bacterial taxa enriched in each larval group. Ninety-three per cent of the bacterial communities belonged to the phylum Proteobacteria, and some may play roles in amino acid and carbohydrate metabolism in the insect gut. Analyses of the 18S rRNA region showed significant taxon-level compositional differences in fungal communities between larvae grown on grapes at different ripening stages. Ascomycota was the dominant phylum (98%) present in the guts of larvae fed on mature grapes, while larvae fed on immature grapes mainly contained fungi within the Cryptomycota (51%). Larvae fed on ripe grapes had a 10-fold higher fungal abundance and were enriched in Saccharomycetales yeasts. Several of the identified microbial taxa in larval guts are commonly found in grapes, which suggests they might be transient insect residents that are ingested with the diet. In conclusion, diet strongly shaped GBM gut-associated fungal communities; specific bacterial taxa also differed between larval groups despite similar overall bacterial diversity. These results contribute to basic knowledge of gut-associated microbes in fruit-feeding insects.}, }
@article {pmid42308045, year = {2026}, author = {Cornman, A and Tranzillo, M and Zulaybar, NG and Bouzit, I and Hwang, Y}, title = {Linear-time prediction of proteome-scale microbial protein interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {25}, pages = {e2610619123}, doi = {10.1073/pnas.2610619123}, pmid = {42308045}, issn = {1091-6490}, support = {GBMF13344//Gordon and Betty Moore Foundation (GBMF)/ ; G-24-67500//Schmidt Futures (Schmidt Futures Projects, LLC)/ ; }, mesh = {*Proteome/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; *Protein Interaction Mapping/methods ; Prediction Algorithms ; Computational Biology/methods ; Protein Interaction Maps ; }, abstract = {Protein-protein interactions (PPIs) underpin biological function, yet proteome-scale interaction prediction remains bottlenecked by the quadratic computational complexity of all-vs.-all pairwise comparisons. Here, we present FlashPPI, a contrastive learning framework, grounded in residue-level interactions, that enables linear-time prediction of physical protein interfaces across a microbial proteome. By leveraging a genomic language model that captures cross-protein coevolutionary signals from metagenomic sequences, FlashPPI aligns interacting partners in a shared latent space. We demonstrate a four-fold performance increase over existing sequence-based methods, while reducing proteome-wide screening time from days to minutes. Crucially, FlashPPI achieves comparable screening performance to state-of-the-art structure-folding models at a fraction of the computational cost. Finally, we integrate FlashPPI into an interactive web platform that combines predicted networks with functional annotations and genomic context, making proteome-wide network analysis rapid and accessible for microbial discovery.}, }
@article {pmid42308105, year = {2026}, author = {Zuffa, S and Allaband, C and Charron-Lamoureux, V and Caraballo-Rodriguez, AM and Patan, A and Mohanty, I and Agongo, J and Bostick, JW and Connerly, TJ and Thron, T and Needam, BD and de Castro Fonseca, M and Benitez, RS and Hansen, L and Tubb, H and Cao, J and Kalecký, K and Bottiglieri, T and MahmoudianDehkordi, S and Schimmel, L and Kueider-Paisley, A and Graham, SF and Siegel, D and Wang, M and Knight, R and Kaddurah-Daouk, R and Dorrestein, PC and Mazmanian, SK and , }, title = {A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117499}, doi = {10.1016/j.celrep.2026.117499}, pmid = {42308105}, issn = {2211-1247}, abstract = {The etiology of Alzheimer's disease (AD) remains unclear but is likely driven by gene-environment interactions. We present a multi-organ untargeted metabolomics atlas (n = 2,271) paired with metagenomics data (n = 666) from two AD transgenic mouse models (3xTg and 5xFAD) under colonized and germ-free conditions. Systems-level analyses revealed clusters of dysregulated molecules across tissues, including carnitines, bile acids, B vitamins, neurotransmitters, and N-acyl lipids. Metabolic shifts were associated with the depletion of Akkermansia muciniphila and enrichment of Mucispirillum schaedleri in the 3xTg model. We identify previously unexplored carnitines linked to microbial metabolism of phenylalanine. Using tissueMASST-a mass spectrometry search tool we developed to translate animal-model findings into a human clinical context-we trace phenylacetyl-carnitine in human plasma and serum samples (n = 1,470) from independent cohorts, revealing associations with aging, cognitive impairment, and diminished memory performance. This public resource and associated tools will aid future research in AD etiology.}, }
@article {pmid42308119, year = {2026}, author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P}, title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42308119}, issn = {2057-5858}, mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation &amp; purification/genetics ; Metagenomics/methods ; Proteomics ; }, abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.}, }
@article {pmid42308338, year = {2026}, author = {Ong, CJN and Nazari, R and Cabuhat, KSP and Ogaya, JB and Ahmed, MM and Shomuyiwa, DO and Musa, SS and Daberechi, OJ and Abdi, YH and Dulay, RMR and Lucero-Prisno, DE}, title = {The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag064}, pmid = {42308338}, issn = {1574-6941}, abstract = {The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes present in pathogenic and non-pathogenic microorganisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.}, }
@article {pmid42308739, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Hoerr, FJ and Robinson, K and Hauck, R}, title = {Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107215}, doi = {10.1016/j.psj.2026.107215}, pmid = {42308739}, issn = {1525-3171}, abstract = {This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 d-old YP x Ross 708 male broilers were assigned to eight treatments. These included an unchallenged control and a challenged control, followed by six dietary treatments applied to challenged broilers. The dietary treatments consisted of fiber supplementation with oat hulls (OH) or soy hulls (SH), either alone or in combination with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. While the enteric challenge induced significant histopathological changes, fiber combinations including OH-WM and OH-SBP significantly (P < 0.05) reduced cumulative pathology scores. The challenge caused a shift toward Lactobacillus crispatus dominance in the microbiome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis. Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes APOB, DSEL, and ENPP7, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. These findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.}, }
@article {pmid42308920, year = {2026}, author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC}, title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {201}, number = {}, pages = {119656}, doi = {10.1016/j.biopha.2026.119656}, pmid = {42308920}, issn = {1950-6007}, abstract = {BACKGROUND &amp; AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.<br><br>METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n&#x202f;=&#x202f;27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.<br><br>RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p&#x202f;<&#x202f;0.05), and increased the respiratory exchange ratio (p&#x202f;<&#x202f;0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p&#x202f;<&#x202f;0.05), while antioxidants primarily reduced adipose tissue (p&#x202f;<&#x202f;0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p&#x202f;<&#x202f;0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p&#x202f;<&#x202f;0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.<br><br>CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.}, }
@article {pmid42309017, year = {2026}, author = {Yang, X and Liu, W and Mao, Y and Wang, H}, title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.}, journal = {Ecotoxicology and environmental safety}, volume = {320}, number = {}, pages = {120390}, doi = {10.1016/j.ecoenv.2026.120390}, pmid = {42309017}, issn = {1090-2414}, abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.}, }
@article {pmid42309163, year = {2026}, author = {Sutthiboonyapan, P and Jungpraditphol, I and Krasaesin, A and Khamwachirapitak, C and Choi, Y and Porntaveetus, T and Wiriyakijja, P}, title = {Supragingival Plaque Microbiome Composition Associated with Oral Lichen Planus Activity and Desquamative Gingivitis Severity: An Exploratory, Cross-Sectional, Shotgun Metagenomic Study.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1824444}, pmid = {42309163}, issn = {1305-7456}, abstract = {OBJECTIVES: The microbial contribution to desquamative gingivitis (DG), a frequent and debilitating form of immune-mediated oral lichen planus (OLP), remains undefined. This study employed shotgun metagenomic sequencing to investigate the role of the oral microbiome in DG site involvement and severity, as well as OLP disease activity.<br><br>MATERIALS AND METHODS: In this exploratory, cross-sectional study, supragingival plaque samples were collected from nine OLP patients at desquamative gingivitis-affected sites (DG sites), sites not affected by desquamative gingivitis (non-DG sites), and pooled full-mouth samples. Shotgun metagenomic sequencing was performed to reveal oral microbial profiles and their functional pathways. Disease severity was assessed using the Oral Lichen Planus Disease Activity Scale (OLP-DAS) and the Desquamative Gingivitis Clinical Score (DGCS).<br><br>STATISTICAL ANALYSIS: Associations between microbial profiles and disease severity were assessed using Spearman's correlation. Microbial and functional pathway profiles were compared between DG and non-DG sites using the paired Wilcoxon signed-rank test. A p-value <0.05 was considered statistically significant.<br><br>RESULTS: Significant differences in microbial composition between DG and non-DG sites were identified, including 6 genera and 17 species (p&#x2009;<&#x2009;0.05). Several taxa showed notable correlations with disease severity (r&#x2009;&#x2265;&#x2009;0.7), according to DGCS, with 10 genera and 16 species positively associated with DGCS, and 5 genera and 8 species associated with OLP-DAS. Notably, the fructan biosynthesis pathway showed a significant inverse correlation with DG severity (r&#x2009;=&#x2009;-&#x2009;0.70, p&#x2009;<&#x2009;0.05) and was linked to Actinomyces sp. oral taxon 448, which was enriched in DG sites. This suggested that increasing disease severity may be associated with reduced microbial polysaccharide-production potential.<br><br>CONCLUSIONS: The DG microbiome shows distinct functional and taxonomic changes. Fructan biosynthesis was more abundant in DG sites than in non-DG sites, but showed an inverse correlation with DG severity, highlighting candidate biomarkers and potential therapeutic targets.}, }
@article {pmid42309238, year = {2026}, author = {R, K and Chandra, A and Pal, S and Tiwari, H and Shekhar, A and Agarwal, R}, title = {Microbial Dysbiosis in Oral Potentially Malignant Disorders: A Systematic Review.}, journal = {Journal of stomatology, oral and maxillofacial surgery}, volume = {}, number = {}, pages = {102876}, doi = {10.1016/j.jormas.2026.102876}, pmid = {42309238}, issn = {2468-7855}, abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs) including oral leukoplakia (OLK), proliferative verrucous leukoplakia (PVL), and oral verrucous hyperplasia (OVH) pose variable malignant transformation risk to oral squamous cell carcinoma (OSCC), yet the role of microbial dysbiosis in their progression remains ambiguous.<br><br>OBJECTIVES: To elucidate microbial shifts in OPMDs, their association with dysplasia progression and malignant transformation, highlighting prospects for early detection and risk stratification.<br><br>MATERIAL AND METHODS: A comprehensive literature search was conducted across scientific databases up to May 2025. Studies investigating microbial dysbiosis in OLK, PVL, or OVH using 16S rRNA sequencing, metagenomic, or transcriptomic analyses were included. Risk of bias was assessed using the modified Newcastle-Ottawa scale.<br><br>RESULTS: OPMDs showed inconsistent alpha diversity and distinct beta diversity compared to controls. Microbial composition differed by lesion type: OLK was enriched with Fusobacterium periodonticum, Porphyromonas pasteri, Streptococcus, and Haemophilus; PVL with Campylobacter concisus, Leptotrichia, and Haemophilus parainfluenzae; and OVH with Porphyromonas gingivalis, Tannerella forsythia, and Saccharibacteria TM7. High-risk OLK showed reduced diversity and enrichment of Fusobacterium nucleatum, Parvimonas, and Streptococcus infantis. Malignant transformation revealed lesion-specific shifts, including increased Fusobacterium, Capnocytophaga and Porphyromonas in OLK-OSCC, while Neisseria was specifically enriched in progressive OLK lesions, Treponema and Campylobacter in PVL-OSCC, and Capnocytophaga sputigena and Prevotella oris in OVH-OSCC.<br><br>CONCLUSION: This review highlights the pivotal role of microbial dysbiosis in the evolution of OPMDs to malignancy. Distinct microbial signatures across OLK, PVL, and OVH may serve as biomarkers for disease stratification and early detection of high-risk lesions.}, }
@article {pmid42309478, year = {2026}, author = {Maya, MA and Raboni, SM and Giamberardino, HIG and Nogueira, MB and Giamberardino, ALG and Ferreira, LH and Torrecilha, VT and Pereira, LA and Usuga, J and Aristizabal-Valencia, M and Vasquez, A and Berg, MG and Rebolledo, PA and Averhoff, F and Cloherty, GA and Hernandez-Ortiz, JP and Osorio, JE}, title = {Clinical and Genomic Characterization of Pediatric Adenovirus-Associated Severe Acute Respiratory Infection: A Binational Study from Brazil and Colombia, 2022-2023.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108893}, doi = {10.1016/j.ijid.2026.108893}, pmid = {42309478}, issn = {1878-3511}, abstract = {BACKGROUND: Human adenovirus (HAdV) is detected in fewer than 10% of hospitalized children with acute respiratory infections, yet several regions reported unusual increases in 2021-2022. We investigated an HAdV outbreak detected through surveillance in Curitiba, Brazil, and Antioquia, Colombia, comparing clinical and genomic characteristics before and during the outbreak.<br><br>METHODS: We conducted a multicenter observational study of HAdV-associated severe acute respiratory infection in hospitalized children. Respiratory samples collected between February 2022 and April 2023 underwent metagenomic sequencing and hexon gene analysis. Clinical and phylogenetic analyses evaluated viral dynamics and genetic diversity.<br><br>RESULTS: A HAdV outbreak occurred in both regions during late 2022. HAdV-C predominated before the outbreak, whereas HAdV-B3 became the dominant genotype at both sites during the outbreak. During the outbreak, bronchiolitis/asthma exacerbation was most common in Antioquia, whereas pneumonia predominated in Curitiba. Phylogenetic analysis of the hexon gene identified two distinct HAdV-B3 clades that diverged from a shared ancestor but expanded independently in Brazil and Colombia.<br><br>CONCLUSION: Following relaxation of non-pharmacological measures, both regions experienced a substantial rise in HAdV-B3-associated disease. Despite increased case numbers, clinical patterns remained stable within sites but differed between regions. Integrated genomic and clinical surveillance provides important insights into adenovirus lineage expansion and outbreak dynamics.}, }
@article {pmid42309606, year = {2026}, author = {Silverstein, J and Chapman, A}, title = {Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {24}, number = {2}, pages = {100702}, pmid = {42309606}, issn = {2090-5920}, abstract = {Ancient DNA (aDNA) research has revolutionised archaeology and forensic science by enabling genomic recovery from highly degraded remains. This review explores the biochemical and environmental factors influencing aDNA preservation, alongside methodological advances that have improved data yield and authenticity. Techniques such as next-generation sequencing (NGS), single-stranded library preparation, and hybridisation capture have transformed the field, allowing recovery from ultrashort fragments and challenging contexts such as warm climates. Authentication strategies-including cytosine deamination profiling, fragment length analysis, and rigorous contamination controls-remain essential to ensure reliability. Applications of aDNA extend beyond ancestry reconstruction and population genetics to include forensic identification, kinship analysis, and pathogen detection. Lessons from forensic genetics, such as stringent validation and contamination mitigation, have informed best practices in archaeological contexts. However, ethical considerations are central to both domains. Issues of Indigenous data sovereignty, consent, repatriation, and culturally sensitive interpretation demand transparent, community-led research frameworks. These principles align with international agreements such as the Nagoya Protocol and emerging guidelines for equitable benefit-sharing. Despite significant progress, challenges persist, including geographic sampling bias, interpretive uncertainty, and the need for interdisciplinary integration. Future directions emphasise long-read sequencing, metagenomic approaches, and artificial intelligence-driven analytics, alongside robust ethical governance. By combining technological innovation with culturally responsible practices, aDNA research continues to advance our understanding of human history while reinforcing the importance of ethical stewardship in forensic and archaeological science.}, }
@article {pmid42309718, year = {2026}, author = {Sakiyama, Y}, title = {[Metagenomic analysis for central nervous system infections: clinical utility and future directions].}, journal = {Rinsho shinkeigaku = Clinical neurology}, volume = {}, number = {}, pages = {}, doi = {10.5692/clinicalneurol.cn-002248}, pmid = {42309718}, issn = {1882-0654}, abstract = {Encephalitis and meningitis are neurological emergencies in which delayed diagnosis may lead to severe neurological sequelae, necessitating accurate and rapid etiological identification. In recent years, metagenomic next-generation sequencing (mNGS), which enables comprehensive analysis of microbial genomes without prespecified hypotheses, has attracted increasing attention. Its clinical application in neuroinfectious diseases has contributed to improved diagnostic yield and the detection of rare pathogens. In particular, mNGS has been shown to be useful in clinically challenging situations such as culture-negative cases, anaerobic infections, mixed infections, and immunocompromised hosts. However, the technology also has inherent limitations, including enormous data volume, challenges in interpreting pathogenic relevance, limited turnaround time, high cost, and a lack of standardized analytical pipelines. Thus, although mNGS represents a valuable complementary tool to conventional diagnostic methods, it is not universally applicable, and its results must be carefully interpreted within appropriate clinical contexts.}, }
@article {pmid42311379, year = {2026}, author = {Saito, Y and Sato, S and Sasanami, Y and Yamashita, T and Yamada, M}, title = {Heterologous expression and structural characterization of polyamide 4-degrading enzyme from a soil bacterium.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1811100}, pmid = {42311379}, issn = {1664-302X}, abstract = {Polyamide 4 (PA4) is a bio-based plastic with thermal stability, excellent mechanical properties, and good biodegradability in various environments. To understand the biodegradation of PA4 under natural environments, PA4-degrading microorganisms and enzymes have been investigated. Although our previous research identified the amino acid sequence and predicted the three-dimensional (3D) structure of a PA4-degrading enzyme from a marine environment (Nyl4A pa), those of an enzyme from terrestrial environments have remained unidentified. In this study, we identified the PA4-degrading enzyme gene (nyl4Apx) from the PA4-degrading soil bacterium Pseudoxanthomonas sp. TN-N1. In addition, nyl4Apx was successfully expressed in Escherichia coli BL21(DE3) and Brevibacillus choshinensis HPD31-SP3. The PA4-degrading activity of the enzyme secreted by recombinant B. choshinensis HPD31-SP3 reached 68.8 Δ655 nm/h/100 mL broth, representing a 2.4-fold increase compared with that produced by recombinant E. coli BL21(DE3). Based on a homology search using the amino acid sequence and predicted 3D structure of the enzyme, Nyl4A px was predicted to be composed of a substrate-binding domain, a middle domain, and a catalytic domain. Among these domains, the substrate-binding and catalytic domains of Nyl4A px are sequentially and structurally similar to those of Nyl4A pa . Furthermore, putative homologs of Nyl4A px and Nyl4A pa were found in marine-associated environmental metagenomes through BLAST searches. To our knowledge, this is the first report describing the structural properties of a PA4-degrading enzyme from a soil bacterium.}, }
@article {pmid42311675, year = {2026}, author = {Zhang, H and Fan, B and Ma, R and Jiang, R and Qin, Z and Qu, X and Wang, J and Xue, J and Wang, C and Liu, X and Guo, L}, title = {Gut microbiota and sepsis-associated acute kidney injury: a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1724266}, pmid = {42311675}, issn = {1664-3224}, mesh = {Humans ; *Acute Kidney Injury/microbiology/etiology/therapy/immunology ; *Sepsis/complications/microbiology/immunology ; Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Intestinal Barrier Function ; Signal Transduction ; }, abstract = {BACKGROUND: Sepsis-associated acute kidney injury (SA-AKI) carries high morbidity and mortality, yet its pathogenesis remains incompletely understood. Emerging evidence underscores the gut-kidney axis as a critical pathway in SA-AKI development.<br><br>OBJECTIVE: This review aims to synthesize current knowledge on how sepsis-driven gut dysbiosis compromises intestinal barrier integrity and contributes to SA-AKI, and to explore potential therapeutic strategies targeting the gut microbiota.<br><br>METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus databases for publications between 2005 and 2026. Studies focusing on gut-kidney crosstalk mechanisms in sepsis/AKI were included. Key findings from human and animal studies were summarized.<br><br>RESULTS: Sepsis induces marked gut dysbiosis characterized by loss of microbial diversity and expansion of pathobionts. This dysbiosis compromises intestinal barrier integrity, facilitating translocation of bacterial products such as lipopolysaccharide (LPS). Upon entering circulation, these mediators activate systemic inflammation and renal signaling cascades, including the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-&#x3ba;B) pathway, leading to tubular injury and impaired renal function. Recent human metagenomic studies have identified specific microbial signatures associated with AKI, such as increased Clostridium asparagiforme and decreased Roseburia spp., alongside elevated uremic toxin-producing bacteria like Gordonibacter pamelaeae. Additionally, gut-derived metabolites including indoxyl sulfate, p-cresol sulfate, and trimethylamine N-oxide (TMAO) have been implicated in promoting renal inflammation and fibrosis. Importantly, renal dysfunction further disrupts gut homeostasis, establishing a pathological gut-kidney feedback loop. Targeting the gut-kidney axis via fecal microbiota transplantation, probiotic supplementation, or short-chain fatty acid administration may offer novel therapeutic avenues.<br><br>CONCLUSIONS: Sepsis induces gut microbiota dysregulation play an important role in the development of SA-AKI. The intestine-kidney crosstalk may provide a basis for the treatment of sepsis-induced organ injury and also provide new ideas for the treatment of SA-AKI.}, }
@article {pmid42311883, year = {2026}, author = {Tan, S and Liao, Q and Wen, Y and Zhu, Y}, title = {Case Report: Invasive pulmonary aspergillosis caused by Aspergillus lentulus in a boy with chronic granulomatous disease.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1813957}, pmid = {42311883}, issn = {2296-858X}, abstract = {Aspergillus lentulus is a slow-growing and drug-resistant fungus, which has been primarily reported in adults, usually immunocompromised ones, suffering from invasive pulmonary aspergillosis (IPA). This condition is rare in children. Here, we report a case of invasive pulmonary aspergillosis due to Aspergillus lentulus in a boy with no history of recurrent infections who presented with a prolonged fever of unknown origin. Based on chest CT scan findings showing typical halo signs, a fungal infection was strongly suspected. Empirical antifungal therapy was initiated at early admission but failed to resolve the persistent fever in this case. The causative pathogen was confirmed by blood metagenomic next-generation sequencing (mNGS). Subsequent genetic analysis identified a pathogenic mutation in the X-linked CYBB gene, confirming chronic granulomatous disease (CGD). Eventually, following a combination therapy of voriconazole and micafungin, the boy became afebrile and was discharged, pending hematopoietic stem cell transplantation (HSCT). To our knowledge, no previous cases of Aspergillus lentulus infection in children with CGD have been reported in the literature. This case underscores the critical importance of identifying the causative microorganism. It also highlights the value of emerging detection methods, such as mNGS. At present, there is no consensus for the optimal antifungal regimen against pediatric Aspergillus lentulus infections. Clinical improvement was achieved in this patient following combination therapy with voriconazole and micafungin, offering a practical therapeutic reference for managing this refractory fungal infection.}, }
@article {pmid42312035, year = {2026}, author = {Radzieta, M and Malone, M and Schwarzer, S and Bergamin, E and Whitely, G and Jensen, S}, title = {Anaerobe-associated microbial shifts at infection onset in diabetes-related foot ulcers revealed by longitudinal metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812721}, pmid = {42312035}, issn = {2235-2988}, mesh = {Humans ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; *Microbiota ; Longitudinal Studies ; Male ; Female ; Aged ; Middle Aged ; Metagenome ; }, abstract = {INTRODUCTION: Diabetes-related foot infections (DRFIs) are a major cause of hospitalisation and carry a significantly increased risk of lower extremity amputation. To date there is a lack of longitudinal studies examining within-patient microbiome dynamics during the transition from non-infected to infected diabetes-related foot ulcers (DRFUs).<br><br>METHODS: We used shotgun metagenomic sequencing to longitudinally profile the wound microbiome of 6 patients with DRFUs who developed clinical infections, utilising taxonomic profiling, metagenome assembly and binning and strain level analysis to characterise within-patient microbial shifts.<br><br>RESULTS: DRFUs with no signs of clinical infection were colonised by virulent pathogens including Staphylococcus aureus, Streptococcus agalactiae, Enterococcus faecalis, Enterobacter hormaechei and Pseudomonas aeruginosa. In most patients, infection onset was associated with a decrease in pathogen abundance and a significant increase in obligate anaerobes including Prevotella spp, Peptoniphilus spp, Porphyromonas spp and Anaerococcus spp.<br><br>CONCLUSION: These findings highlight the potential importance of anaerobes and hypoxia in DRFIs and may support monitoring of tissue oxygen saturation as a predictor of infection onset.}, }
@article {pmid42312150, year = {2026}, author = {Sabogal-Rodriguez, D and Caro-Quintero, A}, title = {PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag150}, pmid = {42312150}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-species genetic variation can reveal adaptive evolution, selection pressures, and ecological dynamics that are hidden when MAGs are treated as homogeneous entities. Existing tools address individual analysis steps in isolation, requiring manual integration and creating barriers for researchers without extensive bioinformatics expertise.<br><br>RESULTS: Here we present PopMAG, a Nextflow pipeline and interactive Shiny application that automates population genetics analysis of MAGs. PopMAG integrates quality control, community profiling, competitive read mapping, functional annotation, and microdiversity estimation into a single reproducible workflow. The pipeline calculates key population genetics metrics including nucleotide diversity (&#x3c0;), p N / p S ratios, fixation index (F S T), Levins' index and SNVs counts with results consolidated into an interactive visualization platform for metadata-driven exploration. We demonstrate PopMAG's utility through analysis of longitudinal cystic fibrosis lung metagenomes, where we identify patterns consistent with antibiotic-driven selection in Pseudomonas aeruginosa efflux pump genes coinciding with treatment intervention.<br><br>PopMAG and corresponding documentation are publicly available at https://github.com/daasabogalro/PopMAG.}, }
@article {pmid42312179, year = {2026}, author = {Chen, X and Xue, CX and Wang, J and Wang, S and Su, M and Liu, R and Zhu, XY and Liu, J and Yao, P and Fu, L and Yang, Z and Greening, C and Todd, JD and Zhang, XH}, title = {Metagenomic expansion of Joyebacterota identifies Cavimicrobium, a dominant sulfide-producing lineage in anoxic marine ecosystems.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag137}, pmid = {42312179}, issn = {2730-6151}, abstract = {Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.}, }
@article {pmid42312182, year = {2026}, author = {Wang, Z and Zhu, Y and Liu, X and Li, Z and Bai, J and Zou, M and Zhang, C and Liu, Y and Li, F and He, K}, title = {iSymBase: an integrative functional-genomic platform for ecological exploration of insect symbionts.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag128}, pmid = {42312182}, issn = {2730-6151}, abstract = {Insect symbionts play essential roles in host biology, influencing nutrition, immunity, reproduction, and environmental adaptation, ultimately shaping insect physiology, ecology, and evolution. With the rapid growth of functional and genomic datasets on insect symbionts, there remains a critical need for a dedicated platform to systematically compile, organize, and analyze these datasets from an integrative ecological perspective. Here, we developed an insect Symbiont database, named as iSymBase, by manually curating functional records and genomic datasets of insect symbionts from published academic literature. Currently, iSymBase contains over 2657 insect symbiont functional records spanning 795 host species, along with 1494 metagenomes, 14 992 amplicon datasets, and standardized genome and gene catalogs, providing a comprehensive resource for ecological and comparative insect symbiont researches. iSymBase offers standardized query functionalities, such as data browsing, keyword associative search, sequence alignment, data download, and submission. Beyond conventional database functionalities, iSymBase provides several innovative tools: insect-symbiont interaction network for host-symbiont ecological relationships, a batch annotation tool for detecting ecologically functional symbionts from microbiome profiles, and an artificial intelligence (AI)-powered chatbot iSymSeek designed to assist researchers with related knowledge queries. Taken together, iSymBase will serve as an open-access and continually updated platform for storing, querying, and analyzing insect symbiont data, supporting ecological exploration of host-symbiont interactions, symbiont functional diversity, and microbiome-driven adaptation. Database URL: http://symbiont.insect-genome.com/.}, }
@article {pmid42312183, year = {2026}, author = {Zheng, YL and Guo, YS and Ren, XY and Wang, YF and Cui, HL and Zhang, LM and Ding, LJ and Zhu, YG}, title = {Unveiling the role of soil microorganisms in indicating paddy soil health via metagenomics combined with machine learning.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag133}, pmid = {42312183}, issn = {2730-6151}, abstract = {The soil microbiome performs various ecological functions, making it a potentially vital component of soil health assessment; however, the indicator taxa of soil health remain unidentified. This study explored these taxa in paddy soils of the black soil region in Northeast China. First, the soil health index (SHI) was evaluated using representative physicochemical and biological parameters, revealing that approximately one-third of the soils had a low health level. A Random Forest model was then developed based on microbial species' relative abundance to predict the SHI, achieving an R [2] value greater than 0.6. Based on the SHapley Additive exPlanations values of this model, 40 microbial species were identified as potential indicator taxa of soil health, with 39 of these taxa occurring in more than 50% of the samples. Specifically, paddy soils with more abundant carbon (C)- and nitrogen (N)-fixing bacteria exhibited higher soil organic matter and total N contents, along with higher health levels. Conversely, soils rich in denitrifying bacteria exhibited lower SHI values because of increased N loss. Furthermore, C-fixing, N-fixing, and denitrifying genes showed functional relationships with the corresponding soil properties and SHI. In addition, halophilic, halotolerant, and eutrophic bacteria indicated soil health by reflecting salinity and nutrient status. The potential of these indicator taxa was validated at multidecadal and regional spatial scales. These results highlight the practical value of such indicator taxa, which elucidate the ecological processes associated with soil health and respond predictably to changes in soil health, thereby serving as rapid diagnostic tools for assessing soil health.}, }
@article {pmid42312244, year = {2026}, author = {Heidrich, V and Fackelmann, G and Ricci, L and Spadazzi, R and Baldanzi, G and Punčochář, M and Catassi, G and Marchi, P and Modesto, M and Piccinno, G and Porcari, S and Rondinella, D and Asnicar, F and Valles-Colomer, M and Mattarelli, P and Ianiro, G and Segata, N}, title = {Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.}, journal = {Cell press blue}, volume = {1}, number = {3}, pages = {None}, pmid = {42312244}, issn = {3051-3839}, abstract = {Interpersonal strain transmission shapes the human microbiome, yet a comparative understanding of the transmission dynamics across body sites is lacking. We analyzed 1,644 paired oral and fecal metagenomes to investigate microbiome transmission among healthy cohabitants and intra-individual oral-gut overlap. Cohabitants shared significantly more oral and gut strains than non-cohabitants. Romantic partners exhibited the highest oral strain-sharing rates, exceeding their gut strain sharing. Higher oral transmissibility was associated with increased longitudinal strain replacement, while the most transmissible gut species were linked to poorer cardiometabolic health. Within individuals, 74.5% of cases of species detected in both sites involved the same strains, primarily related to abundant oral species such as Streptococcus salivarius, suggesting saliva-mediated transmission. Conversely, Bifidobacterium longum strains never overlapped between sites, with the recently proposed B. longum subsp. nexti uniquely colonizing the oral cavity. These findings extend our understanding of microbiome spread and its potential consequences for human health.}, }
@article {pmid42312840, year = {2026}, author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG}, title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0031925}, doi = {10.1128/cmr.00319-25}, pmid = {42312840}, issn = {1098-6618}, abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.}, }
@article {pmid42312855, year = {2026}, author = {Lim, SJ and Thompson, LR and Goodwin, K}, title = {Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0079926}, doi = {10.1128/aem.00799-26}, pmid = {42312855}, issn = {1098-5336}, abstract = {UNLABELLED: The Gulf of Mexico/Gulf of America provides ecosystem services derived from marine biodiversity and oil and gas resources. Threats posed by unintended releases of oil and gas can be attenuated by microbial processes, necessitating the documentation of baseline microbial diversity to better understand spill dynamics and to inform bioremediation strategies. Here, we analyze metagenomic sequencing of 10 water column samples collected from the Green Canyon 233 (GC233) lease block near the mussel-fringed brine lake, Brine Pool NR-1. Bioinformatics processing produced 60 bacterial metagenome-assembled genomes (MAGs), 11 archaeal MAGs, 149 microbial taxa predicted from assembled full-length small subunit (SSU) rRNA genes, and 389 microbial genera predicted from single-copy marker genes. Abundant taxa classified from these analyses included archaeal Nitrosopumilaceae, Nitrosopelagicus, and Thalassarchaeaceae and the bacterial taxa Pelagibacteraceae and SAR324. The MAGs revealed genes that degrade gaseous and non-gaseous hydrocarbons, including methane, other alkanes, and aromatic compounds. These samples were collected in 2009, fortuitously prior to the 2010 Deepwater Horizon (DWH) oil spill. Therefore, we searched for members of the rare biosphere that dominated the DWH plume during the early phase of microbial succession. Sequences related to Bermanella spp. were not detected initially. The search was expanded by mapping reads from ours and an additional 55 metagenomic libraries to two Bermanella MAGs. Read recruitment to Bermanella sp913054445 enriched in DWH plume samples was low (<1%) for our samples, those collected after the spill, and most experimental samples compared to samples collected outside (3%) and inside the DWH plume (19%-23%) during the spill.<br><br>IMPORTANCE: Microbes execute oil spill biodegradation through complex interactions involving whole microbiome communities by harnessing genes distributed across multiple taxa. Therefore, metagenomic data sets provide taxonomic and functional annotations to aid in understanding spill dynamics. Although the Deepwater Horizon oil spill provided opportunities to observe ecosystem recovery, data about the microbiome prior to the spill are scarce and limited to amplicon sequencing. Our metagenomic libraries, although not derived from the same lease block as the blowout, contribute linkages between microbial taxonomy and function in an area of active oil and gas production. This analysis can aid microbial indicator development, machine learning, and modeling efforts to bioremediate hydrocarbon influxes in marine environments.}, }
@article {pmid42313157, year = {2026}, author = {Cardenas Alegria, OV and Torres, MC and Breyer, GM and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Ramos, RTJ and Dorn, M and Kich, JD and Siqueira, FM}, title = {Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42313157}, issn = {1432-0991}, mesh = {Animals ; Swine ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Soil Microbiology ; *Manure/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ponds/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Soil/chemistry ; Metagenomics ; Genes, Bacterial ; *Microbiota ; }, abstract = {The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.}, }
@article {pmid42313166, year = {2026}, author = {Taguchi, R and Ebihara, A and Tsunematsu, Y and Jeelani, G and Suzuki, R and Nozaki, T and Suenaga, K and Iwasaki, A}, title = {Discovery, Genome-Guided Structure Elucidation, and Total Synthesis of Terukufazoline A, a Macrocyclic Docosapeptide, from a Marine Cyanobacterium.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.6c06625}, pmid = {42313166}, issn = {1520-5126}, abstract = {The structure elucidation of large molecules remains a central challenge in natural products chemistry. This challenge has been addressed through spectroscopic methods as well as degradative and synthetic approaches, which have provided effective solutions. Recent advances in genome analysis have enabled an orthogonal approach to structure elucidation based on biosynthetic gene information. In this study, we report the structure elucidation of an unprecedentedly large cyanobactin, terukufazoline A (1), through integration of spectroscopic analysis, metagenome-guided biosynthetic information, chemical degradation, and total synthesis. Terukufazolines A (1) and B (2) were discovered from an undescribed marine cyanobacterium, and the intractable NMR and tandem MS data for 1 prompted us to incorporate biosynthetic gene information. Metagenomic analysis identified the cyanobactin biosynthetic gene cluster, whose core peptide sequence enabled the assignment of the amino acid sequence of 1. The absolute configuration was established by degradation-based analyses, and the proposed structures were verified by convergent total syntheses of 1 and 2.}, }
@article {pmid42313402, year = {2026}, author = {Louine, M and Dandekar, R and Reddy, SP and Karalius, MC and Waldrop, G and Wang, S and Gakuru, J and Kimuda, S and Mugabi, T and Musubire, AK and Kagimu, E and Abassi, M and Kabahubya, M and Williams, DA and Phan, HV and Dai, B and Zia, M and Zorn, KC and Fouassier, C and Gerungan, C and Marra, PS and Skipper, CP and Bahr, NC and Langelier, CR and Creswell, FV and Boulware, DR and Meya, DB and Wilson, MR}, title = {Cerebrospinal fluid transcriptional immune pathways linked to survival in HIV-associated tuberculous meningitis.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag313}, pmid = {42313402}, issn = {1537-6613}, abstract = {BACKGROUND: TB meningitis (TBM) has up to 50% mortality in people living with HIV. We investigated differences in cerebrospinal fluid (CSF) host immune responses associated with short-term mortality.<br><br>METHODS: We enrolled a prospective cohort of adults with definite, probable and possible HIV-related TBM in Kampala, Uganda. Metagenomic next-generation sequencing (mNGS) of bulk CSF RNA was used to detect co-infecting or alternate CNS pathogens and refine cohort diagnosis. Host transcriptomic profiles from the refined cohort were then compared between 14-day survivors and non-survivors.<br><br>RESULTS: CSF mNGS reclassified or excluded 14% of participants based on pathogen detection, yielding 110 participants for transcriptomic analysis, of whom 23% (n=25) died within 14 days. More than 2000 genes were differentially expressed in the CSF based on 14-day mortality (adjusted p-value <0.05). Survivors upregulated T-cell receptor signaling (LCK, FYN, LAT), T-cell survival and differentiation (IL7, CD27, IL12RB1), B-cell receptor signaling (CD81, PLCG2, TNFRSF13C), cytotoxic lymphocyte and NK cell genes (KLRD1, ULBP1), TNF signaling, and class I MHC antigen processing pathways, while downregulating neutrophil chemoattractant CXCL1 and classical complement genes C4A and C4B. Unsupervised clustering identified a hypoinflammatory subgroup with significantly elevated mortality.<br><br>CONCLUSIONS: Short-term TBM survival was associated with upregulation of adaptive immunity - including T-cell, B-cell, NK cell, and cytotoxic lymphocyte signaling - alongside TNF signaling and IFN-&#x3b3;-driven class I MHC antigen processing pathways, with concurrent restraint of complement and neutrophil pathways. This supports investigation of targeted immunomodulatory agents that preserve protective responses while selectively dampening injurious innate pathways, rather than broad immunosuppression with corticosteroids.}, }
@article {pmid42313512, year = {2026}, author = {Han, M and Zhao, H and Lai, J and Zhao, S and Dong, B and Xi, H}, title = {Succession and Functional Adaptation of Bacterial and Fungal Communities in Biological Soil Crusts Responding to Uranium Stress.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70359}, doi = {10.1111/1462-2920.70359}, pmid = {42313512}, issn = {1462-2920}, support = {22106182//National Natural Science Foundation of China/ ; 2022YFC3702500//National Key Research and Development Program of China/ ; SKLNBC2023-03//State Key Laboratory of NBC Protection for Civilian/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification/genetics ; Adaptation, Physiological ; Biodegradation, Environmental ; *Soil Pollutants, Radioactive/metabolism ; *Microbiota ; Stress, Physiological ; }, abstract = {Uranium (U) mining causes severe radioactive contamination threatening ecosystems. Biological soil crusts (BSCs), as pioneer communities in degraded habitats, show strong heavy metal accumulation potential, yet their adaptive mechanisms under U stress remain unclear. In this study, BSCs from a uranium tailings dam in Hunan Province were exposed to simulated U stress. Results showed that BSCs exhibited exceptionally high U accumulation capacity (up to 4131 mg/kg), and effectively immobilised U by converting it into residual and organic-bound fractions (collectively > 70%) via carboxyl complexation and microbial mineralisation, thus significantly reducing environmental mobility. U stress caused damage to the photosynthetic and antioxidant systems of the BSCs. Microbial community complexity decreased, with tolerant taxa including Proteobacteria and Bacilli significantly enriched. Metagenomics revealed distinct cross-kingdom functional adaptation strategies: bacteria upregulated energy metabolism and acetaldehyde metabolism to facilitate efflux detoxification, while fungi strengthened lipid homeostasis and antioxidant metabolism. Several U-tolerant strains (Bacillus, Aspergillus and Penicillium) closely associated with U immobilisation were further isolated and verified. This study systematically reveals the synergistic tolerance mechanisms of BSCs under U stress and provides key microbial resources and theoretical support for the in situ bioremediation of U-contaminated sites.}, }
@article {pmid42313858, year = {2026}, author = {Meijer, S and Hugerth, LW and Nouri, M and Erlandsson, L and Lavasani, S and Hansson, SR}, title = {Comparative analysis of gut microbiome alterations in early- and late-onset preeclampsia: A case control study.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0348943}, pmid = {42313858}, issn = {1932-6203}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Dysbiosis/microbiology ; Metagenomics ; Bacteria/classification/genetics ; }, abstract = {Preeclampsia (PE) is a complication during pregnancy characterized by hypertension, organ damage, and systemic inflammation. Increasing evidence suggests that the gut microbiome may play a role in the pathophysiology of PE. However, previous studies on the gut microbiome have generally overlooked the distinction between subgroups of PE, although clinical manifestations may differ. Also, most studies have not used deep sequencing techniques. Therefore, this study aimed to explore further potential differences in gut dysbiosis in different PE subgroups compared to controls using shotgun metagenomics. We studied the bacterial gut microbiome using shotgun metagenomic sequencing in 37 pregnant patients in the third trimester from a Swedish cohort, separating patients according to subtype (healthy controls N = 21, late-onset PE N = 8, early-onset PE N = 8). Differential relative abundances and alpha diversity were evaluated using Wilcoxon rank sum test, and beta diversity was evaluated using PERMANOVA. Multiple linear regression was used to study associations between gut microbiome composition differences and clinical parameters. Late-onset PE and early-onset PE were both associated with significantly different beta diversity compared to controls. Differences remained significant after adjusting for age, and were not affected by gestational age, BMI or parity. Alpha diversity was lower in late-onset PE compared to controls. While no significant differences in taxonomic abundances were seen after correcting for multiple testing, several interesting leads were identified, including a higher abundance of genus Blautia in late-onset PE, and lower abundance of Coprococcus catus and unclassified Lachnospiraceae in early-onset PE. Functional analysis did not reveal any significant differences after false discovery rate (FDR) correction. In conclusion, our results showed subgroup-specific gut microbiome differences in PE with more pronounced associations in late-onset PE, despite limited power due to the observational design and small cohort. Accordingly, our results highlight the importance of subgroup analysis when studying PE.}, }
@article {pmid42314068, year = {2026}, author = {Lytras, S and Ghafari, M and Grove, J}, title = {Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction.}, journal = {Annual review of virology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-virology-100424-122154}, pmid = {42314068}, issn = {2327-0578}, abstract = {High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically been bottlenecked by experimental determination. The recent revolution in artificial intelligence (AI) structure prediction has fundamentally changed this, enabling the rapid generation of millions of viral protein structures. This review examines the effect of AI-based protein structure prediction methods on our understanding of deep viral evolution. We describe the strengths and limitations of protein structure prediction and consider the questions it can be used to address: illuminating viral dark matter in metagenomic datasets, resolving high-level taxonomy for orphan lineages, and inferring function for divergent proteins. Furthermore, we assess the emerging field of structural phylogenetics, exploring the theoretical and practical challenges of integrating structure and sequence to reconstruct ancient evolutionary events. We conclude that despite remaining challenges, systematic structure prediction will extend our exploration of deep evolution across the virosphere.}, }
@article {pmid42314322, year = {2026}, author = {Zhang, P and Zhu, Y and Wang, Z and Yu, P and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Tan, C and Wu, F and Peng, Q}, title = {Initial exploration of the health effects on Qinghai-Tibetan Plateau yaks following short-term exposure to polystyrene microplastics: Analysis of rumen microbiota, host metabolism, antioxidant function and inflammatory responses.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142707}, doi = {10.1016/j.jhazmat.2026.142707}, pmid = {42314322}, issn = {1873-3336}, abstract = {Microplastics (MPs) are ubiquitous across environments including the Qinghai-Tibet Plateau. Most existing MPs studies focus on aquatic animals and rodents, while MPs influences on yaks (Bos grunniens) remain poorly understood. Using yaks as animal models, we combined metagenomics and metabolomics to explore short-term polystyrene-MPs (PS-MPs) impacts on ruminal microbiota, metabolism, antioxidant capacity and inflammation. Seven-day PS-MPs exposure reshaped rumen microbiota and elevated β-diversity. Four KEGG pathways (peptidoglycan synthesis, vitamin B6/riboflavin metabolism, terpenoid backbone biosynthesis) were enriched alongside altered extracellular polysaccharides composition. Serum metabolomics revealed elevated L-glutamine and indole-3-propionic acid, coupled with reduced 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and indole-3-lactic acid post-exposure. Urinary metabolomics revealed decreased D-erythrose 4-phosphate, dimethyl allyl pyrophosphate, and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate, collectively indicating inhibited terpenoid backbone biosynthesis in yaks. Additionally, PS-MPs triggered inflammatory responses, evidenced by elevated levels of pro-inflammatory cytokines (interferon-γ, interleukin-1β, interleukin-6, interleukin-17, interleukin-22, tumor necrosis factor-α, transforming growth factor-α), yet antioxidant function indexes (total antioxidant capacity, superoxide dismutase, glutathione peroxidase, catalase and malondialdehyde) showed no significant changes. Multi-omics suggested Prevotella ruminicola may help resist PS-MPs invasion. In summary, rumen microbes may alleviate PS-MPs adverse effects, explaining yaks' mild responses to short-term PS-MPs exposure. Long-term MPs effects, tissue deposition and related molecular mechanisms warrant further study.}, }
@article {pmid42315104, year = {2026}, author = {Itoh, H and Mise, K and Kuniyasu, M and Wasai-Hara, S and Ushijima, N}, title = {Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag157}, pmid = {42315104}, issn = {1751-7370}, abstract = {Acidobacteriota, one of the most abundant and ubiquitous bacterial phyla in soils, are well recognized for their role in carbon cycling. In contrast, their roles in soil nitrogen cycling remain largely unexplored, although recent metagenome-assembled genome (MAG) analyses suggest that Acidobacteriota may harbor genes involved in nitrogen cycling. Here, we provide culture-based evidence of diazotrophy within this phylum and demonstrate the widespread occurrence of nitrogen-fixing Acidobacteriota across diverse soil types. From grassland and agricultural soils, we isolated five Acidobacteriota strains representing novel taxonomic lineages, four of which harbor functional nitrogenase (nif) gene clusters. These strains were capable of fixing atmospheric nitrogen in vitro and/or in soil microcosms, as evidenced by acetylene reduction, N2-dependent growth, transcription of nif genes, incorporation of 15N into biomass and soil, and inhibition of nitrogenase activity by ammonium. Furthermore, global-scale meta-analysis of soil metagenomes revealed that nif-harboring Acidobacteriota are widely distributed and locally dominant across soil types. These results demonstrate the nitrogen-fixing capability of Acidobacteriota at the organismal level, complementing MAG-based inferences, and underscore their adaptive capacity in nitrogen-limited environments and their potential contribution to terrestrial nitrogen fixation. We also propose novel taxa within the class Terriglobia of the phylum Acidobacteriota, including diazotrophic strains, comprising one novel family, three novel genera, and four novel species: Koromonadaceae fam. nov., Koromonas soli gen. nov., sp. nov., Koromonas humicola sp. nov., Oryzophilus luti gen. nov., sp. nov., and Humiphilus diazotrophicus gen. nov., sp. nov.}, }
@article {pmid42315187, year = {2026}, author = {Benga, L and Rehm, A and Gougoula, C and Bischoff, S and Janssen, S}, title = {Is the Microbial Status an Extrinsic, Intrinsic, or Intermediate Influence on Experimental Animals?.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {}, number = {}, pages = {1-4}, doi = {10.30802/AALAS-JAALAS-26-036}, pmid = {42315187}, issn = {2769-6677}, abstract = {Living entities, inlcuding laboratory animals, are composed of the host and its associated microbial communities and defined as holobionts. The host genotype and its microbiome drive together as a metagenome, the holobiont phenotype, with the microbiome itself as a well-recognized source of phenotypic variation. Multiple environmental (diet, light/dark cycles, etc.) as well as host-related factors (genotype, maternal effect, etc.) not only influence the animal experimental phenotype but also contribute to the shaping of the microbiome, raising the question of whether the microbiome of experimental animals represents an extrinsic, intrinsic, or intermediate influence. Currently, there is sufficient evidence that microbial communities at different body sites are shaped by distinct endogenous and exogenous factors, indicating that the host does not leave its microbial status to chance but instead actively modulates it through host-specific mechanisms, despite extrinsic influences. This leads to a microbiome that reflects a 'fingerprint' of its own endogenous and exogenous influences. This suggests that the microbiome of experimental animals is an intermediate factor with both intrinsic and extrinsic components and underscores the importance of refining the selection of the appropriate metagenome for each specific rodent experiment.}, }
@article {pmid42315257, year = {2026}, author = {Cramer, C and Marshall, IPG and Abramson, MJ and Jõgi, NO and Khomich, M and Peddada, SD and Skottvoll, BS and Schlünssen, V and Bertelsen, RJ}, title = {Role of oral bacteria composition and functional gene profiles in respiratory diseases.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003938}, pmid = {42315257}, issn = {2052-4439}, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; *Asthma/microbiology ; *Mouth/microbiology ; Adult ; Middle Aged ; *Rhinosinusitis/microbiology ; Norway/epidemiology ; Australia/epidemiology ; Estonia/epidemiology ; Nitric Oxide ; Fractional Exhaled Nitric Oxide Testing ; *Bacteria/isolation &amp; purification/genetics ; Chronic Disease ; Spirometry ; }, abstract = {INTRODUCTION: The oral microbiome has been shown to be associated with respiratory health, primarily in adult case studies or among children. This relationship has been scarcely investigated in adult population-based cohorts.<br><br>OBJECTIVES: To investigate the association between oral microbiome and respiratory health, more specifically asthma, chronic rhinosinusitis (CRS), lung function and fractional exhaled nitric oxide (FeNO) in a population-based cross-continental multicentre study among adults.<br><br>METHODS: Subgingival samples from 355 adult European Community Respiratory Health Survey participants from Norway, Australia and Estonia underwent metagenomic sequencing. Respiratory disease was defined from questionnaires and sensitisation from specific immunoglobulin E (IgE)/skin prick tests. Spirometry and FeNO were measured. The associations between alpha diversity and disease status were evaluated in cross-sectional analyses using logistic regression adjusting for sex, smoking and study centre. Differential abundance analyses were performed using analysis of compositions of microbiomes with bias correction.<br><br>RESULTS: Alpha diversity differed by study centre and sensitisation status and was associated with non-allergic CRS (richness: 1.12, 95%&#x2009;CI 1.03 to 1.22). A similar though not statistically significant pattern was seen for forced vital capacity (FVC) below the lower limit of normal (LLN). Lachnospiraceae and Xanthomonas were more abundant in the oral microbiome of non-asthmatics and individuals without CRS, respectively, as compared with asthmatics and CRS patients. Several functional genes (1477-3391)&#x2009;and genera (54-98) were only present in the non-case groups, whereas individuals with affected respiratory health had 0-74&#x2009;unique functional genes, but no unique genera present only in their respective groups.<br><br>CONCLUSION: Increased alpha diversity was associated with non-allergic CRS and a similar trend was seen for FVC below LLN. Bacterial composition and functional profiles of the oral microbiome differed by respiratory health status. This study is novel in exploring functional gene profiling in relation to asthma and FeNO.}, }
@article {pmid42315409, year = {2026}, author = {Urvoy, M and Baumgart, L and Howard-Varona, C and Sullivan, MB}, title = {Beyond AMGs: Phage-encoded transcription and sigma factors as understudied virocell reprogramming tools.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.05.019}, pmid = {42315409}, issn = {1878-4380}, abstract = {Phages, the most abundant biological entities on Earth, infect bacteria and reprogram them into 'virocells' with altered physiology and ecology. While metagenomic studies have largely inferred reprogramming through virus-encoded auxiliary metabolic genes (AMGs), phages can reprogram cells through many other tools. In this review, we explore how phage-encoded, host-acting transcription and sigma factors (TSFs) reshape host transcriptional networks beyond simply regulating phage replication. We synthesize emerging genomic evidence for TSF prevalence in phages, mechanistic insights into how host-acting TSFs might influence ecologically relevant cellular functions, and highlight recent experimental and bioinformatic advances that make TSFs particularly tractable for large-scale bioinformatic studies. Together, we position TSFs as AMG-complementary mechanisms of viral reprogramming, tractable for metagenomic inferences, with potential cellular- and ecosystem-level consequences that can power translational applications.}, }
@article {pmid42315843, year = {2026}, author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, DM and Teixeira, M and Earl, AM and Worby, CJ and Kong, HH and Huang, SS and Segre, JA}, title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74611-x}, pmid = {42315843}, issn = {2041-1723}, support = {ZIA-HG200382-14//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, abstract = {Antimicrobial resistance (AMR) is a health threat disproportionately affecting nursing home (NH) residents. Surveillance and infection control in NHs are restricted to nares or perirectal cultures, overlooking skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here, within the PROTECT trial NCT03118232, we show, that NH residents' skin serves as a reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using metagenomics, culturing, and genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including 4 (10.5%) with ESBL-producing Escherichia coli sequence type (ST)131/ST648 and 7 (18.4%) with methicillin-resistant Staphylococcus aureus. Skin microbiome analysis by metagenome-assembled genomes identified broader MDRO colonization, including 27 (71.1%) with E. coli ST93, 14 (36.8%) with Staphylococcus epidermidis ST2, 16 (42.1%) with Proteus mirabilis, 7 (18.4%) with Providencia stuartii, 7 (18.4%) with Enterococcus faecalis, and 5 (13.2%) with Pseudomonas aeruginosa. Colonization persisted after bathing. Clonal E. coli ST93 was shared by 27 residents across 9 facilities, and 5 resident pairs carried clonally related strains of ≥2 MDRO species, suggesting polymicrobial transmission. We confirmed skin as a reservoir of MDROs, utilizing metagenomics to detect colonization and transmission pathways, supporting AMR surveillance in long-term care.}, }
@article {pmid42315898, year = {2026}, author = {Mishra, S and Mutnuri, S}, title = {Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57926-z}, pmid = {42315898}, issn = {2045-2322}, abstract = {Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.}, }
@article {pmid42316154, year = {2026}, author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y}, title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08462-x}, pmid = {42316154}, issn = {1479-5876}, support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.<br><br>METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n&#x2009;=&#x2009;45), fecal samples collected within 48&#xa0;h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n&#x2009;=&#x2009;25), infants with RDS who did not receive SRT (RDS(S-) group, n&#x2009;=&#x2009;7), and infants with RDS who received SRT (RDS(S+) group, n&#x2009;=&#x2009;13). In the probiotic discovery cohort (n&#x2009;=&#x2009;40), gut microbiota of infants without RDS (CON group, n&#x2009;=&#x2009;17) and infants with RDS (RDS group, n&#x2009;=&#x2009;23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.<br><br>RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.<br><br>CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.}, }
@article {pmid42316249, year = {2026}, author = {Li, R and He, X and Chen, Z and Shao, J and Feng, J and Wan, L and Zhang, M and Yang, J and Tong, Y and Dong, B and Huang, C and Qiu, H and Cai, Y and Niu, J and Xu, X and Song, X and Ma, J and Ge, H and Zhou, K}, title = {Microbial DNA analysis of paired blood-bronchoalveolar lavage fluid in post-HSCT patients with pneumonia implying application conditions of blood as a surrogate in pathogen detection.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03779-z}, pmid = {42316249}, issn = {1465-993X}, support = {82341114//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Blood testing aids pneumonia diagnosis, but its effectiveness varies. Given the invasiveness of bronchoalveolar lavage fluid (BALF) sampling versus blood testing's simplicity, this study investigates when blood can reliably substitute for BALF in detecting microbial presence, especially for pathogens.<br><br>RESULTS: Metagenomic sequencing was performed on paired BALF-blood samples from 21 post-HSCT immunocompromised (ICP) and 21 immunocompetent (ICT) patients. The ICP cohort was expanded to 62 for biomarker validation. Host responses were profiled via metatranscriptomics (30 BALF samples). Microbial alpha and beta diversity differed significantly between blood and BALF in ICP, but not ICT, patients. ICP patients' BALF contained a greater diversity and abundance of microbes. A higher proportion of microbial DNA sequences in ICP patients' blood was also present in their BALF, suggesting a potentially more permeable alveolar-capillary barrier. Related genes (e.g., NABA CORE MATRISOME, extracellular matrix organization, cell-cell adhesion) were downregulated. Upregulated pathways like VEGFA-VEGFR2 signaling and Rho GTPases suggested increased vascular permeability. In ICP patients, 419 microbial sequences in blood indicated their presence in the lower respiratory tract with >&#x2009;70% certainty.<br><br>CONCLUSION: Host immune status significantly influences blood-BALF microbial diversity differences. Shared blood-BALF microbial DNA sequences show potential for aiding pneumonia pathogen diagnosis, offering a novel biomarker identification approach.}, }
@article {pmid42316284, year = {2026}, author = {Wang, X and Cheng, L and Yin, K and Wang, B and Yan, X and Chen, S}, title = {Chronic proton pump inhibitor exposure aggravates intestinal injury by impairing intestinal stem cell self-renewal through the microbiota-7-ketolithocholic acid Axis.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08448-9}, pmid = {42316284}, issn = {1479-5876}, abstract = {BACKGROUND: Long-term proton pump inhibitor (PPI) use is associated with increased intestinal disease risk, but its damaging mechanisms remain unclear.<br><br>METHODS: Mice were administered rabeprazole (Rab) for 4&#x2009;weeks before dextran sulfate sodium (DSS) or ionizing radiation (IR) injury. We employed RNA sequencing, metabolomics, and metagenomics, evaluated intestinal stem cell (ISC) function, and used organoids for validation.<br><br>RESULTS: Long-term Rab induced small intestinal mucosal injury and exacerbated DSS/IR-induced damage, manifesting as crypt/villus atrophy and reduced ISC numbers. Mechanistically, Rab downregulated the Wnt pathway and impaired mucosal defense and regeneration. Microbiota involvement was indicated by fecal transplantation. Integrated metagenomic and metabolomic analyses revealed that Rab induced intestinal dysbiosis and reduced ileal bile acids, particularly 7-ketolithocholic acid (7KLCA) and chenodeoxycholic acid (CDCA). Faecalibaculum rodentium supplementation restored ISC self-renewal by converting CDCA to 7KLCA. In vitro, 7KLCA activated Wnt signaling to rescue Rab-induced stem cell impairment. In vivo, both 7KLCA and Gly-&#x3b2;-MCA (intestinal FXR antagonists) suppressed the FXR-FGF15 axis, restored the expression of hepatic bile acid synthesis enzymes, and promoted epithelial repair, thereby mitigating DSS-induced injury.<br><br>CONCLUSIONS: Chronic PPI use impairs ISC self-renewal by disrupting the microbiota-7KLCA-Wnt axis. F. rodentium or 7KLCA supplementation ameliorates PPI-induced effects, highlighting a microbe-metabolite axis as a pivotal mechanism and potential therapies for PPI-associated intestinal damage.}, }
@article {pmid42316350, year = {2026}, author = {Zhao, J and Su, Q and Wang, S and Li, Q and Chen, L and Kang, X and Xu, Q and Liu, C and Zhao, H}, title = {Differentiating hemorrhagic shock and organophosphate poisoning through integrated skin microbiome-metabolome signatures.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05276-1}, pmid = {42316350}, issn = {1471-2180}, support = {2024B04J0022//Guangzhou Science and technology planning project/ ; 82371901//National Natural Science Foundation of China/ ; 2023JC36//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; }, abstract = {Accurate determination of cause of death and estimation of postmortem interval (PMI) are critical yet challenging tasks in forensic science, particularly in cases with rapid demise and absence of obvious morphological abnormalities. We employed an integrative multi-omics approach to characterize postmortem microbial succession and metabolic alterations on facial skin in mouse models of hemorrhagic shock (HS) and organophosphorus poisoning (OP) across three decomposition stages: bloating (2 days), active decay (8 days), and advanced decay (16 days). Metagenomic profiling revealed significantly reduced α-diversity in HS compared with OP throughout all stages (p < 0.001), accompanied by stage-dependent compositional shifts, including early enrichment of Firmicutes in HS and Proteobacteria in OP. A total of 237 differential taxa were identified, with Providencia and Morganella predominating in OP, whereas Staphylococcus and Corynebacterium dominated bloating stage of HS. Untargeted metabolomics uncovered distinct cause-of-death-linked metabolites, notably elevated 2'-deoxycytidine-5'-diphosphate in early OP and persistent cholic acid/cholate accumulation in HS at later PMI. Functional analysis highlighted histidine and phosphate/phosphonate metabolism as key discriminatory pathways, exhibiting stage-specific oscillations and strong correlations with characteristic taxa. These findings demonstrate that skin-based metagenomic-metabolomic integration provides robust, mechanistically informed biomarkers for both PMI estimation and cause-of-death differentiation, offering a minimally invasive and temporally dynamic tool for forensic investigations.}, }
@article {pmid42316926, year = {2026}, author = {Goldsworthy, A and Olsen, M and Obonyo, NG and Jones, P and McKirdy, S and Senok, A and Alghafri, R and Ghemrawi, R and Almheiri, R and Tronstad, O and Suen, JY and Fraser, JF and Tajouri, L}, title = {Hospital-Associated Antimicrobial Resistant Bacteria on 95 Mobile Phones: An International Metagenomic "Phonome" Analysis.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70321}, pmid = {42316926}, issn = {2045-8827}, mesh = {*Bacteria/genetics/drug effects/isolation &amp; purification/classification/pathogenicity ; Metagenomics ; *Cell Phone ; *Drug Resistance, Bacterial/genetics ; Humans ; *Cross Infection/microbiology/epidemiology ; Bacteriophages/genetics/isolation &amp; purification ; *Fomites/microbiology ; Anti-Bacterial Agents/pharmacology ; Hospitals ; High-Throughput Nucleotide Sequencing ; Virulence Factors/genetics ; }, abstract = {Antimicrobial resistant healthcare-associated infections present an increasing threat to public safety and the sustainability of healthcare systems around the world. Mobile phones have been highlighted as a fomite that negates hand hygiene and contributes to the dissemination of pathogenic microorganisms in healthcare settings. The objective of the current stidy was to investigate the presence of bacteria, antimicrobial resistance and virulence genes associated with high morbidity on 95 mobile phones within healthcare settings. Next-Generation Metagenomic Sequencing was undertaken and FastQ files were subsequently analyzed within COSMOSid to enable taxonomic identification. Antibiotic resistant genes, virulence genes and bacteriophages were co-located with bacteria associated with the highest global mortality. Antibiotic resistant genes were manually annotated and cross referenced with the Comprehensive Antibiotic Resistance Database (CARD) to identify gene-drug interactions. On average, mobile phones were identified to be contaminated with 3.62 of the top 10 highest mortality-causing bacteria and 2.49 ESKAPE pathogens. A total of 262 unique ARGs, 448 unique VFGs, and 314 bacteriophages were identified. Mobile phones within healthcare settings harbor pathogens alongside genes associated with increased virulence and antimicrobial resistance. Additionally, mobile phones, known to be infrequently sanitized, may increase antimicrobial resistance by providing a contaminated platform which facilitates continued horizontal genetic transfer.}, }
@article {pmid42316995, year = {2026}, author = {Gu, Y and Li, L and Zhang, H and Ye, T and Zhu, Q and Zhao, X and Xie, K and Ge, R and Han, J and Qin, Y}, title = {Dietary purple sweet potato anthocyanin extracts attenuate intestinal barrier decline in naturally aged mice via the microbiota-autophagy-stem cell axis.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00039h}, pmid = {42316995}, issn = {2042-650X}, abstract = {Age-related deterioration of the intestinal epithelial barrier exacerbates systemic metabolic and functional decline, highlighting the gut as a key target for dietary interventions in healthy aging. Here, using naturally aged mice and intestinal organoids, we demonstrate that supplementation with purple sweet potato anthocyanins (PSPAs) alleviates systemic aging phenotypes, including impaired motor coordination, hepatic lipid dysregulation, insulin resistance, and cellular senescence, while concurrently restoring intestinal barrier integrity. PSPAs enhanced tight junction protein expression and epithelial architecture, independently of inflammation resolution, and promoted the proliferative and differentiation capacity of intestinal stem cells (ISCs). Metagenomic profiling revealed that PSPAs remodeled aging-associated gut microbiota composition and functions. Fecal microbiota transplantation established the causal contribution of microbiota remodeling to ISC rejuvenation, while luminal content-organoid assays confirmed the role of microbial metabolites. Integrative metabolomics identified metabolic changes linked to autophagy-related processes, including altered SCFA profiles, while transcriptomic analysis highlighted PI3K-AKT signaling as a major pathway associated with microbial and metabolic remodeling. Collectively, this multi-omics study establishes a mechanistic framework in which PSPAs alleviate aging-associated barrier decline through a "microbiota-autophagy-stem cell" axis, providing important insights into polyphenol-based strategies for gut-centered healthy aging.}, }
@article {pmid42317351, year = {2026}, author = {Lou, Y and Ma, D and Gan, Q and Xu, X and Xiao, Y and Wang, J and Li, Z and Zhang, T and Qi, L and Feng, S}, title = {Inflammatory protein mediators linking gut microbiota to degenerative lumbar spine disorders: cross-disease genetic evidence.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1855966}, pmid = {42317351}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Intervertebral Disc Degeneration/genetics/microbiology/immunology/metabolism ; Humans ; *Lumbar Vertebrae/pathology ; Rats ; Mendelian Randomization Analysis ; *Inflammation Mediators/metabolism ; *Spondylolisthesis/genetics/microbiology ; Biomarkers ; *Spinal Stenosis/genetics/microbiology ; Disease Models, Animal ; }, abstract = {BACKGROUND: Degenerative lumbar spine disorders (DLSD), including intervertebral disc disorders (IDD), degenerative spondylolisthesis, and lumbar spinal stenosis (LSS), are major contributors to low back pain and disability. Associations among gut microbiota (GM), inflammatory proteins, and DLSD have been demonstrated in prior studies. Yet, two key questions persist: whether specific circulating inflammatory proteins (IPs) mediate this association, and whether such mediation is shared across different diseases.<br><br>METHODS: We performed two-sample Mendelian randomization (MR) to evaluate causal associations among 473 GM taxa, 91 circulating IPs, and three DLSD outcomes using FinnGen R12 summary statistics. Causal estimates were obtained using inverse-variance weighted MR with complementary sensitivity analyses, pleiotropy and heterogeneity testing, and bidirectional MR. Two-step MR mediation was applied to quantify indirect effects of GM through IPs. Experimental validation was performed using rat models, with qPCR and ELISA assessing inflammatory markers in lumbar tissues and metagenomic sequencing evaluating gut microbiota profiles.<br><br>RESULTS: Genetically predicted GM taxa were associated with LSS (28 taxa), spondylolisthesis (20 taxa), and IDD (41 taxa). IP MR identified risk-increasing associations for LSS (4E-BP1 and interleukin-4), spondylolisthesis (CXCL1, CXCL5, FGF-5, IL-15RA, and IL-4) and IDD (IL-20RA and IL-6), while IL-18 showed a protective association with IDD that remained robust after multiple-testing correction. Mediation analyses identified 13 genetically supported putative GM-IPs-DLSD pathways, highlighting convergent mediators including PD-L1 for spondylolisthesis and IL-6 and IL-18 for IDD, with mediation proportions ranging from 7.55% to 13.22% across key pathways. Experimental results showed inflammatory activation and gut microbiota alterations in disease models, with partial concordance with the MR findings.<br><br>CONCLUSIONS: These findings support a genetically determined microbiota-inflammation axis in DLSD. Furthermore, they identify circulating inflammatory proteins as mediators to prioritize mechanistic studies and guide translational follow-up research.}, }
@article {pmid42317755, year = {2026}, author = {Rout, AK and Tripathy, PS and Rout, SS and Kumar, N and Parida, SN and Panda, A and Suman, D and Tyagi, A and Behera, BK and Pandey, PK}, title = {Metagenomic insights into microbial diversity, xenobiotic and plastic-degrading enzymes in sediments of river Yamuna at Agra.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1828736}, pmid = {42317755}, issn = {1664-302X}, abstract = {The river Yamuna is one of the most polluted rivers in India and is heavily impacted by urban, industrial, and agricultural inputs. In this study, shotgun metagenomics was used to investigate microbial diversity and functional potential in sediments from three locations: Balkeshwar Shivpuri Agra (BSA), Taj Ganj Yamuna (TGY), and Yamuna Expressway Agra (YEA). A total of 38.3-46.5 million reads per sample were generated, yielding 3.08-5.54 million predicted ORFs. Taxonomic profiling revealed that BSA exhibited higher microbial diversity, with a more even distribution of dominant taxa compared to TGY and YEA. Functional analysis indicated that core metabolic pathways (e.g., glycolysis and TCA cycle) were more abundant in BSA, whereas pathways related to aromatic compound degradation were relatively enriched in TGY. Plastic-degrading enzyme homologs were detected across all sites, with the strongest signals associated with biodegradable polymers such as polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), and polyethylene glycol (PEG). The normalized abundances of PHA-associated enzymes were approximately 60-75% higher in YEA compared to BSA and TGY, while homologs linked to recalcitrant plastics such as polyethylene (PE) and low-density polyethylene (LDPE) were detected at low levels across all sites (< 10-15%). Similarly, xenobiotic degradation pathways, including chlorocyclohexane and chlorobenzene degradation, showed relatively higher abundance in YEA, whereas bisphenol degradation was more prominent in BSA. Overall, the results indicate that sediment microbial communities along the river Yamuna harbor diverse metabolic capabilities and functional potential for pollutant degradation, with site-specific variations driven by local environmental conditions.}, }
@article {pmid42317759, year = {2026}, author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A}, title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1850075}, pmid = {42317759}, issn = {1664-302X}, abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.<br><br>METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.<br><br>RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.}, }
@article {pmid42317762, year = {2026}, author = {Joshi, G and Rani, S and Bharti, D and Panda, N and Chavan, P and Mathpal, S and Ramaiah, S and Anbarasu, A}, title = {The role of the gut microbiome in antibiotic-driven antimicrobial resistance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1856738}, pmid = {42317762}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role in normal growth and physiological processes of the human body. It serves both as a target of antibiotic-mediated disruption and as a reservoir for the propagation of antimicrobial resistance genes. Although antibiotics remain indispensable for the treatment of bacterial infections, their broad ecological impact on the gut microbiota can undermine the microbial balance that protects the host against pathogen invasion and metabolic dysfunction. The gut microbiome also functions as a reservoir of antimicrobial resistance genes collectively termed the "resistome," which can be mobilised and transferred between commensal and pathogenic bacteria via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. This review examines the composition and functions of the human gut microbiota, the mechanism of antibiotic-induced gut dysbiosis, and the role of host factors like age, genetics, diet and immune status, on microbiome dynamics and AMR development. We further evaluate emerging methods for resistome characterisation, which include PCR, next-generation sequencing, functional metagenomics and artificial intelligence-driven tools. Finally, we discuss microbiome-targeted therapeutic strategies such as faecal microbiota transplantation (FMT), phage therapy, CRISPR-based therapies, and antimicrobial peptides for combating AMR and restoring gut microbial homeostasis. Overall, this review highlights that maintaining and re-establishing the integrity of the gut microbiome should be considered a fundamental component of antimicrobial stewardship strategies aimed at controlling AMR worldwide.}, }
@article {pmid42318385, year = {2026}, author = {Fu, J and Qi, Y and Zhan, J and Su, L and Gao, Y and Zhou, Q and Zhang, Y}, title = {Clinical effects of Yiqi-Yangyin-Huoxue granules in the management of type 2 diabetes mellitus and early vascular aging: a randomized, double-blind, placebo-controlled trial protocol.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1768610}, pmid = {42318385}, issn = {2296-858X}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) has become a major global public health challenge, affecting more than 500 million adults worldwide. Early vascular aging (EVA) is one of the key pathological changes for diabetic vascular complications. However, targeted and effective therapeutic strategies remain limited. Based on our previous research and clinical experience, we developed a granulated natural herbal formulation, Yiqi-Yangyin-Huoxue (YQYYHX). This trial aims to evaluate the clinical efficacy and safety of YQYYHX in patients with T2DM and EVA, and to preliminarily explore its potential mechanisms.<br><br>METHODS: This is a single-center, randomized, double-blind, placebo-controlled, parallel-group clinical trial. It will enroll 120 participants with T2DM and EVA, who will be randomized in a 1:1 allocation ratio to two groups. In addition to standard therapy, the treatment group will receive the YQYYHX granules, while the control group will receive a matched placebo. Based on mass spectrometry analysis, daidzin, salvianolic acid L, and oleamide were identified as the compounds with the largest peak area in YQYYHX. After a 12-week intervention, brachial-ankle pulse wave velocity (baPWV) is planned to be assessed as the primary outcome. Secondary outcomes are expected to include the ankle-brachial index, blood glucose levels, lipid profiles, inflammatory cytokines, 6-min walk test and questionnaires. Safety will be evaluated using liver transaminases, serum creatinine, and related indicators. Serum and fecal samples will be collected before and after treatment. The serum will be used for metabolomic and proteomic sequencing analysis, and feces will be used for metagenomic sequencing. Electronic case report forms are generated within the clinical record system, ensuring that all follow-up information is traceable. Subsequently, the data will be entered into a specific electronic data capture, and the data administrator will verify it.<br><br>RESULTS: The recruitment began on March 27, 2025 and is expected to end on December 31, 2026. As of March 10, 2026, 72 participants have been enrolled.<br><br>CONCLUSION: This rigorously designed trial is expected to generate reliable evidence. As a complementary and alternative therapeutic option, YQYYHX has the potential to benefit patients with T2DM and EVA.<br><br>CLINICAL TRIAL REGISTRATION: This trial has been registered with the International Traditional Medicine Clinical Trial Registry Platform (http://itmctr.ccebtcm.org.cn/, ITMCTR2024000388).}, }
@article {pmid42318413, year = {2026}, author = {Hu, Z and Hou, L and Huang, A}, title = {Case Report: Methylprednisolone-induced pheochromocytoma crisis resulting in cardiac arrest.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1779740}, pmid = {42318413}, issn = {2296-858X}, abstract = {Pheochromocytoma crisis, a rare yet life-threatening endocrine emergency, is characterized by acute hemodynamic instability that can lead to severe cardiovascular collapse, including cardiac arrest. Systemic glucocorticoid administration has been shown to trigger such crises in patients with pheochromocytoma. This report describes a 38-year-old female who developed symptoms including chest tightness, dyspnea, and vomiting shortly after receiving a methylprednisolone injection for urticaria, suggesting a possible association between glucocorticoid administration and the subsequent crisis. On admission, she suffered cardiac arrest and was managed with extracorporeal membrane oxygenation (ECMO). Coronary angiography, blood microbial RNA analysis, and metagenomic testing revealed no abnormalities. Despite comprehensive pharmacological treatment, the patient's symptoms persisted, with recurrent ventricular fibrillation detected on electrocardiogram, prompting further investigations. A computed tomography (CT) scan identified an adrenal mass, and biochemical tests confirmed the diagnosis of pheochromocytoma. Following successful laparoscopic adrenalectomy, the patient experienced significant clinical improvement. This case demonstrates the potential for methylprednisolone to trigger or contribute to a pheochromocytoma crisis. However, it is important to acknowledge that other concurrent factors, such as use of medication, systemic inflammatory response, and physiological stress of resuscitative interventions, may have also played a role. The challenges posed by the diagnosis of this condition underscore the need for caution when administering glucocorticoids to patients with suspected pheochromocytoma.}, }
@article {pmid42319209, year = {2026}, author = {Parsons, DAJ and Vos, RA and Price, BW}, title = {BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70170}, pmid = {42319209}, issn = {1755-0998}, support = {101059492//European Commission/ ; 22.00173//Swiss State Secretariat for Education, Research and Innovation/ ; 24.00054//Swiss State Secretariat for Education, Research and Innovation/ ; //UK Research and Innovation/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Workflow ; *Metagenomics/methods ; }, abstract = {Natural history collections are unparalleled archives of global biodiversity, yet most specimens remain molecularly uncharacterised due to the technical challenges of historical DNA (hDNA), including degradation, low endogenous content and contamination. Genome skimming offers a scalable alternative to PCR-based barcoding, but existing bioinformatic workflows are not optimised for the heterogeneous, metagenomic nature of museum-derived data. Here we present BeeGees (Barcode Extraction and Evaluation from Genome Skims), a high-performance computing (HPC) integrated, Snakemake-based workflow designed for protein-guided recovery and validation of mitochondrial and plastid barcode genes from degraded short-read genome sequences. BeeGees integrates dual read pre-processing, systematic per-sample parameter sweeps, sequential consensus cleaning to remove contaminant sequences and rigorous structural and taxonomic validation against curated reference databases. We benchmarked BeeGees on 1518 museum specimen-derived genome skims spanning eight phyla. The workflow completed in approximately 120 h (< 5 min per sample) on HPC infrastructure. When excluding sequencing failures (< 1 M reads), validated COI barcodes were recovered for 73.2% of specimens (1050/1435). Barcode recovery success was influenced by endogenous content, preservation quality and parameter choice rather than raw read count alone, highlighting the importance of systematic parameter optimisation. Sequential consensus cleaning eliminated ambiguous bases and reduced chimeric artefacts, proving essential for robust museomic analyses. BeeGees provides a reproducible, scalable framework for high-throughput barcode recovery and biodiversity genomics and reference gap-filling initiatives from natural history collections. The BeeGees pipeline is available at: https://github.com/bge-barcoding/BeeGees/.}, }
@article {pmid42319454, year = {2026}, author = {Xie, M and Jie, Y}, title = {From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42319454}, issn = {1432-0991}, support = {82371022//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; *Dry Eye Syndromes/microbiology/diagnosis ; Bacteria/genetics/classification/isolation &amp; purification ; *Eye/microbiology ; Fungi/isolation &amp; purification/genetics/classification ; Tears/microbiology ; }, abstract = {Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.}, }
@article {pmid42319554, year = {2026}, author = {Wang, Q and Xiao, H and Liu, W and Dang, X and Bai, Y and Xiao, R and Tong, L and Wang, Y and Li, M and Wang, S and Pu, S and Pei, D and Zhang, D and Wang, X and Hu, G and Guo, J and Jin, X and Qin, L and Zhang, C and Li, Y and Zhang, T and Yang, J and Wang, Q and Sun, H}, title = {Fusobacterium varium Exacerbates Neutrophil-driven Intestinal Inflammation Associated with Succinate-SUCNR1-NF-κB Signaling.}, journal = {Inflammation}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10753-026-02547-x}, pmid = {42319554}, issn = {1573-2576}, support = {24ZDNA003//Gansu Provincial Major Science and Technology Special Project Plan/ ; 82572004//National Natural Science Foundation of China/ ; lzujbky-2023-eyt04//Fundamental Research Funds for the Central Universities/ ; 25YFFA067//Key Research and Development Program of Gansu Province/ ; 2023RCXM65//Gansu Province key talent project/ ; 2021-RC-115//Lanzhou Talent Innovation and Entrepreneurship Project/ ; yjrckyqdj-2020-01, yjrckyqdj-2022-01//Talent Introduction Plan of the Second Hospital of Lanzhou University/ ; }, abstract = {Disruption of gut microbial homeostasis is a hallmark of ulcerative colitis (UC), yet the specific pathobionts and effector molecules driving mucosal inflammation remain unclear. In this study, metagenomic sequencing of fecal samples from 37 patients with UC and 30 healthy controls was performed to identify differentially enriched bacterial species. Fusobacterium varium (F. varium) was found to be significantly enriched in patients with UC and was therefore selected for further functional investigation. Germ-free mice colonized with F. varium developed more severe dextran sulfate sodium (DSS)-induced colitis, accompanied by enhanced mucosal inflammation. In addition, F. varium culture supernatants increased NF-κB reporter activity and inflammatory signaling at the protein level. Bioactivity-guided fractionation combined with mass spectrometry identified succinate as a major candidate bacterial-derived bioactive metabolite. Succinate exacerbated colonic inflammation in vivo and promoted neutrophil recruitment, whereas inhibition of CXCR2 signaling reduced neutrophil infiltration and alleviated disease severity. In vitro experiments further demonstrated that succinate activated NF-κB signaling in HL-60-derived neutrophils through succinate receptor 1 (SUCNR1) and induced the production of inflammatory mediators, including CXCL8. Collectively, these findings support a role for F. varium in exacerbating intestinal inflammation under colitic conditions, at least in part through succinate-associated neutrophil recruitment.}, }
@article {pmid42319773, year = {2026}, author = {Ali, H and Rieuwpassa, IE and Hamrun, N and Marlina, E and Yulianty, R and Akbar, FH and Siti Hartina Dewang, DA}, title = {Longitudinal effects of antiretroviral therapy on the oral microbiota in people living with HIV: A systematic review.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02910}, pmid = {42319773}, issn = {1588-2640}, abstract = {People living with HIV frequently experience oral microbial dysbiosis, contributing to oral disease burden and reduced quality of life. Although antiretroviral therapy (ART) effectively suppresses viral replication and promotes immune recovery, its longitudinal effects on the oral microbiota remain incompletely understood. This systematic review aimed to evaluate longitudinal changes in oral microbiota composition and diversity in people living with HIV before and after ART initiation. A systematic review was conducted in accordance with PRISMA guidelines and registered in PROSPERO (CRD420251164326). Electronic searches were performed in PubMed, ScienceDirect, Wiley Online Library, DOAJ, and Google Scholar for studies published between 2015 and 2024. Eligible studies included longitudinal human studies reporting pre- and post-ART oral microbiota data using 16S rRNA gene sequencing or metagenomic approaches. Methodological quality was assessed using Joanna Briggs Institute critical appraisal tools. Due to substantial heterogeneity, findings were synthesized narratively. Six longitudinal studies met the inclusion criteria. ART was associated with partial and non-uniform modulation of the oral microbiota. Changes in beta diversity and selective taxonomic shifts were commonly reported, whereas changes in alpha diversity were inconsistent. Taxonomic alterations were more evident at the genus level, while several dominant oral genera remained stable before and after ART. Evidence linking oral microbiota changes with immune recovery was limited. Longitudinal evidence indicates that ART induces selective and heterogeneous changes in the oral microbiota without consistent normalization toward a non-HIV microbial profile, underscoring the importance of integrating oral health into long-term HIV care.}, }
@article {pmid42320204, year = {2026}, author = {Ma, S and Cao, M and Wang, F and Geng, H and Xu, Q and Gao, Z and Li, J and Russel, M and Sun, K}, title = {DOM-microbe interactions shape carbon storage strategies in rhizosphere and detritus-rich wetland soils.}, journal = {Journal of environmental management}, volume = {412}, number = {}, pages = {130250}, doi = {10.1016/j.jenvman.2026.130250}, pmid = {42320204}, issn = {1095-8630}, abstract = {Wetland macrophytes are associated with carbon storage through photosynthetic CO2 uptake and interactions with microbes. Rhizodeposition and detritus accumulation represent two key pathways examined in this study. However, how dissolved organic matter (DOM) interacts with microbial carbon storage remains incompletely understood. Here, we investigated links between DOM characteristics and microbial carbon transformation pathways in Wuchang Lake using FT-ICR-MS, metagenomics, and geochemical analyses. Macrophyte presence was associated with a higher relative abundance of genes related to microbial carbon storage potential compared to macrophyte-free areas. Microbial taxa and carbon transformation strategies varied between rhizosphere and detritus-enriched soils and were associated with differences in DOM properties. In the rhizosphere, DOM with low H/C ratios (<1.5) and high number of transformations (>10) was associated with taxa linked to biomass degradation. In detritus-enriched soils, DOM with higher H/C ratios and lower carbon-to-phosphorus ratios (C:P) was associated with higher relative abundance of genes related to intracellular carbon storage, while genes associated with CO2 and CH4 production showed lower relative abundance. These communities also showed higher relative abundance of CO2 fixation genes. Overall, DOM molecular characteristics were associated with niche-specific microbial carbon transformation patterns, providing a conceptual framework for wetland carbon dynamics.}, }
@article {pmid42320375, year = {2026}, author = {Srisakvarangkool, W and Rosyidah, A and Yasawong, M and Suriyachadkun, C and Pitiwittayakul, N and Ganta, P and Tanasupawat, S and Nantapong, N}, title = {Comparative genomics and taxonomic characterization of Streptomyces diversicolor sp. nov.: a novel species exhibiting intraspecific genomic divergence and biotechnological potential.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126737}, doi = {10.1016/j.syapm.2026.126737}, pmid = {42320375}, issn = {1618-0984}, abstract = {Two actinomycete strains, designated SSUT88A[T] and SSUT88R, were isolated from distinct soil samples in Nakhon Ratchasima, Thailand. While both belong the genus Streptomyces, they exhibited phenotypic divergence; strain SSUT88A[T] produced yellowish-white mycelia with potent antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), whereas SSUT88R produced red colonies with limited inhibitory effects. Genomic analyses confirmed the isolates are conspecific, sharing high ANI (99.99%) and dDDH (99.6%) values, yet exhibiting genomic divergence; the 11.2 Mb genome of SSUT88A[T] exceeded the 8.3 Mb genome of SSUT88R. Comparative genome mining revealed this variation extended to secondary metabolism, as SSUT88A[T] encoded a more diverse biosynthetic potential. Furthermore, ANI and dDDH values against the closest phylogenomic neighbors were below species thresholds (79.69-87.55% and 25.7-30.2%, respectively), supporting their classification as a novel species. Metagenomic screening using IMNGS and Branchwater revealed a predominantly terrestrial distribution. While the broader lineage appeared ecologically versatile, high-confidence conspecific populations (cANI ≥0.97) were restricted to soil and rhizosphere habitats, with evidence of regional persistence in Thailand. Chemotaxonomic characteristics including ll-diaminopimelic acid, MK-9(H8) and whole-cell sugars contained ribose, mannose, and glucose. The polar lipid profile included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, and an unidentified glycolipid. Major fatty acids included iso-C16:0, anteiso-C15:0, anteiso-C17:0 and iso-C15:0. Based on this polyphasic evidence, strains SSUT88A[T] and SSUT88R are proposed to represent a novel species, for which the name Streptomyces diversicolor sp. nov. is proposed. The type strain is SSUT88A[T] (InaCC A1220[T] = TISTR 10074[T]). Strain SSUT88R is deposited as InaCC A1221 = TISTR 10075.}, }
@article {pmid42320776, year = {2026}, author = {Cho, MS and Lee, IS and Kim, J and Park, JW and Kim, J and Ko, SJ}, title = {Multi-herb formulations modulating gut microbiota: A systematic review and data-driven analysis.}, journal = {Journal of ethnopharmacology}, volume = {370}, number = {}, pages = {122082}, doi = {10.1016/j.jep.2026.122082}, pmid = {42320776}, issn = {1872-7573}, abstract = {Multi-herb formulations, characterized by their complex synergistic compositions, are widely used in traditional medicine to modulate the gut microbiota. However, identifying reproducible herb-microbiota associations across disparate clinical settings remains a significant methodological challenge.<br><br>AIM OF THE STUDY: This study aims to systematically synthesize human clinical evidence to map the modulation patterns of multi-herb formulations on the gut microbiota and to identify the herbal components associated with reported directional microbial shifts.<br><br>MATERIALS AND METHODS: We conducted a systematic review and data-driven analysis of 29 clinical trials involving 954 participants in multi-herb formulation groups. To integrate findings from heterogeneous clinical settings, we employed a binarization strategy focused on statistically significant directional shifts (+1 for increase, -1 for decrease). An extreme gradient boosting (XGBoost) learning framework combined with SHapley Additive exPlanations (SHAP) was used to deconstruct these formulations and explore the predictive importance of individual constituents. To ensure the highest level of scientific integrity and prevent data leakage, the model's generalizability was rigorously validated using Leave-One-Study-Out (LOSO) cross-validation at the independent study level.<br><br>RESULTS: The LOSO validation yielded a mean accuracy of 0.84 and a macro F1-score of 0.42, indicating limited but informative cross-study pattern recognition despite the inherent heterogeneity of clinical data. Our analysis identified recurrent directional associations: formulas containing Scutellaria baicalensis Georgi were associated with reported reductions in genus-level taxa such as Escherichia-Shigella within neuropsychiatric disease contexts. Formulas containing Zingiber officinale Roscoe were associated with reported increases and decreases in selected genus-level taxa across heterogeneous disease contexts.<br><br>CONCLUSIONS: This study provides a comprehensive, evidence-based map of how multi-herb formulations modulate the human gut microbiota. By prioritizing rigorous validation and accounting for the complexity of synergistic preparations, we have identified hypothesis-generating patterns that transcend individual study variations. These findings provide a realistic foundation for future high-resolution metagenomic research and the development of standardized ethnopharmacological therapies.}, }
@article {pmid42320811, year = {2026}, author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L}, title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and synergizes with αPD-1 therapy.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153116}, doi = {10.1016/j.ijbiomac.2026.153116}, pmid = {42320811}, issn = {1879-0003}, abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-dependent mechanisms and potentiates anti-PD-1 therapy.<br><br>MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.<br><br>RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-&#x3b1; reduced. In vitro, butyrate enhanced T-cell IFN-&#x3b3;/IL-2/granzyme-B, inhibited tumor HDAC activity, and counteracted IFN-&#x3b3;-induced PD-L1; in vivo, PSP-H created a T-cell-activating milieu with adaptive STAT1/PD-L1 up-regulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H&#x202f;+&#x202f;anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.<br><br>CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by converting systemic immunity while inducing targetable adaptive resistance.}, }
@article {pmid42321256, year = {2026}, author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L}, title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01068-7}, pmid = {42321256}, issn = {2055-5008}, support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&amp;D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; }, abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.}, }
@article {pmid42321634, year = {2026}, author = {Pandey, S and Parmar, B and Gupta, A and Singh, A and Chauhan, A and Huang, KW and Karan, R}, title = {Eco-technological potential of salinity-driven functional specialization in Indian solar salterns revealed by integrated culturomics and whole-metagenome profiling.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05253-8}, pmid = {42321634}, issn = {1471-2180}, support = {RFS #5974//King Abdullah University of Science and Technology/ ; IoE/2024-25/12/FRP and IoE/2025-26/12/FRP//University of Delhi/ ; }, abstract = {Solar salterns are environmentally stable yet biologically extreme ecosystems that serve as vital models for understanding and managing hypersaline environments, including industrial saline effluents. Despite their ecological and biotechnological significance, Indian solar salterns remain functionally underexplored. In this study, we integrated culture-dependent isolation with whole-metagenome sequencing to investigate microbial community assembly, functional specialization, and eco-technological potential across four geographically distinct Indian salterns.Physicochemical analyses revealed pronounced spatial variation in salinity, pH, and electrical conductivity, which together strongly structured microbial communities. Metagenomic sequencing generated between 4.84 and 8.68 Gb of raw data across individual site, yielding between 429,420 and 669,991 predicted genes in high-salinity locations. Taxonomic reconstruction demonstrated archaeal dominance at extreme salinity, particularly among Euryarchaeota, whereas comparatively moderate salinity sites supported more balanced bacterial-archaeal assemblages. Alpha diversity patterns indicated higher richness in Tamil Nadu and Rajasthan, while Gujarat exhibited reduced evenness consistent with environmental filtering.Culture-dependent approaches recovered 42 halophilic and polyextremophilic isolates, primarily affiliated with Halobacteriaceae and Bacillaceae, complementing the broad taxonomic detection of these lineages inferred from metagenomic data. Functional annotation revealed extensive enrichment of genes involved in ion transport, energy production, osmoprotectant biosynthesis, and DNA repair, reflecting an adaptive mechanism critical for survival in high-salinity industrial processes. Amino acid metabolism genes exceeded 25,000 hits in selected sites, and replication and repair genes reached 32,554 in Gujarat, indicating heightened stress-response activity. Secondary metabolite biosynthetic gene clusters, including pathways for novel antimicrobial peptides, terpene, ribosomally synthesized and post-translationally modified peptide-like, and type III polyketide synthase pathways, were widely distributed, offering new biological control mechanisms for environments impaired by stress. Antimicrobial resistance signatures were limited and unevenly distributed across sites.These findings demonstrate that salinity acts as a dominant ecological filter driving both taxonomic composition and functional specialization in Indian solar salterns. By linking environmental gradients to adaptive genomic traits, this study establishes a functional baseline for hypersaline ecosystems.}, }
@article {pmid42321797, year = {2026}, author = {Igriczi, B and Zsiborás, L and Albert, E and Német, Z and Balka, G and Dénes, L}, title = {High genetic diversity of porcine rotavirus A, B, and C in Hungary with putative novel VP4 genotypes.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05649-8}, pmid = {42321797}, issn = {1746-6148}, abstract = {BACKGROUND: Rotaviruses (RVs) are important enteric pathogens of swine, contributing significantly to neonatal and post-weaning diarrhea worldwide. Although rotavirus A (RVA) is the best characterized species, much less is known about the epidemiology and genetic diversity of RVB and RVC, especially in Central Europe. This study aimed to investigate the presence and genetic diversity of RVA, RVB, and RVC in diarrheic piglets in Hungary using Nanopore third-generation sequencing.<br><br>RESULTS: A total of 77 fecal swab samples collected from diarrheic piglets across 19 swine farms were analyzed. All three RV species were detected, RVA and RVC were each identified in 54.5% of samples, while 40.3% was RVB positive. Coinfections involving multiple RV species were frequent, highlighting the complex etiology of piglet diarrhea. Altogether, 8 RVA, 3 RVB, and 4 RVC full-genome sequences, comprising all 11 segments, were identified. Genotyping of RVA strains revealed multiple G/P genotype combinations, with G9P[23] being the most prevalent. Whole-genome analysis demonstrated a Wa-like genomic backbone of porcine origin. In RVB, three complete VP4 sequences were obtained that could not be assigned to any known P genotype, suggesting the presence of a novel lineage. Hungarian RVC strains showed high genetic diversity, including five distinct G genotypes and one potential novel P genotype, underlining evolutionary diversity of porcine RVs.<br><br>CONCLUSIONS: This study provides a comprehensive molecular characterization of RVA, RVB, and RVC circulating in Hungarian pig populations. The high prevalence of coinfections and the detection of genetically diverse and potentially novel strains emphasize the complexity of RV epidemiology in swine. These findings highlight the need for continued surveillance to better understand their role in pig health and zoonotic risk.}, }
@article {pmid42321844, year = {2026}, author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H}, title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08501-7}, pmid = {42321844}, issn = {1479-5876}, support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; }, abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.<br><br>METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.<br><br>RESULTS: Dokdonia (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;5.704) and Cocleimonas (q&#x2009;=&#x2009;0.026, LDA&#x2009;=&#x2009;5.329) were enriched in the early-stage group, whereas Barnesiella (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.784), Pedobacter (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;4.913) and unclassified Bacteroides (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.926), rfaD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.918), nudF (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;4.283) and sfsA (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8&#x207a; T lymphocytes (q&#x2009;<&#x2009;0.001), whereas it showed a lower proportion of CD4&#x207a; T cells and a decreased CD4/CD8 ratio (q&#x2009;<&#x2009;0.001; q&#x2009;<&#x2009;0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q&#x2009;=&#x2009;0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.<br><br>CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.}, }
@article {pmid42322841, year = {2026}, author = {Wang, L and Li, X and Cao, Y and Meng, F and Xu, J and Hao, J}, title = {Microbial adaptation to benzethonium chloride exerts a double‑edged sword effect on long‑term sludge anaerobic fermentation: Volatile fatty acids promotion and antibiotic resistance genes propagation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142682}, doi = {10.1016/j.jhazmat.2026.142682}, pmid = {42322841}, issn = {1873-3336}, abstract = {The widespread use of benzethonium chloride (BZC) leads to its significant input into wastewater treatment and then accumulation in waste activated sludge (WAS). However, the long-term consequences of BZC accumulation in WAS anaerobic fermentation still remain unexplored. This study established a continuous fermentation system with stepwise increase and decrease in BZC content to simulate fluctuating pollutant levels. The concentration-dependent effects of BZC on acidogenic fermentation were displayed: low-to-medium-level BZC (10-100 mg/L) inhibited volatile fatty acids (VFAs) production from the baseline of 1150 mg COD/L to approximately 800 mg COD/L, whereas high-level BZC (1000 mg/L) increased VFAs production to 1800 mg COD/L, representing an absolute increase of 650 mg COD/L (70% relative to control) and facilitated the solubilization of organic substrates. Molecular docking modelling showed that BZC could bind with extracellular polymeric substances (EPS) and enzyme. Microbial community analysis showed that the resilience of fermentation system was maintained mainly by the functionally redundant rare subcommunity, whereas the enrichment of specific fermentative bacteria (e.g., Proteiniclasticum) contributed directly to the enhanced VFAs production. Based on metagenomic data, BZC stress activated microbial quorum sensing (QS) response and this QS-mediated adaptation strategy increased the relative abundance of related genes for hydrolysis, transport, and VFAs biosynthesis. Critically, this adaptive success carried a hidden cost, i.e., persistently enriching high-risk antibiotic resistance genes (e.g., bacA, mepA, vanY) (20% relative to the control) and activating mobile genetic elements. These findings reveal a trade-off between the increased VFAs production and environmental resistance propagation during the BZC affected sludge anaerobic fermentation.}, }
@article {pmid42323142, year = {2026}, author = {Yang, J and Zhu, D and Liu, R and Shi, L and Dai, X}, title = {Excessive biomass retention decouples ammonia-oxidizer abundance and activity in sidestream partial nitritation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135208}, doi = {10.1016/j.biortech.2026.135208}, pmid = {42323142}, issn = {1873-2976}, abstract = {Partial nitritation (PN) underpins two-stage anaerobic ammonium oxidation-based nitrogen removal, but biomass management in sidestream PN reactors remains largely empirical. This study tested three PN sequencing batch reactors maintained at contrasting biomass-retention states (2, 4, and 6 g L[-1] MLSS) under stepwise loading. Among the tested conditions, the intermediate-biomass reactor showed the most favorable performance, shortening recovery periods by 40.0-67.0% and reaching the highest apparent stable nitrogen loading rate of 2.30 g N L[-1] d[-1]. Metagenomic analysis linked this response to more deterministic community assembly and stronger species-level dominance of Nitrosomonas stercoris, whereas the low- and high-biomass states showed greater stochasticity and enrichment of heterotrophic or stress-tolerant taxa. Metatranscriptomics further showed that the intermediate-biomass state maintained the strongest ammonia oxidizing bacteria (AOB)-centred transcriptional configuration, together with peak expression of amoABC and hao, and higher AMO and HAO levels. This state was also associated with higher expression of Calvin-Benson-Bassham cycle and electron transport genes, indicating stronger coupling among ammonia oxidation, energy metabolism, and autotrophic carbon fixation. By contrast, the high-biomass reactor retained nitrifier-related potential, but this potential was not converted into proportional transcriptional or functional output. It showed weakened AOB-centered dominance and a broader reduction in chemolithoautotrophic functional expression. These findings reveal abundance-activity decoupling under excessive biomass retention and show that PN control should move beyond biomass concentration alone. A more informative operational perspective is the loading-to-biomass state, which helps indicate whether retained biomass is translated into active nitritation function.}, }
@article {pmid42323145, year = {2026}, author = {Zhang, S and Lv, H and Cui, B and Zhou, D}, title = {Low-substrate nitrogen drives functional succession toward a cooperative Candidatus Brocadia consortium in anammox systems.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135206}, doi = {10.1016/j.biortech.2026.135206}, pmid = {42323145}, issn = {1873-2976}, abstract = {Mainstream anammox treatment is promising but limited by slow acclimation and unstable performance under low nitrogen. Community succession is often observed, but it is usually explained by kinetic differences among anammox bacteria, which cannot fully account for competitive outcomes. Here, we operated an anammox biofilter under sustained low‑nitrogen stress and combined metagenomics, metatranscriptomics, co‑occurrence networks, and SMETANA to identify ecological adaptation mechanisms. During early acclimation, Ca. Kuenenia reduced the expression of costly biosynthetic pathways, including aromatic amino acid synthesis by 25.6%-38.8%. In contrast, Ca. Brocadia showed broad transcriptional activation, with anammox genes upregulated by ∼18-fold. During long-term operation, the community shifted to a multispecies Ca. Brocadia assemblage characterized by complementary model-inferred auxotrophies, stronger positive associations around the dominant Brocadia species (68.0%), and lower predicted metabolic resource overlap than that observed in the high-nitrogen system (0.66 ± 0.12 vs. 0.77 ± 0.10). Ultimately, Ca. Brocadia replaced Ca. Kuenenia as the dominant functional lineage, increasing from 1.0% to 44.7% in relative abundance and contributing 71.5% of total transcriptional activity. These findings suggest that low-nitrogen stress favors a metabolically complementary and potentially cooperative Ca. Brocadia assemblage rather than a single superior competitor, offering ecological guidance for stabilizing anammox processes in low-strength wastewater.}, }
@article {pmid42323301, year = {2026}, author = {Li, C and Feng, Y and Sáez-Sandino, T and Xiong, C and Eldridge, DJ and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and Zhou, G and García-Gómez, M and Valencia, E and Berdugo, M and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Berhe, AA and Cutler, NA and Abades, S and Alcántara, J and Alfaro, F and Arroyo, AI and Barrett, M and Bastida, F and Blaum, N and Boldgiv, B and Bowker, M and Branquinho, C and Hart, SC and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fraser, LH and Gallardo, A and García Velázquez, L and Geissler, K and Grebenc, T and Gusman Moltanvan, E and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Liang, J and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Muñoz-Rojas, M and Mussery, A and Unuk Nahberger, T and Nair, GR and Neuhauser, S and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and de Los Ríos, A and Rodríguez, A and Rodriguez Lozano, B and Roman, R and C Ruppert, J and Salah, A and Serôdio, J and Siles, JA and Singh, J and Travers, S and Undrakhbold, S and Valkó, O and Vivas, M and Wang, L and Williams, MA and Zaady, E and Maestre, FT and Singh, BK and Delgado-Baquerizo, M}, title = {Aridity-related differences in soil elemental ratios reshape microbial functional traits across global biomes.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73215-9}, pmid = {42323301}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407401//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Aridity alters soil carbon (C), nitrogen (N) and phosphorus (P) stoichiometry, yet the implications of these processes for soil microbial functional traits and potentials at the genomic level remain poorly synthesized. Here we combine measurements of soil C, N and P pools and ratios with shotgun metagenomes from 200 natural ecosystems spanning major biomes worldwide. Across sites, increased aridity is associated with lower soil C:N and N:P (and C:P) ratios and with a coordinated shift in microbial functional potential. Genes linked to catabolic resource acquisition-including carbohydrate-active enzymes and pathways for degradation of plant litter and organophosphorus compounds-are declined as C becomes relatively scarce. In contrast, genes supporting anabolic investment in growth and drought resistance, such as RNA transcription, protein synthesis and intracellular transport, are increased. These patterns indicate that aridity-related change in soil elemental ratios is coupled to a broad shift from catabolic to anabolic strategies in soil microbiomes. By linking soil elemental ratios to microbial functional traits across biomes, our study provides a framework for anticipating how climate-driven drying may reorganize microbial metabolism with consequences for carbon and nutrient cycling.}, }
@article {pmid42323352, year = {2026}, author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Pei, Y and Wan, Z and Zhang, T and Zhang, C}, title = {Investigating the human anellome across the lifespan reveals sex-specific biphasic trajectories.}, journal = {npj aging}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41514-026-00412-7}, pmid = {42323352}, issn = {2731-6068}, support = {BJWS2025082//Shanghai Eastern Talent Plan/ ; 32441099//National Natural Science Foundation of China/ ; }, abstract = {Anelloviruses dominate the human plasma virome, yet their lifespan dynamics and relationships with the immune system are unclear. We integrated metagenomics with cytokines, HERV-K, and CMV profiling across 405 individuals (0-100 years) and found that prevalence, abundance, and diversity varied non-linearly with age and by sex. Alphatorqueviruses accumulated progressively with age, while betatorqueviruses and gammatorqueviruses displayed biphasic, female-specific patterns. Alphatorquevirus species diversity had significant inflection points at ages 54-58 years in females. We identified a stable core of 12 age-uniform species, with their abundance trajectories diverging significantly by sex. Male bias in anellovirus metrics widened with age, and community dispersion reversed across lifespan. CMV IgG titers correlated significantly with anellovirus genus richness. In young adult females, anellovirus ORF1 was associated with IL-1β. These findings suggest altered anellovirus ecology as a correlate of age-related immune changes, positioning these viruses as strong indicators of immune status and offering new perspectives on age-modulated host-virus dynamics.}, }
@article {pmid42323440, year = {2026}, author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD}, title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57628-6}, pmid = {42323440}, issn = {2045-2322}, support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; }, abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.}, }
@article {pmid42323523, year = {2026}, author = {Hatwar, N and Qureshi, A}, title = {Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42323523}, issn = {1432-0991}, support = {UGC August 2021-Grant Number -191620062301//UGC/ ; }, mesh = {*Polyvinyl Chloride/metabolism/chemistry ; Biodegradation, Environmental ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/enzymology/isolation &amp; purification ; Composting ; *Microbiota ; Soil/chemistry ; *Plastics/metabolism ; }, abstract = {Polyvinyl chloride (PVC) plastic films accumulate in the environment and cause ecological damage due to their persistent, high-density polymeric nature. To mitigate PVC pollution, a sustainable bioremediation approach needs to be designed. Biodegradation of PVC using pure bacterial cultures has been reported as a sustainable option. However, PVC biodegradation studies in the presence of a soil/compost indigenous microbiome have not been conducted. In the present study, attempts have been made to understand and show the biodeterioration and biodegradation of PVC under soil and compost burial conditions. The study revealed that the PVC films, when buried under soil and compost at different conditions (ambient, sun-exposed, and 37 °C conditions), resulted in gravimetric weight loss with CO2 release. Under soil burial at 37 °C, PVC films showed 13.32 ± 0.10% weight reduction with 9.9 ± 0.9% CO2 evolution in 90 days, whereas compost conditions resulted in 6.89 ± 0.11% weight reduction. Another unique feature of the study is the metagenomic profiling of PVC buried soil/compost microbiomes, which revealed Proteobacteria and Actinobacteria as dominant phyla with Bacillus, Staphylococcus, Streptomyces, Arthrobacter, and Exiguobacterium as predominant genera. Also, the bioinformatics analysis revealed that these microbes possess potential metabolic capability associated with PVC biodeterioration and biodegradation (laccases, peroxidases, and oxidoreductases). Overall, the novelty reflects integrating metagenomic, spectroscopic, and morphological characterization of buried PVC plastic and linking microbial community dynamics with their enzymatic machinery and physico-chemical transformations of PVC. These multi-analytical approaches provided mechanistic evidence that the soil/compost microbial community initiates the PVC biodegradation process, offering a scientific basis for designing sustainable plastic waste management and remediation practices.}, }
@article {pmid42323568, year = {2026}, author = {Alves, CPP and Pinto, OHB and Pappas, GJ and Mota, SS and Rahlff, J and Krüger, RH}, title = {Taxonomic and functional diversity of the microbiome associated with the freshwater sponge Metania sp. (Haplosclerida: Metaniidae) from the Brazilian Cerrado, a metagenomic approach.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42323568}, issn = {1471-2180}, mesh = {Animals ; Brazil ; *Porifera/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Fresh Water/microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; Symbiosis ; Phylogeny ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Sponges, the oldest metazoans on the planet, have an evolutionary history shaped by symbiotic associations with microorganisms. Although well studied in marine sponges, these associations are poorly understood in freshwater species. This study explored the taxonomic diversity and functional potential of the microbiome of the freshwater sponge Metania sp. and its distinction from the surrounding water, using a metagenomic approach. The samples were collected in the Brazilian Cerrado.<br><br>RESULTS: Taxonomic assignment identified 17 phyla, including bacterial and archaeal, with 19 sequence variants successfully assigned to the species level. Bacteria comprised 16 phyla, with a predominance of Pseudomonadota, Actinomycetota, and Bacteroidota in both microbiomes. The sponge microbiome is distinct from the water microbiome (PERMANOVA; F&#x2009;=&#x2009;21.6, p&#x2009;=&#x2009;0.04), sharing only 27% of the identified taxa. Functional prediction resulted in 7,201 KEGG Orthologs (KOs), assigned to 117 significantly enriched metabolic pathways. Although 95 pathways are shared, differential abundance analysis identified 1,024 KOs more abundant in the sponge microbiome and 1,275 in the water. The presence of bacterial defense systems such as CRISPR-Cas in the sponge microbiome suggests a crucial role in protecting against phages while maintaining symbiosis. In contrast, the water microbiota is enriched with pathways linked to environmental adaptation, such as secondary metabolite biosynthesis and pollutant degradation. Although the water microbiome harbored 1.3 times more biosynthetic gene clusters (BGCs), the sponge microbiome also demonstrated biotechnological potential for producing secondary metabolites, especially antimicrobial.<br><br>CONCLUSIONS: These findings demonstrate that the freshwater sponge Metania sp. hosts a complex and functionally specialized microbial community that plays fundamental roles in adaptation, nutrition, and defense, highlighting the critical importance of symbiotic associations for the host.}, }
@article {pmid42323877, year = {2026}, author = {Gagniuc, PA and Gagniuc, E}, title = {The sequence alignment problem: boundary conditions as the unifying principle.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42323877}, issn = {1477-4054}, mesh = {Algorithms ; *Sequence Alignment/methods/statistics &amp; numerical data ; Humans ; }, abstract = {Sequence alignment provides a formal framework for comparison of biological sequences through score maximization over matches, mismatches, and insertion-deletion events. Classical formulations distinguish between global alignment, which enforces end-to-end correspondence through fixed boundary conditions, and local alignment, which extracts high-scoring subsequences without global consistency. Both paradigms arise from the same dynamic programing (DP) recurrences, shaped by substitution matrices and gap-penalty models that approximate molecular evolution. Canonical algorithms such as Needleman-Wunsch and Smith-Waterman establish the foundations of exact alignment, while later extensions introduce affine and convex gap costs, statistical score distributions, and probabilistic significance models. Modern work builds on these principles through bit-parallel techniques, band-restricted computation, cache-aware layouts, single instruction, multiple data and graphics processing unit parallelism, hardware accelerators, and index-assisted heuristics that enable large-scale genomic analysis. Sequence alignment underpins applications ranging from whole-genome comparison and metagenomics to protein annotation, variant detection, human leukocyte antigen typing, and microbial surveillance. Persistent challenges include scalability to ultra-long sequences, faithful models of complex mutation processes, avoidance of parameter bias, and formal limits on exact subquadratic solutions. Emerging directions emphasize adaptive data-driven scoring, hybrid global-local formulations, privacy-preserving computation, and real-time or incremental alignment. These developments reaffirm sequence alignment as a closely related DP framework shaped primarily by boundary conditions rather than distinct paradigms.}, }
@article {pmid42324063, year = {2026}, author = {Stancheva, R and Valadez-Cano, C and Van Aken, B and Selckmann, GM and Lawrence, J and Cahoon, AB}, title = {Limnofasciculus delicatus (Coleofasciculaceae, Coleofasciculales), a Novel Mat-Forming Cyanobacterium From Shenandoah River, Virginia, USA.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70377}, doi = {10.1111/1758-2229.70377}, pmid = {42324063}, issn = {1758-2229}, support = {//4-VA, A Collaborative Partnership for Advancing the Commonwealth of Virginia/ ; //Virginia Interstate Commission on The Potomac River Basin/ ; //VA Department of Environmental Quality/ ; 2222322//United States National Science Foundation/ ; }, mesh = {Phylogeny ; *Cyanobacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Virginia ; *Rivers/microbiology ; Genome, Bacterial ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Benthic cyanobacterial mats in flowing waters are complex communities typically composed of taxa from the orders Coleofasciculales and Oscillatoriales, many of which have unresolved taxonomic positions and poorly characterized toxic potential. We collected field mats of a benthic non-heterocytous filamentous cyanobacterium from the North and South Forks of the Shenandoah River in Northern Virginia (USA) that were dominated by a novel morphotype. Whole-genome and 16S rRNA gene phylogenetic analyses placed this cyanobacterium within the recently described genus Limnofasciculus (Coleofasciculaceae). Genome-based species delimitation metrics fell below accepted thresholds for bacterial species delineation relative to Limnofasciculus baicalensis, the only formally described species in the genus to date, supporting recognition of the cyanobacterium from Shenandoah River as a distinct species. Furthermore, the two Limnofasciculus species exhibited marked structural differences in the Box B helix of the 16S-23S ITS region. Comparative genomic analyses revealed a genome size similar to L. baicalensis and a conserved core gene repertoire alongside substantial divergence in biosynthetic gene cluster composition. Neither species contains biosynthetic gene clusters associated with the production of known cyanotoxins. Based on morphological, phylogenetic and genomic evidence, we describe Limnofasciculus delicatus sp. nov., supported by light microscopy and whole-genome characterization.}, }
@article {pmid42324270, year = {2026}, author = {Ma, Y and Yang, M and Xu, A and Zhao, X and Dong, X and Li, W and Tu, H and Guo, Y and Song, Z and Wu, X}, title = {Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01059-8}, pmid = {42324270}, issn = {2055-5008}, support = {K20230085//Healthy Zhejiang One Million People Cohort/ ; 2020E10004//Zhejiang Key Laboratory of Intelligent Preventive Medicine/ ; 2019R01007//the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2020C03002//Cancer Center, Zhejiang University and Key Research and Development Program of Zhejiang Province/ ; }, abstract = {This cross-sectional study compared the gut microbiota between metabolic dysfunction associated steatotic liver disease (MASLD) patients and healthy controls. A total of 1401 participants, including 392 MASLD patients and 1009 healthy controls, were enrolled from one project site of the Healthy Zhejiang One Million People Cohort (HOPE) between January 2022 and June 2023. Shotgun metagenomic sequencing was conducted to compare the composition and functional profiles of the gut microbiome between MASLD patients and healthy controls. Compared to the control group, MASLD patients exhibited significant alterations in both alpha and beta diversity, along with reduced connectivity and robustness of the gut microbial network. We identified significant changes in the abundance of 12 microbial strains between the two groups with two strains (t_SGB4749 and t_SGB4753) enriched and ten strains depleted in MASLD patients. In comparison to the control group, MASLD patients demonstrated distinct differences in the genomic potential related to increased glycolysis, decreased pyruvate metabolism, and elevated lipopolysaccharide (LPS) biosynthesis in both metagenomic functional profiling and single-strain genome analysis. These findings suggest that alterations in specific microbial strains and metabolic pathways may contribute to MASLD pathogenesis.}, }
@article {pmid42324618, year = {2026}, author = {Hernandez, JB and Abiodun, M and Hayer, SS and Dickson, T and Ayayee, P and Clayton, JB}, title = {Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687925}, doi = {10.1080/19490976.2026.2687925}, pmid = {42324618}, issn = {1949-0984}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Metagenome/drug effects ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Callithrix/microbiology ; Metagenomics ; Shotgun Sequencing ; Real-Time Polymerase Chain Reaction ; Genome, Bacterial ; Feces/microbiology ; }, abstract = {Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.}, }
@article {pmid42324716, year = {2026}, author = {Niloy, RK and Jewel, NA and Karim, D and Rolin, MH and Khan, T and Akter, A and Mondal, SI}, title = {Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70344}, doi = {10.1002/mbo3.70344}, pmid = {42324716}, issn = {2045-8827}, support = {LS/2022/1/05//SUST Research Center/ ; 37.01.0000.073.04.030.23.2134//University Grants Commission of Bangladesh/ ; }, mesh = {Humans ; *Bacteriophages/genetics/enzymology/classification/isolation &amp; purification ; *Endopeptidases/genetics/chemistry/metabolism ; *Gastrointestinal Tract/virology/microbiology ; Genome, Viral ; Bacteria/virology ; Metagenome ; Metagenomics ; }, abstract = {The escalating threat of antimicrobial resistance has renewed global interest in bacteriophages as precise and powerful tools for controlling bacterial populations in the human gut. These viruses owe much of their antibacterial potential to phage-encoded endolysins, enzymes capable of rapidly degrading bacterial cell walls with high specificity and low potential for resistance development. Despite their therapeutic promise, the overall composition of the gut phageome and the structural modularity of its endolysins remain poorly understood. In this study, we performed a large-scale analysis of 9141 human gut metagenomic samples from 34 independent studies. Using standardized workflows for assembly, genome clustering, host prediction, and protein domain annotation, we reconstructed 15,267 phage genomes and identified 3794 corresponding endolysins. The recovered genomes showed substantial variation in size and coding density, with an average GC content of 43%. Host prediction indicated that most phages targeted bacterial members of the phyla Bacillota (41%) and Bacteroidota (23%). Endolysin sequences grouped into 296 protein families and displayed striking domain modularity. Catalytic domains such as Amidase_2 and Glyco_hydro_25 frequently co-occurred with cell wall-binding motifs including LysM and CW_7. Remarkably, one endolysin contained 15 distinct domains, the highest natural domain diversity reported to date. Collectively, this study represents the most comprehensive characterization of the human gut phageome and its encoded endolysins to date. The exceptional modular diversity uncovered highlights the gut phageome as a rich reservoir of endolysin variants, providing a strong foundation for developing next-generation therapeutics against multidrug-resistant bacterial pathogens.}, }
@article {pmid42324848, year = {2026}, author = {Santos-Perdomo, I and Salces-Castellano, A and Moraza, ML and Mateos, E and Muñoz-Barrera, A and González-Montelongo, R and Suárez, D and Vega-Pita, N and Falcón-López, L and Lorenzo-Salazar, JM and Flores, C and Arribas, P and Andújar, C}, title = {Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70166}, doi = {10.1111/1755-0998.70166}, pmid = {42324848}, issn = {1755-0998}, support = {CGL2015-74178-JIN//Agencia Estatal de Investigaci&#xf3;n/ ; PID2021-126883NA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2022-143291NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; RYC2020-029196-I//Agencia Estatal de Investigaci&#xf3;n/ ; RYC2021-034291-I//Agencia Estatal de Investigaci&#xf3;n/ ; TESIS2022010039//Agencia Canaria de Investigaci&#xf3;n, Innovaci&#xf3;n y Sociedad de la Informaci&#xf3;n/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Spain ; Phylogeography ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; *Metagenomics/methods ; Soil ; }, abstract = {Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.}, }
@article {pmid42324919, year = {2026}, author = {Zhang, H and Xie, H and Liu, J and Xue, Y and Fan, Y and Chen, M and Wang, R and Zhao, Q}, title = {Dynamic CSF metagenomic next-generation sequencing to guide duration of therapy in Listeria monocytogenes ventriculitis: a multi-modal strategy with intraventricular gentamicin and neurosurgical intervention.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {7}, pages = {}, doi = {10.1093/jac/dkag184}, pmid = {42324919}, issn = {1460-2091}, support = {2023ZD0506502//National Science and Technology Major Project/ ; Z155080000004//National Key Clinical Specialist Construction Project/ ; }, }
@article {pmid42325417, year = {2026}, author = {Zhang, X and Yang, X and Hu, J and Zhang, W and Shen, W}, title = {Treatment of brain abscess rupturing into ventricle: a case report and literature review.}, journal = {Frontiers in surgery}, volume = {13}, number = {}, pages = {1782105}, pmid = {42325417}, issn = {2296-875X}, abstract = {Brain abscess is a focal intraparenchymal infection. Brain abscess breaking into ventricles is a potentially fatal complication of brain abscess, which can lead to sudden deterioration of neurological function. Its incidence rate is 0.3%-35.0%, and the mortality rate is 84.0%-100.0%. This paper reports a case of a 50-year-old male patient who had previously undergone intracranial hematoma evacuation and skull fixation for traumatic brain injury. He was admitted to the hospital with dizziness for 20 days and bradyphrenia for 4 days. After admission, enhanced computerized tomography(CT) and magnetic resonance imaging(MRI) indicated a left frontal lobe brain abscess. During empirical treatment with ceftriaxone and metronidazole, the abscess ruptured into the ventricle, leading to ventriculitis. Bilateral external ventricular drainage (EVD) combined with ventricular lavage was performed using stereotactic technology. Metagenomic next-generation sequencing (mNGS) of the pus identified the infecting bacteria as Parvimonas micra and Fusobacterium. According to clinical guidelines, the anti-infective regimen was adjusted, short-term low-dose methylprednisolone was used, and combined with hyperbaric oxygen therapy. The patient recovered and was discharged. This paper emphasizes that timely identification of brain abscess rupture leading to ventriculitis, adoption of bilateral external ventricular drainage combined with ventricular lavage, determination of abscess pathogens using mNGS technology, and selection of sensitive antibacterial drugs can improve the cure rate of ventriculitis.}, }
@article {pmid42325651, year = {2026}, author = {Mourad, A and Lupu, DS and Richey, M and Steven, P and Fowler, VG and Perkins, B and Holland, TL and Bergin, SP}, title = {Timing of Bronchoscopy and Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Host Pneumonia.}, journal = {Open forum infectious diseases}, volume = {13}, number = {6}, pages = {ofag361}, pmid = {42325651}, issn = {2328-8957}, abstract = {BACKGROUND: Immunocompromised patients are at high risk of pneumonia, with associated poor outcomes. Rapid microbiologic diagnosis is crucial, yet diagnostic yields vary widely. We evaluated the variability in diagnostic yield of usual care testing and plasma microbial cell-free DNA (mcfDNA) sequencing in the prospective observational Pneumonia in the Immunocompromised-Use of the Karius Test for the Detection of Undiagnosed Pathogens (PICKUP) study, specifically focusing on timing of testing relative to the onset of pneumonia.<br><br>METHODS: In this exploratory analysis, patient characteristics, variability in diagnostic yield, and the timing of bronchoscopy and mcfDNA sequencing from date of first abnormal imaging associated with suspected pneumonia were evaluated across enrolling sites.<br><br>RESULTS: A total of 222 patients from 10 enrolling sites were analyzed. Usual care diagnostic yield varied across sites (range, 7.7%-57.7%). Patient characteristics did not differ between sites, and median time from abnormal imaging to bronchoscopy was not different across sites (3 days [IQR, 3]). Diagnostic yield of bronchoscopy was significantly higher when performed &#x2264;3 days (early) from abnormal imaging (38.5% [52/135]) versus >3 days (delayed) (21.8% [19/87]) (difference, 16.7% [95% CI, 2.5%-28.3%]; P = .009). Adding mcfDNA sequencing to usual care testing increased overall diagnostic yield by 7.9% for patients undergoing early bronchoscopy, and by 16.3% for delayed bronchoscopy.<br><br>CONCLUSIONS: Early bronchoscopy enhances diagnostic yield in immunocompromised patients with suspected pneumonia. Irrespective of timing, plasma mcfDNA sequencing increases overall diagnostic yield in this clinical scenario. These findings underscore the importance of prompt diagnostic strategies in this patient population.}, }
@article {pmid42325854, year = {2025}, author = {Fan, L and Guan, J and Feng, L and Wang, Y and Zeng, H and Zhu, Y and Li, H and Chen, Q and Li, L and Qian, J and Liu, L and Li, Y}, title = {A patient with long-term diabetes dies following infection with Francisella novicida in Guangdong province, China: a case report.}, journal = {Infectious diseases &amp; immunity}, volume = {5}, number = {1}, pages = {68-71}, pmid = {42325854}, issn = {2693-8839}, abstract = {The rarity of Francisella novicida infection in humans is well-known, and the F. novicida cases occur in immunocompromised patients or those with underlying health problems. Herein, we report the case of a patient with long-term diabetes who died following F. novicida infection that caused multiple organ failure, although F. novicida was effectively eliminated using antimicrobial therapy. Microbiological confirmation of F. novicida infection relies on metagenomic next-generation sequencing (mNGS) and pdpD-2 gene-specific identification. This study highlights the importance of early pathogen diagnosis in severely infected patients, particularly in cases of F. novicida, and indicates that mNGS is a useful tool for early diagnosis.}, }
@article {pmid42326050, year = {2026}, author = {He, F and Yang, Y and Ma, D and Liu, P}, title = {Disseminated Cryptococcosis in a Non-HIV Patient: Diagnostic Value of Integrating mNGS, Culture, and Antigen Testing.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {597466}, pmid = {42326050}, issn = {1178-6973}, abstract = {Cryptococcus neoformans is an opportunistic fungal pathogen most commonly observed in individuals with human immunodeficiency virus (HIV) infection. Disseminated infections involving multiple organs, such as lungs, bloodstream, urinary tract, pleural cavity and central nervous system, are uncommon in patients without HIV. This work describes the case of a 72-year-old man who developed high fever and increased inflammatory markers after coronary artery bypass surgery. C. neoformans (8 sequence reads) was initially detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and was subsequently isolated from blood, urine and pleural effusion culture. Additionally, the cerebrospinal fluid tested positive for cryptococcal capsular polysaccharide antigen (CrAg), confirming disseminated infection involving multiple anatomical sites. The patient received liposomal amphotericin B combined with flucytosine antifungal treatment, which led to improvement in inflammatory parameters; however, the patient developed secondary multiorgan failure due to the severity of the illness. After 98 days of hospitalization, the patient was eventually discharged. This case highlights the diagnostic challenges of disseminated cryptococcosis in non-HIV hosts, particularly when involving atypical sites such as the urinary tract and pleural cavity. The integration of conventional microbiological methods, CrAg testing, and mNGS facilitated early diagnosis and enabled timely, standardized antifungal therapy.}, }
@article {pmid42326398, year = {2026}, author = {Zhao, S and Peng, S and Li, H and Yang, G and Gao, X and Xu, K and Shi, L and Yu, H and Qiao, S}, title = {An approach for diagnosis of diarrhea in neonatal piglets based on the core gut microbiota and machine learning.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852304}, pmid = {42326398}, issn = {1664-302X}, abstract = {Diarrheal diseases, such as yellow dysentery and white dysentery caused by pathogens or viruses, in newborn piglets lead to substantial economic losses in the swine industry worldwide. Gut microbiota dysbiosis is frequently observed in diarrheic piglets and is thought to play a role in disease pathogenesis, although causal relationships remain to be established. However, developing reliable microbiome-based diagnostic tools still poses a significant challenge. This study aimed to develop a diagnostic model for piglet diarrhea by integrating core microbiota analysis with machine learning. Fecal samples from diarrheic and healthy piglets were subjected to metagenomic sequencing to characterize archaeal, bacterial, and fungal communities. We identified diarrhea-associated bacterial biomarkers via LEfSe, DESeq2, and microbial cooccurrence network analysis. These microbial features were used to construct and compare multiple machine learning classifiers. Our results revealed significant disparities in the structure and diversity of the gut microbiota between diarrheic and healthy piglets, with the bacterial community showing the most notable changes. Among the models developed, the decision tree classifier based on bacterial genus-level features achieved the highest prediction accuracy of 91.18%. Furthermore, a simplified model utilizing a panel of 18 core bacterial genera also demonstrated high efficacy, with a support vector machine model achieving 88.24% accuracy. In independent validation using our internal dataset, the random forest model exhibited the best generalizability and stability. This study establishes a robust, microbiota-based diagnostic model for diarrhea in neonatal piglets, highlighting the potential of machine learning in leveraging microbiome data for disease classification and health management in livestock production.}, }
@article {pmid42326408, year = {2026}, author = {Cha, J and Yang, J and Zhang, Z and Qian, L and Yang, F and Li, S and Li, J and Jian, Z and Cheng, W}, title = {Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807081}, pmid = {42326408}, issn = {1664-302X}, abstract = {INTRODUCTION: The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses.<br><br>METHODOLOGY: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds.<br><br>RESULTS: The results showed no significant differences between the two breeds in core phylum composition or overall microbial diversity. A total of 146 bacterial genera were identified with significant differences at the genus level. Functional analysis revealed that the gut microbiota of Yunnan ponies was significantly enriched in pathways related to carbohydrate metabolism and pectin degradation, which are involved in basic energy acquisition. In contrast, Dutch warmblood horses were more enriched in host immune interaction pathways such as Toll-like receptor signaling. Analysis of ARGs indicated that while there was no difference in the overall diversity of ARGs between the two groups. Their association networks with specific bacterial hosts were markedly distinct, and the dominant ARG subtypes differed.<br><br>DISCUSSION: This study provides a descriptive characterization of the gut microbiome of Yunnan ponies, offering baseline data for future research on the conservation of this genetic resource and its health management in breeding.}, }
@article {pmid42326413, year = {2026}, author = {Peng, C and Delle Grazie, G and Ghanbari, M and May, A and Abeel, T}, title = {Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1702973}, pmid = {42326413}, issn = {1664-302X}, abstract = {BACKGROUND: Efforts to replace antibiotic growth promoters (AGPs) in livestock are often hindered by a limited mechanistic understanding of how sub-therapeutic antibiotic doses enhance animal growth. Since AGP concentrations are typically too low to directly suppress pathogens, their effects on the gut microbiome, particularly its ecological dynamics, warrant closer investigation. A critical but underexplored dimension is how these additives influence the structure and stability of microbial communities as interconnected ecosystems.<br><br>METHODS: We conducted a comparative network-based analysis to examine the effects of zinc-bactracin, a commonly used AGP, and Digestarom[&#xae;], an alternative phytogenic feed additive (PFA) on cecal microbiome dynamics in broiler chickens. Using metagenomic data from a repeated cross-sectional randomized controlled trial of 96 broiler chickens assigned to three dietary groups: Basal (Control), AGP and PFA, we constructed microbial co-occurrence networks using Spearman's correlation for birds raised on basal, AGP-, or PFA-supplemented diets at key developmental stages (Day 3, 14, 21, and 35). We assessed changes in network topology, modular organization and node centrality. We evaluated whether the network-prioritized keystone taxa could discriminate among diets using a Random Forest classifier.<br><br>RESULTS: Compared to the Control group, both AGP and PFA treatments induced consistent shifts in network topology, including reduced connectivity, increased modularity, increased percentage of positive interactions, enhanced mucosa connectivity, and improved structural robustness over experiment time. Overall, these treatment-induced changes were more pronounced under AGP than under PFA. Despite these changes, we identified conserved subgraphs with stable interconnections across diets and time points during the experiment. The node centrality analysis revealed condition-specific keystone taxa, but Linear Discriminant Analysis (LDA) and Random Forest (RF) struggled to accurately differentiate between diets using their abundance, particularly between PFA and the two other groups.<br><br>CONCLUSION: Our findings reveal that feed additives can reshape gut microbial dynamics without producing marked compositional shifts. The consistent network-level changes observed for both AGP and PFA highlight the value of ecological network analysis in uncovering microbial community responses. These insights improve our understanding of cecal microbiome responses in chickens, highlight potential modes of action of AGPs, and offer a comparative framework for assessing the microbial impacts of alternative feed additives.}, }
@article {pmid42326425, year = {2026}, author = {Wang, X and Yang, N and Hu, Y and Wang, X and Wu, Y and Zhang, A and Wang, Y}, title = {Vegetation restoration restructures soil sulfur allocation and sulfur-cycling functional potential in the Mu Us Sandy Land.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1845938}, pmid = {42326425}, issn = {1664-302X}, abstract = {Vegetation restoration in semi-arid sandy ecosystems can alter soil sulfur cycling not only through changes in sulfur stocks, but also through shifts in the partitioning between organic sulfur and sulfate and their microbial regulation. Here, we investigated soil sulfur pool allocation and sulfur-cycling functional potential along a five-stage vegetation restoration gradient in the Mu Us Sandy Land by integrating sulfur fraction measurements with metagenomic analyses. Vegetation restoration markedly reshaped the soil physicochemical and microbial context, as reflected by lower pH and higher TN, microbial biomass carbon, and enzyme activity in restored soils. In contrast, sulfur pools responded asynchronously: total sulfur and organic sulfur declined substantially from bare sandy land to restored vegetation types, whereas sulfate showed a weaker and comparatively more stable response. At the functional level, dominant sulfur-cycling genes were generally more abundant in bare sandy land, declined across restored vegetation types, and showed only partial recovery in forestland, indicating that restoration reorganized sulfur-cycling functional composition rather than uniformly enhancing sulfur-cycling potential. Taxonomically, dominant sulfur-cycling genes were consistently affiliated mainly with Actinomycetota and Pseudomonadota, but restored vegetation types exhibited more partitioned host compositions, with greater contributions from Acidobacteriota, Chloroflexota, and, for some genes, Thermoproteota. MAG-based analyses further showed that key sulfur-cycling genes were phylogenetically widespread but unevenly distributed across specific host lineages. Co-variation and Mantel analyses showed that sulfur-cycling genes formed coordinated functional modules and were most strongly associated with soil sulfur pools and fractions. Overall, vegetation restoration in the Mu Us Sandy Land primarily reshaped sulfur allocation and sulfur-cycling functional potential rather than promoting simple sulfur accumulation. These findings highlight that sulfur recovery in sandy drylands is better characterized by pool reallocation and functional reorganization.}, }
@article {pmid42326426, year = {2026}, author = {Nelon, JN and Eltaher, SS and Abdelhamid, AG}, title = {Shotgun metagenomic and phenotypic characterization of indigenous lactic acid bacteria from raw milk artisanal cheeses: metagenomic functional insight and starter culture traits.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820264}, pmid = {42326426}, issn = {1664-302X}, abstract = {The diversity of commercial starter cultures of lactic acid bacteria (LAB) used in fermented dairy products is limited. This has created strong demand to discover novel starter culture strains to develop unique products with appealing sensory characteristics. The current study used an integrated shotgun metagenomic and culture-based pipeline to (a) define taxonomic composition and functional potential of selected artisanal raw milk cheese microbiomes and (b) isolate and evaluate native LAB strains as potential starter cultures. Five artisanal cheeses (brie, bleu, plain gouda, mustard seed gouda, and nettle gouda) were analyzed. Shotgun metagenomics profiled the cheese microbiomes and revealed a high abundance of Lactococcus cremoris and Lactococcus lactis in gouda cheeses, whereas brie cheese contained high abundances of L. lactis and Streptococcus thermophilus. Functional profiling of metagenome-assembled genomes recovered from cheese microbiomes identified abundant pathways linked to carbon utilization, energy metabolism, and organic nitrogen metabolism. In parallel, 12 LAB isolates were recovered from all cheeses, of which five strains were classified taxonomically as L. lactis using whole genome sequencing. These five L. lactis strains displayed desirable milk and cream fermentation properties, achieving coagulation within 6 h, with final pH values of 4.5. The resulting fermented products contained 2.9%-4.2% protein content, displayed a relative increase in long-chain fatty acids, and a relative decrease in short-chain fatty acids compared to unfermented controls. The current study links cheese metagenome functional potential to dairy adaptation and identifies indigenous L. lactis strains as promising candidates for novel starter cultures in fermented dairy products.}, }
@article {pmid42326431, year = {2026}, author = {Mei, X and Wu, W and Fang, N and Guo, Y and Dai, X}, title = {Sludge compost: a double-edged sword for depleted soil restoration revealed by integrated multi-omics analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1731456}, pmid = {42326431}, issn = {1664-302X}, abstract = {The prospective use of sludge compost for restoring depleted soils requires balancing its agronomic benefits against potential ecological risks. This study employed an integrated metagenomic and metabolomic approach to evaluate the dose-dependent effects of sludge compost on soil properties, maize growth, and rhizosphere microbial communities. Results showed that moderate compost application (≤15% w/w) enhanced soil nutrient availability, promoted root development, and enriched beneficial microbial taxa (Streptomyces, Mesorhizobium, Flavisolibacter), while upregulating plant stress-response metabolites (terpenoids, flavonoids). Conversely, excessive application (>20%) induced salinity stress, impaired root growth, and altered the microbial community, favoring thermophilic and xenobiotic-metabolizing taxa. Critically, high application rates led to the accumulation of residual pharmaceuticals (anti-neoplastic and anti-epileptic agents) and pesticides (insecticides and rodenticides), which correlated with the enrichment of microbial pathways associated with human diseases, highlighting a significant ecological risk. In addition, root integrity was the primary determinant of a sustainable plant-microbe feedback loop. These findings underscore the necessity for tailored application strategies to harness the soil-restorative potential of sludge compost while mitigating contaminant-driven risks, providing a framework for its safe use in sustainable agriculture.}, }
@article {pmid42326513, year = {2026}, author = {Knight, R and Khatib, L and Patel, L and MahmoudianDehkordi, S and Labus, J and Agongo, J and Borkowski, K and Ambre, M and Brydges, C and Schimmel, L and Blach, C and Consortium, AGMP and Karu, N and Taylor, M and Diaz, E and Brosch, J and Bendlin, B and Swerdlow, R and Henderson, V and Chen, D and Saykin, A and Craft, S and Brewer, J and Wisniewski, T and Roberson, E and Dorrestein, PC and Kaddurah-Daouk, R}, title = {Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9917711/v1}, pmid = {42326513}, issn = {2693-5015}, abstract = {Cognitive impairment is increasing with global aging, yet mechanisms linking diet, the gut microbiome, and metabolism to cognitive function remain unclear. To investigate a diet-microbiome-metabolome axis associated with cognition, we integrated fecal metagenomics, diet, and multi-platform plasma metabolomics in 505 older adults from four ADRCs. Several microbes broadly associated with circulating metabolites were also linked to multiple measures of cognitive performance. These taxa exhibited coordinated metabolic signatures, with cognition-positive microbes associated with antioxidant, lipid, and microbial-host co-metabolites, and microbes negatively associated with cognition were linked to inflammatory and aromatic amino acid-derived metabolites. Dietary patterns, particularly the Healthy Eating Index Greens and Beans component, were associated with microbial composition and metabolomic structure. Mediation analyses supported a diet-microbe-metabolite-cognition pathway, while metabolites remained associated with cognition after accounting for microbial features. These findings highlight the metabolome as a central integrator of diet, microbial activity, and cognitive function.}, }
@article {pmid42326540, year = {2026}, author = {Yang, J and Nie, D and Zhang, Y and Li, C}, title = {Exploratory Pilot Multi-Omics Profiling of Gut Microbiota and Metabolic Features in Patients with Prolactinoma.}, journal = {Cancer management and research}, volume = {18}, number = {}, pages = {608026}, pmid = {42326540}, issn = {1179-1322}, abstract = {BACKGROUND: Growing evidence suggests a potential role of the gut microbiota in pituitary neuroendocrine tumors (PitNETs). This exploratory study focused on prolactinoma, the most prevalent PitNET subtype, to preliminarily characterize gut microbial and metabolic features associated with the disease.<br><br>MATERIALS AND METHODS: Fecal samples were collected from five patients with hyperprolactinemic prolactinoma and five patients with nonfunctioning (NF) PitNETs. Exploratory metagenomic and metabolomic analyses were performed to profile gut microbiota composition and metabolic alterations.<br><br>RESULTS: Compared with NF PitNET controls, prolactinoma patients showed distinct trends in gut microbial composition, including increased abundances of Bacteroides and Eubacterium and decreased abundances of Blautia and Clostridium. Metabolomic profiling identified differential metabolic features, including elevated fatty acid esters of hydroxy fatty acids (FAHFAs) and palmitoleic acid, which were mainly associated with glucose and lipid metabolism pathways.<br><br>CONCLUSION: This pilot multi-omics analysis provides preliminary evidence of altered gut microbiome-metabolite profiles in prolactinoma. These findings are hypothesis-generating and may support further investigation of gut-pituitary axis interactions in larger, well-powered cohorts.}, }
@article {pmid42326568, year = {2026}, author = {Stacul, A and Valido, E and Nyfeler, N and Bertolo, A and Zeh, RM and Fontana, AO and Pannek, J and Krebs, J and Leichtle, A and Glisic, M and Stoyanov, J}, title = {Precision Rehabilitation in Spinal Cord Injury: A Systematic Review of Omics Applications for Intervention Monitoring in Spinal Cord Injury.}, journal = {Archives of rehabilitation research and clinical translation}, volume = {8}, number = {2}, pages = {100598}, pmid = {42326568}, issn = {2590-1095}, abstract = {OBJECTIVE: To systematically evaluate the application and utility of omics technologies, high-throughput methods measuring the complete or targeted set of molecules inside a biological system at a certain timepoint, in monitoring and optimizing rehabilitation interventions in traumatic spinal cord injury.<br><br>DATA SOURCES: Embase, Medline/Ovid, and Web of Science were searched from inception to November 27, 2024.<br><br>STUDY SELECTION: Eligible studies included adults (&#x2265;18 years) with spinal cord injury undergoing rehabilitation interventions assessed using omics technologies (genomics, epigenomics, transcriptomics, proteomics, metabolomics, or metagenomics).<br><br>DATA EXTRACTION: Following PRISMA guidelines, independent screening, data extraction, and risk of bias (RoB) assessment (National Institutes of Health Quality Assessment Tools) were performed by 2 investigators. Based on RoB assessment, studies were classified from level 1 (most reliable) to level 4 (least reliable).<br><br>DATA SYNTHESIS: Twenty-three trials were included: 8 randomized controlled trials, 5 non-randomized controlled trials, and 10 pre-post trials. Twenty-two studies (96%) exhibit a moderate RoB due to small sample size and heterogeneity. Omics technologies were primarily applied to exercise and electrical muscle stimulation interventions (65%), followed by hormonal and cellular therapies (22%), and diet (13%). Transcriptomic analyses revealed consistent molecular adaptations, including increased mitochondrial biogenesis (proliferator-activated receptor gamma coactivator 1-alpha) and reduced muscle atrophy gene expression (myostatin), correlating with enhanced insulin sensitivity and improved aerobic capacity. Metagenomics consistently identified microbiome shifts, such as decreased inflammatory taxa and increased beneficial taxa, associated with improved metabolic profiles and bowel function. Proteomics and metabolomics highlighted systemic changes related to neurorecovery, immune modulation, and sperm motility, linking molecular signatures directly to clinical outcomes.<br><br>CONCLUSIONS: Omics technologies enable early identification of molecular alterations. However, given small sample sizes and heterogeneity of the current studies, these findings should be interpreted with caution. Gradual integration of omics, particularly epigenomics which may capture long-term, injury-related changes holds promise for developing personalized rehabilitation protocols and monitoring clinical progression in spinal cord injury.}, }
@article {pmid42326740, year = {2026}, author = {Avina-Bravo, EG and García-Lorenzo, I and Alfaro-Ponce, M and Breton-Deval, L}, title = {Machine learning-based classification of COVID-19 severity using respiratory microbiome profiles from shotgun metagenomic sequencing.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1801685}, pmid = {42326740}, issn = {2673-7647}, abstract = {Accurate clinical triage is critical for optimizing decision-making and resource allocation during infectious disease outbreaks such as COVID-19. In this study, we present an AI-driven decision-support tool for the triage of COVID-19 patients based on respiratory microbiome profiles derived from shotgun metagenomic sequencing. We analyzed 477 shotgun respiratory metagenomes from three independent public cohorts and generated genus-level taxonomic profiles, which were integrated with minimal clinical metadata (age, sex, and antibiotic exposure) to train supervised machine-learning models, including Random Forest, Support Vector Machine, and XGBoost. Model performance was evaluated using standard classification metrics, cross-validation, and particle swarm optimization for hyperparameter tuning. Across cohorts, we observed a consistent transition from microbiomes dominated by commensal taxa to dysbiotic states enriched in opportunistic and clinically relevant genera, particularly Acinetobacter and Staphylococcus, in severe and deceased patients. Among the evaluated models, XGBoost consistently achieved the best performance, reaching up to 96.1% accuracy, 97.6% F1-score, and 98.2% ROC-AUC in individual cohorts. When trained on the integrated dataset, XGBoost maintained robust performance (95.1% accuracy, 97.2% F1-score, 94.3% ROC-AUC) and demonstrated greater stability and lower variance compared to alternative models. Feature-importance analyses identified a compact and interpretable set of recurrent microbial predictors, and reduced-feature models retained substantial discriminative power when augmented with key clinical variables. These results support the respiratory microbiome as a valuable source of information for outcome-oriented clinical triage and position microbiome-informed machine learning as a scalable and interpretable decision-support approach for managing COVID-19 and future infectious disease scenarios.}, }
@article {pmid42326837, year = {2026}, author = {Virwani, PD and Qian, G and Cheung, CN and Pijarnvanit, TKKTS and Hsu, MSS and Chow, YH and Tang, LK and Tse, YH and Xian, JW and Lam, SS and Lee, CPI and Lo, CCW and Liu, RKC and Ho, TL and Chow, BY and Leung, KS and Lo, EKK and Yuen, MF and Leung, SY and Hung, IF and Louie, JCY and Teo, KC and El-Nezami, H and Ho, JWK and Lau, KK}, title = {Associations between gut microbiome and 24-hour blood pressure variability: a cross-sectional study highlighting sex differences and potential therapeutic targets.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e9}, pmid = {42326837}, issn = {2632-2897}, abstract = {Blood pressure (BP) variability is an independent risk factor for cardiovascular disease. Gut microbiome (GM) regulates BP, but its association with BP variability remains unclear. We examined the association of GM, determined by stool shotgun metagenomic sequencing, with 24-hour BP average real variability (ARV) assessed by ambulatory BP monitoring in 235 community-dwelling adults from Hong Kong (111 men and 124 women, mean age 54 ± 6 years) using covariate-adjusted statistical models. The GM alpha diversity was negatively associated with systolic BP (SBP) ARV in the full cohort, driven by women. In men, beta diversity of both GM species and function was associated with SBP ARV, while Bacteroides nordii and the steroid hormone biosynthesis pathway had a positive association with SBP ARV. Bacteroides nordii emerged as the key species driving the significant positive association of steroid hormone biosynthesis and other pro-pathogenic pathways with SBP ARV, including lipopolysaccharide biosynthesis, phenylalanine, and sulfur metabolism in men, warranting further investigation for its causal role. We demonstrated distinct signatures of GM dysbiosis, composition, and function with minimal overlap between men and women with increased 24-hour SBP variability. Our work suggests that sex differences should be an important consideration in mechanistic and therapeutic investigations of GM-mediated BP variability.}, }
@article {pmid42327082, year = {2026}, author = {Loya, O and Villarreal, ES and Carneiro, A and Agarwal, S and Fraidenburg, D and Sun, J and de Jesus Perez, V and Lahm, T and Oliveira, SD}, title = {Sex-linked Lung Estrobolome May Contribute to Pulmonary Hypertension Penetrance of Bmpr2 R899X Mutation via an ET-1 [high] Endoregulatory Macrophage Phenotype.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.08.729693}, pmid = {42327082}, issn = {2692-8205}, abstract = {Mutations in the bone morphogenetic protein receptor 2 (BMPR2) are a major genetic driver of pulmonary arterial hypertension (PAH), yet their penetrance is strikingly sex-biased: females are disproportionately affected, while males experience poorer outcomes. While hormonal and chromosomal factors have been implicated, the biological basis for this disparity remains not fully understood. Here, we investigated the role of the lung microbiome in sex-linked PAH pathogenesis. We hypothesized that increased BMPR2 mutation penetrance in females is partly driven by the accumulation of potent vasoactive molecules, such as endothelin-1 (ET-1), in response to lung microbiome dysbiosis. Using humanized Bmpr2 [+/R899X] mice, we integrate lung metagenomics with basic functional immune profiling to show that females develop a distinct microbiome profile, characterized by increased microbial-derived lipopolysaccharide (LPS), potentially fueling the pathogenic effects of the estrogen metabolite 16α-hydroxyestrone (16α-OHE). These signals converge on macrophages, where co-exposure led to a hyperactivated state characterized by enhanced phagocytosis and ET-1 secretion. Tissue-level analyses confirmed immune cell infiltration and spatial association with elevated ET-1, providing evidence that these factors may contribute to the onset of sex-linked PAH. Taken together, these findings identify a previously unrecognized microbiome-estrogen-immune axis that amplifies BMPR2 dysfunction and provides a mechanistic basis for female-biased disease penetrance.}, }
@article {pmid42327127, year = {2026}, author = {Troman, L and Kim, J and Rose, JJA and Johnson, M and Banfield, JF and Petrovski, S and Ghosal, D}, title = {A Novel Pilus System in Candidate Phyla Radiation Bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.03.709456}, pmid = {42327127}, issn = {2692-8205}, abstract = {The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15-50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primarily identified through metagenomic approaches. Candidatus Mycosynbacter amalyticus is a parasitic CPR bacterium that specifically targets Gordonia amarae , an actinobacterium with a hydrophobic, mycolic acid-rich cell envelope. Previous cryo-electron tomography indicated that Ca . M. amalyticus assembles thin extracellular filaments that are important for host interaction, yet their molecular identity remains unknown. Here, we applied single-particle cryo-electron microscopy to determine high-resolution structures of these filaments (2.8 and 3.6 Å), enabling the unambiguous identification of two previously uncharacterized pilins from the experimental density maps. These pilins, designated PamA and PamB, assemble into unique helical filaments distinct from all previously characterized filaments in both domain architecture and assembly mechanism. Despite low sequence identity, both PamA and PamB share conserved structural principles, including Ig-like folds and donor-strand exchange-mediated assembly. Phylogenetic analysis indicates that Pam pilins are exclusive to CPR bacteria, with homologues distributed predominantly across the classes Saccharimonadia and Microgenomatia. Analysis of the conserved pam operon identifies putative chaperones (PamC and PamD) and assembly factors structurally homologous to chaperone-usher pili components, suggesting an analogous but distinct assembly pathway. These findings expand the known diversity of bacterial pilus systems and demonstrate the power of structural approaches for characterizing uncharacterized proteins encoded within CPR genomes.}, }
@article {pmid42327471, year = {2026}, author = {Li, YM and He, FF and Donge-Liu,  and Bin-Xu,  and Shuyi-Li, }, title = {Multi-Omic Profiling of Gut Microbiota and Fecal Metabolites in Patients With Polycystic Ovary Syndrome: A Cross-Sectional Study.}, journal = {Health science reports}, volume = {9}, number = {6}, pages = {e72593}, pmid = {42327471}, issn = {2398-8835}, abstract = {BACKGROUND AND AIM: Intestinal flora composition in polycystic ovary syndrome (PCOS) varies, and the relationship between intestinal flora, fecal metabolites, clinical characteristics, and PCOS pathogenesis remains unclear. This study aimed to elucidate the gut microbiota characteristics of patients with PCOS, focusing on changes in normal-weight individuals, to provide new insights into its pathogenesis.<br><br>METHODS: We combined 16S rRNA gene sequencing re-analysis with metagenomics and metabolomics to investigate gut microbiota and fecal metabolome alterations in PCOS. We re-analyzed our previous data on normal-weight women with PCOS (PCOS, n&#x2009;=&#x2009;24; healthy controls [HC], n&#x2009;=&#x2009;12) and the public databases (PCOS, n&#x2009;=&#x2009;98; HC, n&#x2009;=&#x2009;71) to further investigate the structure and function of the PCOS intestinal flora. Subsequently, from our previous study samples, we selected 10 patients residing in the Kaifu district, and their fecal samples (normal-weight PCOS group, n&#x2009;=&#x2009;6; HC group, n&#x2009;=&#x2009;4) were analyzed using metagenomic sequencing and non-targeted fecal metabolomics. Finally, the correlations among intestinal flora, fecal metabolites, and clinical indicators were evaluated.<br><br>RESULTS: Based on the 16S rRNA data reanalysis, there were no significant differences in beta and alpha diversity between PCOS and normal controls. However, the PCOS group displayed a significantly higher relative abundance of Ruminococcus, Lachnospiraceae, and Escherichia-Shigella (p&#x2009;<&#x2009;0.05) but a significantly lower relative abundance of Prevotella (p&#x2009;<&#x2009;0.05) compared with the HC group. Subsequent metagenomics and metabolomics analyses revealed functional alterations, particularly in pathways related to secondary bile acid and lipid metabolism. Furthermore, Ruminococcus and Roseburia were positively correlated with Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) and negatively correlated with high-density lipoprotein (HDL) in patients with normal-weight PCOS.<br><br>CONCLUSIONS: This study highlights gut microbial dysbiosis as a key feature of PCOS. Reanalysis of 16S rRNA data revealed specific taxonomic shifts without altering overall diversity, notably an enrichment of Ruminococcus and a depletion of Prevotella. Furthermore, our metagenomics study identified functional reprogramming in pathways related to secondary bile acid and lipid metabolism. Crucially, even in normal-weight PCOS patients, these microbial alterations significantly correlated with adverse metabolic profiles (heightened insulin resistance and lower HDL levels), highlighting the microbiome as a potential therapeutic target.<br><br>ETHICAL REVIEW NO: CHiECRT1900028223.}, }
@article {pmid42327525, year = {2026}, author = {Maity, H and Hiwale, K and Meshram, S and Shishodiya, M and Pratyeke Maraskolhe, D and Narang, P}, title = {Zoonotic Nontuberculous Mycobacteria: Transmission Pathways, Laboratory Diagnosis, Detection Methodologies, and One Health Priorities.}, journal = {Infectious diseases &amp; clinical microbiology}, volume = {8}, number = {3}, pages = {232-252}, pmid = {42327525}, issn = {2667-646X}, abstract = {Nontuberculous mycobacteria (NTM) are an ecologically diverse group of environmental mycobacteria that are increasingly recognized as an important cause of human and animal disease. While most infections arise from environmental exposure, evidence from outbreak reports and genomic epidemiology suggests animal- associated and device-associated transmission pathways that intersect with human occupational and clinical risk. This review synthesizes current knowledge on zoonotic and animal-associated NTM, including recent taxonomy updates driven by genomic approaches, major reservoirs (including aquaculture, livestock, wildlife, and engineered water systems), as well as clinical and veterinary manifestations, and operational laboratory approaches for detection and characterization. We present a tiered diagnostic framework, ranging from microscopy and culture to targeted polymerase chain reaction (PCR), whole-genome sequencing, and emerging metagenomic and artificial intelligence (AI)-based pipelines, and we discuss biosafety considerations, reporting standards, and One Health surveillance priorities. Key research gaps include distinguishing true animal-to-human transmission from shared-source exposure, harmonizing One Health metadata and antimicrobial resistance (AMR) surveillance, and validating climate-sensitive predictive models. We propose practical, resource-adaptive recommendations for surveillance, laboratory workflows, and outbreak response. A coordinated global investment in integrated One Health genomic surveillance, harmonized metadata standards, and capacity building is urgently required to detect, attribute, and mitigate zoonotic NTM threats.}, }
@article {pmid42327630, year = {2026}, author = {Katarzyna, BS and Danuta, CL and Wiktoria, K and Małgorzata, T and Natalia, K and Dominika, MM and Karina, R and Joanna, P and Karina, K and Barbara, G and Danuta, LK and Helena, G and Wiśniewska, M and Karolina, S&#x17b; and Stachowska, E}, title = {The impact of freeze-dried food on gut microbiota composition: a preliminary study.}, journal = {Current research in food science}, volume = {13}, number = {}, pages = {101470}, pmid = {42327630}, issn = {2665-9271}, abstract = {Freeze-dried food is widely used during space expeditions or flights. However, evidence on how this affects the gut microbiota is limited. This study aimed to assess changes in the composition of gut microbiota in volunteers subjected to a 14-day stay in a controlled space-analogue habitat. Five adults provided stool samples at baseline and after two weeks. Meals were freeze-dried and standardized for portion size and composition. Meals were served according to a daily schedule with no additional snacks allowed. Coffee and tea were permitted. Compliance was monitored by returning and verifying the packaging. Bacterial community profiles were assessed using shallow shotgun metagenomics and analyzed using paired statistical methods, including alpha diversity indices and beta diversity ordination with permutation-based testing. Differential abundance analyses were performed to identify taxa showing trends toward change during the intervention. Overall gut bacterial diversity and community structure were essentially stable over 14 days among all participants. No statistically significant changes in alpha diversity were observed, and global beta diversity patterns did not indicate a consistent separation of the entire community between baseline and day 14. Exploratory analyses suggested small changes within individuals in the relative abundance of selected taxa; however, inter-individual variability prevailed, and the small sample size limited statistical power. It appears that a diet consisting entirely of freeze-dried foods, consumed for 14 days, did not significantly affect the overall diversity of the gut microbiota or the structure of its communities. However, these studies are preliminary in nature and provide hypotheses for use in larger, controlled studies aimed at elucidating the microbiome's response to dietary regimens based on freeze-dried products.}, }
@article {pmid42328576, year = {2026}, author = {Wu, Y and Gao, Y and Fang, Z and Huang, W and Guo, F}, title = {Time-dependent microbiology of peripancreatic drainage fluid in severe acute pancreatitis: a prospective real-world observational study using metagenomic sequencing and culture.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1795250}, pmid = {42328576}, issn = {2296-858X}, abstract = {OBJECTIVE: The microbiological characteristics of peripancreatic collections in severe acute pancreatitis (SAP) evolve over time, yet prospective data linking pathogen detection to disease timing and first intervention remain limited.<br><br>METHODS: This prospective single-center observational study enrolled 20 patients with SAP undergoing first-time percutaneous catheter drainage (PCD) for suspected infected pancreatic necrosis (IPN). Peripancreatic drainage fluid samples were simultaneously analyzed by conventional microbiological culture and metagenomic next-generation sequencing (mNGS). Microbiological positivity rates were compared according to time from disease onset (&#x2264;14 vs. >14&#x202f;days).<br><br>RESULTS: Overall, mNGS was positive in 9/20 cases (45.0%) and conventional culture in 6/20 cases (30.0%). When stratified by time from disease onset, microbiological positivity was low within 14&#x202f;days (mNGS: 1/7, 14.3%; culture: 1/7, 14.3%), but increased in patients undergoing drainage beyond 14&#x202f;days (mNGS: 8/13, 61.5%; culture: 5/13, 38.5%). mNGS identified a broader spectrum of pathogens, particularly polymicrobial, anaerobic, and fungal organisms. Enterococcus species and Klebsiella pneumoniae were the most frequently detected pathogens.<br><br>CONCLUSION: In this prospective observational cohort, peripancreatic collections were predominantly culture- and mNGS-negative during the early phase of SAP, supporting the concept that early necrosis is commonly sterile. In later stages, mNGS provides complementary microbiological information beyond conventional culture. These findings offer descriptive real-world evidence on the time-dependent microbiology of suspected IPN and may inform future studies on optimized diagnostic and antimicrobial strategies.}, }
@article {pmid42328632, year = {2026}, author = {Alnasser, SM and Ravikumar, S and Jayaraman, S and Selvaraj, D and Gunasekaran, V}, title = {Modulatory effect of porous silicon water-formulated catechin on gut microbiome in chronic unpredictable mild stress-induced dementia in a rat model.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1778580}, pmid = {42328632}, issn = {1663-9812}, abstract = {Stress-induced dysbiosis exacerbates mental health by modulating the nervous system and gut permeability. In this study, we investigate the therapeutic potential of porous silicon water-mixed catechin in alleviating chronic stress-induced dementia in rats. In a 28-day study, chronic unpredictable mild stress (CUMS)-induced rats were treated with Lactobacillus acidophilus (2.5 × 10^9 CFU, p.o), porous silicon water (7 mg/kg, p.o), catechin (30 mg/kg, p.o), and porous silicon water-mixed catechin (PSC) (7 mg and 30 mg/kg, p.o). The effect of porous silicon water-mixed catechin was evaluated through behavioral studies, plasma acetylcholinesterase activity, plasma glutamate, brain reactive oxygen species (ROS), brain endogenous anti-oxidant enzymes, metagenomics analysis, and histological examination of the prefrontal cortex and hippocampus. Administration of PSC significantly improved spatial learning and memory by reducing escape latency time and increased exploratory behavior in the open platform. PSC significantly inhibited acetylcholinesterase enzyme activity and restored endogenous antioxidants such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GSH) while reducing lipid peroxidation (LPO) compared to the CUMS group. In addition, PSC decreased the brain ROS levels, as determined by a fluorescence assay, and reduced plasma glutamate levels. 16S rRNA V3-V4 metagenomic analysis revealed a significant increase in microbial diversity (Shannon index: 7.52), microbial richness (Chao1 index: 1059.41), β-diversity index, and overall taxonomic abundance in treated rats. CUMS-induced morphological alterations in the hippocampus and prefrontal cortex were significantly improved following PSC administration. In the present study, Pearson correlation coefficient (r) demonstrates an association between gut microbial abundance and AChE activity. Hence, it has been concluded that PSC treatment may significantly modulate the gut microbiome and improve cognition in chronic unpredictable mild stress-induced dementia.}, }
@article {pmid42328867, year = {2026}, author = {Wang, Y and Sheng, P and Wang, S and Zhong, X and Cao, H and Li, D and Yan, J and Yang, J and Wang, Y and Peng, J and Sun, F and Wang, S and Feng, Y and Sun, J and Zhang, F}, title = {Gut microbiota translocation contributes to early islet apoptosis in streptozotocin-induced diabetes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0017226}, doi = {10.1128/msystems.00172-26}, pmid = {42328867}, issn = {2379-5077}, abstract = {Dysbiosis of the gut microbiota and impaired intestinal barrier are associated with diabetes development. The translocation of gut microbiota induced by streptozotocin (STZ) has been confirmed to damage pancreatic islets. However, it remains uncertain whether dysregulated gut microbiota plays an essential role in the translocation leading to pancreatic injury. In specific pathogen-free (SPF) and germ-free (GF) mice treated with STZ, we measured glucose metabolism levels, pancreatic islet damage, intestinal barrier integrity, and bacterial content in the pancreas to investigate the role of gut microbiota translocation in diabetes development. Shotgun metagenomic sequencing was used to analyze the impact of STZ on gut microbiota structure and function. Fecal microbiota transplantation was performed to explore if gut microbiota translocation depends on STZ-induced structural dysregulation. STZ induced intestinal damage in SPF mice, resulting in gut microbiota translocation to the pancreas, pancreatic apoptosis, and dysregulated glucose metabolism. Despite inherent intestinal barrier damage, absence of pancreatic apoptosis in GF mice further indicates that gut microbiota translocation is an essential prerequisite for STZ-induced pancreatic islet apoptosis. STZ significantly altered mouse gut microbiota composition and function. Transplantation of fecal microbiota from STZ-treated or saline-treated mice into STZ-induced GF mice also resulted in microbial translocation and pancreas apoptosis. Apoptosis of β cells in STZ-treated mice results from gut microbiota translocating to the pancreas through impaired intestinal barrier caused by STZ treatment independent of alterations in the gut microbial community.IMPORTANCEIn our study, the apoptosis of β cells in STZ-treated mice is the result of the translocation of gut microbiota to the pancreas through the impaired intestinal barrier induced by STZ, independent of alterations in the gut microbiota. These findings proposed the potential role of compounds in impairing the intestinal barrier integrity, promoting microbiota migration and finally damaging pancreatic islets.}, }
@article {pmid42328985, year = {2026}, author = {Pallotti, S and Nigro, ME and Albini, E and Russo, E and Carpi, FM and Falconi, M and Torbidoni-Baldassari, B and Giuliodori, AM and Petrelli, D and Beccacece, L and Pezzotti, G and Magistrali, CF and Massacci, FR and Napolioni, V}, title = {Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156226}, doi = {10.1128/spectrum.01562-26}, pmid = {42328985}, issn = {2165-0497}, abstract = {Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota, along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation-flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.IMPORTANCEAntimicrobial resistance is a growing global health concern that extends beyond clinical settings into agricultural and environmental systems. Slaughterhouses represent critical interfaces where microbial communities from livestock, processing environments, and wastewater converge, creating opportunities for the persistence and dissemination of antimicrobial resistance genes. Despite the widespread use of physicochemical treatments to reduce organic load and suspended solids in slaughterhouse wastewater, their impact on microbial communities and resistome remains poorly characterized. By applying long-read metagenomic sequencing, this study provides a comprehensive characterization of the microbiome and resistome in slaughterhouse wastewater before and after treatment. Our findings show that commonly applied coagulation-flocculation treatments do not substantially alter the relative structure of microbial communities or the diversity of resistance genes. These results highlight the potential role of slaughterhouse wastewater as an environmental reservoir for antimicrobial resistance and emphasize the need for improved treatment technologies and systematic surveillance strategies to mitigate the environmental dissemination of resistance determinants in line with the One Health approach.}, }
@article {pmid42329047, year = {2026}, author = {Villanelo, SAR and Vestergaard, SZ and Liu, L and Yang, Y and Pedersen, IS and Nielsen, PH and Dueholm, MKD}, title = {Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0147726}, doi = {10.1128/spectrum.01477-26}, pmid = {42329047}, issn = {2165-0497}, abstract = {The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation properties are essential for retaining active biomass while producing a clarified effluent. Understanding the microbial composition of AS and the functions of individual taxa is crucial for improving wastewater treatment practices and developing new treatment technologies. Although DNA-based studies have identified abundant taxa and inferred their metabolic roles, many of these organisms remain uncultured, limiting experimental validation of genome-based predictions. Here, we investigated whether antibiotics can transiently reduce community complexity and alleviate competitive exclusion during cultivation, thereby facilitating isolation of previously uncultured activated sludge bacteria. Dispersed single cells from AS were cultivated on agarose plates containing filter-sterilized AS fluid and 1 of 11 antibiotics at three concentrations. Full-length 16S rRNA gene amplicon sequencing indicated that antibiotics reduced microbial diversity and altered community composition in an antibiotic- and concentration-dependent manner. Two antibiotic conditions were selected for pure-culture isolation, resulting in 74 isolates that represented 28 different species based on genomic average nucleotide identity. These include 13 putatively novel species based on GTDB classification, and 19 species belonging to nine globally abundant AS core genera. Although several isolates belonged to genera with cultured representatives, they likely represent distinct species with potentially different ecological functions and physiological traits. These findings demonstrate that antibiotics can function as ecological selectors during cultivation and aid the targeted isolation of ecosystem-relevant activated sludge bacteria.IMPORTANCEBiological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.}, }
@article {pmid42329229, year = {2026}, author = {Yao, C and Wang, Y and Zhou, J and Liu, B and Qi, L and Wang, B and Chen, F and Hou, L and Liu, M and Zheng, Y}, title = {Acidification Dominates over Hypoxia in Controlling Estuarine Nitrogen Removal Dynamics under Coupled Stressors.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02533}, pmid = {42329229}, issn = {1520-5851}, abstract = {As critical transitional zones between land and sea, estuaries are confronting the dual threats of increasing acidification and hypoxia driven by human activities and climate change. However, the combined effects of these stressors on estuarine nitrogen removal processes remain poorly understood. In this study, using stable-isotope tracing and molecular techniques in the Yangtze estuary, we found that hypoxia promoted N removal, yet concurrent acidification can override this effect, leading to net inhibition and a consequent reduction in estuarine nitrogen removal capacity. However, in seasonally hypoxic zones, these combined stressors generally enhanced nitrogen removal rates (by up to 34.4%), which suggests a degree of resilience under such perturbations. Nevertheless, the concurrent acidification-hypoxia in seasonally hypoxic areas stimulated N2O emissions (8.5-44.4%), which may intensify climate forcing and thereby further exacerbate these environmental stressors. Metagenomic and quantitative PCR analyses corroborated these response patterns, revealing coordinated changes in the abundance and expression of key nitrogen-removal genes, as well as divergent microbial response strategies and niche differentiation under acidification-hypoxia stress. This study elucidates the previously overlooked interactive effects of acidification and hypoxia on estuarine nitrogen removal, providing a mechanistic basis for refining biogeochemical models to improve the reliability of simulations under multiple stressors.}, }
@article {pmid42329244, year = {2026}, author = {Gallichan, S and Mäklin, T and Picton-Barlow, E and McKeown, C and Forrest, S and Corander, J and Moore, M and Feasey, NA and Heinz, E and Graf, FE and Lewis, JM}, title = {A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producing Escherichia coli using post-enrichment metagenomics.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001757}, pmid = {42329244}, issn = {2057-5858}, mesh = {*Escherichia coli/genetics/enzymology/isolation &amp; purification ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Polymorphism, Single Nucleotide ; Humans ; Escherichia coli Infections/microbiology/transmission ; Feces/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Metagenome ; }, abstract = {Inferring transmission relies on accurately distinguishing between isolates from the same source and those from different sources, and high-quality genomic data are frequently used to model transmission scenarios. The post-enrichment metagenome sequencing (pe-MGS) method uses a sequencing approach to analyse the diversity of a target pathogen enriched by pre-culturing and has been effectively used to analyse the transmission of nosocomial infections. However, a direct comparison of single nucleotide variant (SNV) call accuracy, cost and feasibility between single-colony whole-genome sequence (sc-WGS) data and pe-MGS for an antimicrobial resistant bacteria of clinical importance, extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC), is required for implementation in large-scale clinical studies. A spiked stool sample and rectal swabs from six study participants were pre-enriched in buffered peptone water and cultured on MacConkey agar with 1 mg l[-1] cefotaxime. Seven single colonies were picked, and the remaining biomass of all colonies was collected from each plate, sequenced and analysed using the mSWEEP/mGEMS pipeline. We created a custom SNV calling workflow that allows heterozygous SNVs in a bacterial population and found that the choice of reference changed the number of measurable SNV distances between the sc-WGS and pe-MGS. Using our custom workflow with a core-gene reference captured 99% of all the SNV calls from multiple sc-WGS data in the pe-MGS data of the same culture. The plate sweep method offers a feasible, cost-effective alternative to multiple single colony picks for describing within-host ESBL-EC diversity. The workflow we developed allows for effective SNV calling from pe-MGS data that were comparable to SNV calls from multiple sc-WGS data from the same sample.}, }
@article {pmid42330062, year = {2026}, author = {Mason, CJ and Weaver, M and Kissinger, KR and Johnson, MA and Copeland, DC and Anderson, KE and Geib, SM}, title = {Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: impacts on error rates and sequence distributions.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0029526}, doi = {10.1128/msphere.00295-26}, pmid = {42330062}, issn = {2379-5042}, abstract = {The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, errors introduced during library preparation remain a major limitation, particularly during PCR amplification of full-length amplicons, where error accumulation may be elevated due to longer sequence lengths. These challenges are amplified when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated PCR cycle autonormalization for PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional fixed-cycle PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Under the workflow tested here, autonormalized libraries generally retained a high proportion of sequences following denoising and chimera removal, exhibited low residual error rates (<0.005%), and yielded relatively even read distributions across heterogeneous sample inputs. Overamplified reactions (30 cycles) showed elevated residual error rates and greater sequence loss, particularly in samples with higher microbial biodiversity, whereas low-cycle libraries produced more variable read output among specimens. Importantly, the PCR protocol had relatively minor effects on overall community composition compared with specimen type. These results support PCR cycle autonormalization as a useful workflow strategy for heterogeneous full-length 16S library preparation, while also highlighting the importance of library design, pooling strategy, and downstream processing in shaping technical outcomes.IMPORTANCEAmplicon-based sequencing of the 16S rRNA gene is a foundational tool in microbiome research, yet PCR amplification remains a major source of library-preparation error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can underamplify low-biomass samples or overamplify high-titer samples, increasing artifacts and sequence loss during downstream processing. Here, we show that PCR cycle autonormalization can be integrated into a PacBio full-length 16S rRNA workflow and, under the conditions tested, provides low residual error rates and relatively even sample representation across heterogeneous inputs. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale library preparation applications handling diverse specimen types.}, }
@article {pmid42330763, year = {2026}, author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH}, title = {Dietary polyphenols from shredded, steam-exploded pine particles mitigate the adverse effects of heat stress in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107298}, doi = {10.1016/j.psj.2026.107298}, pmid = {42330763}, issn = {1525-3171}, abstract = {The current study investigated the impact of supplementing polyphenols extracted from shredded, steam-exploded pine particles (PSPP) on the performance, gene expression, and gut metagenome of broilers exposed to cyclic heat stress (CHS). A total of 216 chickens were distributed into a 2 (temperature) by 3 (diets) design, with each treatment consisting of six replicates of six chickens. Specifically, chickens were fed diets containing 0% PSPP, 0.5% PSPP, and 1% PSPP and exposed to two temperature conditions: CHS (31°C) and Thermoneutral (NT, 21°C). The CHS was conducted for 6 hours every day for 7 consecutive days. Final body weight, average daily gain, and average daily feed intake (ADFI) were decreased, while feed conversion ratio and rectal temperature were increased in heat-exposed chickens. Dietary PSPP supplementation enhanced ADFI. The weight of the liver, bursa, and length of the jejunum and ileum were decreased in heat-exposed chickens. Plasma cholesterol was increased, and triglycerides were decreased in heat-exposed chickens. After heat exposure, gene expression of ZO1, ZO2, GLP2, NOX1, SOD, GPX, HSP70, HSP90, NRF2, TLR2, and TLR4 increased in the jejunum. GLP2 gene expression was similar in 1%PSPP exposed to HS in comparison to the entire NT-exposed chickens. Concerning microbiota analysis, alpha diversity indices, such as Shannon and Gini-Simpson, were increased following CHS exposure. Beta diversity, measured through unweighted and weighted UniFrac distances, showed temperature, dose, and interaction effects. The relative abundance of the phylum Candidatus Melainabacteria was increased, while Tenericutes populations were decreased in heat-exposed chickens. Furthermore, a total of thirty genera were identified as microbial biomarkers of CHS. Interestingly, the relative abundance of five pathogenic bacterial genera was found to be decreased in the 0.5%PSPP treatment. Overall, CHS negatively influences growth performance, modulates the expression of the gut antioxidant-related genes, and favors the colonization of pathogenic bacteria. However, 0.5% PSPP may mitigate CHS by reducing pathogen colonization in the gut of broilers.}, }
@article {pmid42330797, year = {2026}, author = {Gebert, JT and Huleatt, EM and Scribano, FJ and Eledge, MR and Dorn, LE and Hasmi, SK and Hyser, JM}, title = {High-throughput quantitation of pathogen-induced calcium signals captured through live-cell fluorescence microscopy.}, journal = {Cell calcium}, volume = {136}, number = {}, pages = {103160}, doi = {10.1016/j.ceca.2026.103160}, pmid = {42330797}, issn = {1532-1991}, abstract = {Many intracellular pathogens manipulate host cell calcium to facilitate their survival and replication. Live-cell microscopy using fluorescent calcium indicators has become an indispensable tool for characterizing the mechanisms underlying both homeostatic and pathogen-induced cellular calcium dynamics, but such imaging must be coupled with robust quantitative analysis. Further, calcium imaging is most powerful when paired with reductive studies targeting calcium-modulating proteins. The lack of specific inhibitors or agonists to directly target most pathogen-induced calcium signals precludes many of the approaches that have allowed for robust characterization of major eukaryotic cell calcium signaling mechanisms, such as ER Ca[2+] release by inositol triphosphate receptors. Given this, we sought to develop quantitative imaging pipelines tailored for the characterization of pathogen-induced calcium signals. Using rotavirus as a prototypical calcium-modulating pathogen, we developed and optimized a suite of computational tools for automated quantitation of both intra- and inter-cellular calcium signals detected via live-cell imaging of infected epithelial monolayers expressing genetically encoded calcium indicators. Using recombinant strains of rotavirus that express fluorescent markers, we developed a system that allows for automated detection of rotavirus-infected cells and normalization of signals to infectivity. All tools were built in ImageJ, making them freely available and adaptable across operating systems and microscope setups. These tools required minimal active time from the user and allowed for the extraction of signal parameters previously unquantifiable, increasing the speed and breadth of characterization.}, }
@article {pmid42330834, year = {2026}, author = {Cabrera, C and Carrión, N and Mateo, D and Heredia, L and Pino, M and Galvez, S and Forcadell-Ferreres, E and Vicens, P and Torrente, M}, title = {Shotgun metagenomic profiling of the gut microbiota in Parkinson's disease dementia and dementia with Lewy bodies.}, journal = {Parkinsonism &amp; related disorders}, volume = {149}, number = {}, pages = {108400}, doi = {10.1016/j.parkreldis.2026.108400}, pmid = {42330834}, issn = {1873-5126}, abstract = {BACKGROUND: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are related α-synucleinopathies that share Lewy pathology, but they differ clinically. Increasing evidence links gut microbiota (GMB) dysbiosis and microbially derived metabolites to Parkinsonian disorders yet reported associations remain heterogeneous across cohorts and the Lewy body dementia syndromes are comparatively under characterized. This study integrated clinical characterization and GMB profiling in Parkinson's disease dementia (PDD), DLB, and healthy controls (HC) to identify shared and syndrome specific features, and to relate these patterns to cognitive, neuropsychiatric, and functional outcomes.<br><br>METHODS: The present cross-sectional case-control study in Spain included 76 adults aged 60 to 85 years (HC&#x202f;=&#x202f;38, PDD&#x202f;=&#x202f;27, DLB&#x202f;=&#x202f;11). Stool samples underwent shotgun metagenomic sequencing, with species-level taxonomic profiling using Kraken2. Community diversity was assessed using observed species and Chao1 richness, Shannon alpha diversity, and Bray-Curtis dissimilarity for beta diversity. LEfSe and multivariate linear modeling with MaAsLin2 were performed to identify GMB species associated with PDD and DLB and their clinical correlates.<br><br>RESULTS: PDD showed higher richness compared with HC. Shannon alpha diversity did not differ between groups. Bray-Curtis differed by separation of HC from both PDD and DLB, with no significant difference between Lewy body dementia syndromes. LEfSe identified 19 significantly differential taxa. Furthermore, several taxa showed significant multivariable associations with clinical outcomes.<br><br>CONCLUSIONS: PDD and DLB shared a broadly similar GMB alteration away from HC, with multivariable associations between several taxa and clinical outcomes. Longitudinal and functional studies are needed to clarify causality and biomarker potential.}, }
@article {pmid42330882, year = {2026}, author = {Li, X and Wang, W and Liu, Y and Xu, Z and Wang, M and Zhao, J and Hua, Y}, title = {Role of nitrate-dependent Fe(II)-oxidizing bacteria in coupling nitrogen and phosphorus cycling in nearshore sediments of shallow lakes.}, journal = {Water research}, volume = {304}, number = {}, pages = {126323}, doi = {10.1016/j.watres.2026.126323}, pmid = {42330882}, issn = {1879-2448}, abstract = {The nearshore shallow-water zones of lakes serve as critical interfaces for the interception and transformation of land-derived nitrogen and phosphorus pollutants. Nitrate-dependent Fe(II)-oxidizing bacteria (NDFOB) may promote the formation of Fe(III) (hydr)oxides through nitrate reduction and Fe(II) oxidation, thereby potentially enhancing the adsorption of phosphorus in pore water and coupling of nitrogen removal and phosphorus immobilization; however, their ecological role in shallow lakes remains poorly understood. This study focused on six shallow lakes, analyzing the relationships between most probable number (MPN) counts of NDFOB, nitrogen, iron, and phosphorus contents, and using metagenomic techniques to explore their associations with functional genes involved in nitrogen, iron, and phosphorus cycling. The results showed that the number and spatial distribution of NDFOB were associated with lake trophic status. In moderately eutrophic lakes, elevated nitrogen loads were correlated with NDFOB enrichment possibly due to the provision of abundant electron acceptors (NO3[-]) for nitrate-dependent Fe(II) oxidation, and NDFOB number was positively correlated with nitrogen concentrations and negatively correlated with phosphorus content in pore water. Meanwhile, it was also associated with relative abundances of iron reduction-related genes and the presence of iron oxidation-associated genes. Network analysis further provided statistical clues for putative functional links between the ferrous iron oxidation process linked to NDFOB genera (e.g., Aquabacterium) and iron reduction, denitrification, and organic phosphorus mineralization. This study highlights the potential role of NDFOB in intercepting nitrogen and phosphorus within nearshore sediments and provides a microbial perspective for mitigating the risk of internal phosphorus release in shallow lakes.}, }
@article {pmid42330901, year = {2026}, author = {Barbe, V and Saint-Picq, C and Odobel, C and Hingant, M and Pujo-Pay, M and Cruaud, C and Petit, JL and Fischer, C and Boulard, Y and Cébron, A and Ter Halle, A and Eyheraguibel, B and Lemechko, P and Bruzaud, S and Ghiglione, JF}, title = {Unveiling plastic biodegradation pathways through [13]C-DNA stable isotope probing and metagenomics.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142755}, doi = {10.1016/j.jhazmat.2026.142755}, pmid = {42330901}, issn = {1873-3336}, abstract = {Polyhydroxyalkanoates (PHAs) are promising biobased and biodegradable alternatives to conventional plastics, yet their degradation mechanisms and the diversity of microorganisms involved remain poorly characterized in marine ecosystems. Here, we used [13]C-labeled poly(3-hydroxybutyrate) (PHB) and combined DNA-stable isotope probing (DNA-SIP) with metagenomic to identify and functionally characterize active PHB-degrading bacteria in seawater. We identified three metagenome-assembled genomes (MAGs) affiliated with the genus Agarilytica that exhibited an exceptional expansion of preficted extracellular short-chain-length PHA depolymerase genes (ephaZscl) with up to 14 copies per genome, far exceeding the one-to-two copies typically reported. Comparative genomic and structural analyses revealed gene duplication and fusion events, given rise to tandem or chimeric depolymerases that may enhance catalytic diversity and substrate accessibility. Three-dimensional structural modeling confirmed that these fusion proteins retained functional catalytic domains with potential cooperative or independent activity. Such genomic redundancy and structural diversification likely confer an adaptive advantage for PHB biodegradation in marine environment. Collectively, our findings provide new insights into the ecological and evolutionary strategies of marine PHB degraders and highlight the power of DNA-SIP metagenomic for elucidating active plastic biodegradation pathways under natural conditions.}, }
@article {pmid42331262, year = {2026}, author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R}, title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.}, journal = {Genomics}, volume = {}, number = {}, pages = {111282}, doi = {10.1016/j.ygeno.2026.111282}, pmid = {42331262}, issn = {1089-8646}, abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.<br><br>METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.<br><br>RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).<br><br>CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.}, }
@article {pmid42331273, year = {2026}, author = {Chen, D and Wang, Y and Cao, A and Hou, Y and Kong, F and Shi, J and Wang, S}, title = {Manganese-based activated carbon composites promote nitrogen removal in low temperature constructed wetlands via enhanced extracellular electron transfer.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125092}, doi = {10.1016/j.envres.2026.125092}, pmid = {42331273}, issn = {1096-0953}, abstract = {Constructed wetlands (CWs) provide cost effective, nature based wastewater treatment but suffer performance losses at low temperatures. We tested granular activated carbon-supported manganese composites (MnX-GAC; X = Fe or Zn) positioned within CWs to enhance microbial extracellular electron transfer (EET). MnX-GAC increased electron acceptors/donors, strengthened EET activity, and improved nitrogen removal while mitigating temperature impacts. At 15°C, the MnX-GAC system (CW6) raised ammonium (NH4[+]-N) removal by 31.0% versus CW1. Although CW6 generated more CO2 due to intensified carbon mineralization, it effectively suppressed the emissions of potent greenhouse gases (N2O and CH4) and achieved the lowest GWP per unit of nitrogen removed of 4.53 mg CO2-eq/mg N. Metagenomics showed the enrichment of key functional taxa (e.g., Chloroflexota, Thermodesulfobacteriota, and Bacteroidota) and the upregulation of nitrogen metabolism genes and carbon metabolism genes, alongside increases in electron-transport chain and mediator genes, collectively facilitated electron production and utilization. These changes indicate that MnX-GAC enhances EET mediated pathways to sustain nitrogen removal under low temperature. Overall, MnX-GAC offers a practical strategy to overcome low-temperature limitations in CWs, delivering higher nitrogen removal and lower life-cycle climate impacts.}, }
@article {pmid42331805, year = {2026}, author = {Shan, Z and Chen, Y and Chen, F and Zhang, Y and Chen, H and Wang, Z and Wang, X and Zhong, J and Wong, IN and Chen, J and Li, X and Lin, Z and Purcell, R and Guo, Y and Li, X and Li, X}, title = {Dietary yacon concentrate reshapes microbial-metabolite crosstalk to inhibit colorectal cancer.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00931-3}, pmid = {42331805}, issn = {2396-8370}, support = {82203520//National Natural Science Foundation of China/ ; 82203264//National Natural Science Foundation of China/ ; SHAX-LC-202332//Shanghai Anti-Cancer Association "Soar" Program/ ; }, abstract = {Yacon concentrate, which is rich in fructan, phenolic compounds, and flavonoids, exhibits notable nutritional and antioxidant properties. This study explored the potential of New Zealand yacon concentrate to modulate the gut microbiota and host metabolism, alleviate inflammation, and enhance antitumor immunity. The anti-inflammatory and antitumor effects of yacon concentrate were evaluated in mouse models of dextran sulfate sodium (DSS)-induced colitis and colorectal cancer (CRC). Ex vivo gut chemostat model experiments were performed to assess the impact of yacon concentrate on human gut microbiota remodeling. The gut microbiota composition was then analyzed via metagenomic sequencing, and metabolomic profiling was conducted to identify the key bioactive metabolites. Yacon concentrate significantly ameliorated DSS-induced colitis by reducing weight loss, lowering the disease activity index scores, and alleviating colonic shortening in mice. In CRC models, yacon concentrate markedly suppressed tumor growth, reduced tumor incidence, and decreased tumor burden. Microbiota derived from the chemostat after yacon supplementation not only enriched beneficial bacteria and inhibited the growth of immunotherapy-resistant bacteria but also enhanced energy and short-chain fatty acid metabolism. Moreover, transplantation of this microbiota into mice significantly improved the tumor microenvironment and inhibited tumor growth. Collectively, these findings indicate that yacon concentrate is associated with changes in the gut microbiota and metabolomic profiles, supporting a potential link between yacon intake and modulation of the gut microbiota-metabolome axis. These observations provide a rationale for further mechanistic and interventional studies evaluating yacon concentrate as a dietary strategy for colitis prevention and CRC prevention, and as an adjunctive treatment.}, }
@article {pmid42331835, year = {2026}, author = {Yan, X and Shan, Z and Zhao, Y and Wu, W and Tao, Z and Yang, C and Wang, Y and Zhang, Y and Wang, Y and Zhang, C}, title = {Multi-omics insights into floral-fruity aroma formation during Pu'er tea fermentation inoculated with a synthetic fungal community.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00945-x}, pmid = {42331835}, issn = {2396-8370}, support = {202101BA070001-239//Yunnan provincial science and technology department science and technology project/ ; CXTD020//Pu'er tea science and technology research innovation team/ ; FWCY-ZNT2025021//Yunnan province higher education institutions science and technology projects for key industries/ ; 32360771//National natural science foundation of China/ ; 2020XJGH08//Yunnan provincial university center for Pu'er tea processing, key scientific research project of Pu'er university/ ; 2023PEXYCXTD001//Pu'er university outstanding innovation team/ ; 2024J1099//Yunnan provincial education department project/ ; }, abstract = {Pu'er tea fermentation relies on complex microbial activities. This study explored aroma formation in ripe Pu'er tea inoculated with a synthetic fungal consortium using a multi-omics approach across six sampling stages. Sensory evaluation, physicochemical analysis, volatile profiling (HS-SPME-GC×GC-TOFMS), non-volatile metabolomics (UHPLC-Q-Exactive/MS), and metagenomic sequencing were integrated. Inoculation was associated with a distinct floral-fruity aroma. Combined ROAV and VIP analyses identified four volatile compounds, namely phenylethyl alcohol, trans-β-ionone, geraniol, and 1-octen-3-ol, as potentially important aroma-active contributors. Among them, phenylethyl alcohol, trans-β-ionone, and geraniol might play a major role in the floral-fruity character, and their accumulation appeared associated with tea moisture content. Nonanal exhibited a high ROAV but a low VIP value. Non-targeted metabolomics revealed 154 significantly altered metabolites, 38 of which were associated with these volatile compounds. Metagenomic analysis indicated substantial shifts in microbial community structure and function, correlated with physicochemical parameters and volatile profiles. Random forest modeling identified Sphingomonas, Rothia, and Bacteroides as potentially involved in aroma formation. These findings provide insights into the metabolic and microbial dynamics underlying floral-fruity aroma development, offering a scientific basis for tailored starter culture design.}, }
@article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {19}, number = {1}, pages = {}, pmid = {41928235}, issn = {1755-8794}, support = {K99 ES034086/ES/NIEHS NIH HHS/United States ; R00 ES034086/ES/NIEHS NIH HHS/United States ; R01 ES027224/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Alterations to the gut microbiome have been linked to cardiometabolic disease, like type 2 diabetes and hypertension, in adults, but few studies have investigated these associations in adolescents. We examined the relation between the gut microbiome and cardiometabolic risk in adolescence and determined whether sex and race/ethnicity modified these associations. METHODS: In 144 adolescents (age range: 11–14 years) from the Health Outcomes and Measures of the Environment (HOME) Study, we quantified gut microbiome alpha diversity using the Shannon index and species’ relative abundances (i.e., centered log-ratio normalized abundances) in stool DNA that underwent metagenomic sequencing. We assessed adolescent cardiometabolic risk using a cardiometabolic risk summary score, its individual components (i.e., visceral fat, leptin to adiponectin ratio, HOMA-IR, triglyceride to high-density lipoprotein cholesterol ratio, and systolic blood pressure), as well as total cholesterol and hemoglobin A1c. We used linear regression models to estimate covariate-adjusted cross-sectional associations of the Shannon diversity index and species’ relative abundances with cardiometabolic risk, and examine differences in these associations by sex and race/ethnicity. At the species level, the false discovery rate (FDR) correction, with q-value < 0.20, was considered statistically significant. RESULTS: Among all adolescents, a higher Shannon diversity index was associated with lower systolic blood pressure [β: -0.18 (95% CI: -0.35, -0.01)] in covariate-adjusted models. However, the associations of the Shannon diversity index with cardiometabolic risk did not differ significantly by sex or race/ethnicity. Although associations of the relative abundances of species, prevalent in at least 10% of samples, with cardiometabolic risk were not statistically significant tamong all adolescents after correcting for multiple comparisons (qFDR ≥ 0.20), sex modified the association of the relative abundance of Ruminococcus lactaris with HOMA-IR (qinteraction = 0.151), with positive association among females [β: 2.05 (95% CI: 0.93, 3.17), q = 0.155] and suggestive negative association among males [β: -0.84 (95% CI: -1.59, -0.09), q = 0.983]. Associations of the relative abundances of Streptococcus parasanguinis (qinteraction = 0.097), Enterocloster SGB14313 (qinteraction = 0.097), and Alistipes ihumii (qinteraction = 0.097) with total cholesterol also differed between female and male adolescents. We observed differences between adolescents of non-Hispanic black and non-Hispanic white race/ethnicity in the association of the relative abundance of Lachnospira pectinoschiza (qinteraction = 0.028) with total cholesterol. CONCLUSIONS: Our findings suggest that the gut microbiome is associated with cardiometabolic risk in adolescence in a sex-specific manner, and may differ by race and ethnicity.}, }
@article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, mesh = {Animals ; *Feces/microbiology ; *Sus scrofa/microbiology ; *Metagenomics/methods ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Dietary Fiber/metabolism ; Carbohydrate Metabolism ; Sequence Analysis, DNA ; Diet ; Animals, Wild/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.<br><br>RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.<br><br>CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, }
@article {pmid41928791, year = {2026}, author = {Sommer, AJ and Auch, B and Khoruts, A and Bajaj, JS}, title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41928791}, issn = {2693-5015}, abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.}, }
@article {pmid41929040, year = {2026}, author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ}, title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714183}, pmid = {41929040}, issn = {2692-8205}, abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.<br><br>IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.}, }
@article {pmid41929113, year = {2026}, author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R}, title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714056}, pmid = {41929113}, issn = {2692-8205}, abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.}, }
@article {pmid41929272, year = {2026}, author = {Biesheuvel, MM and Barkema, HW and Morley, PS and Pinnell, LJ and Doster, E and Valeris-Chacin, R}, title = {In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1770245}, pmid = {41929272}, issn = {2297-1769}, abstract = {Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of a targeted enrichment (TE) shotgun sequencing approach to detect and classify M. bovis strains in milk metagenomic samples. As a proof of concept, the accuracy of this approach was assessed using milk-derived M. bovis strains. A total of 620 M. bovis whole-genome sequences were downloaded from NCBI, of which 162 (26.1%) originated from milk samples. Genomes were grouped into Genomically Clustered Sequence Variants (GSVs) using MashTree and TreeCluster to enable strain-level classification. To simulate TE sequencing data, genomes from different milk-associated GSVs were randomly selected and fragmented in silico into 150-bp reads. Mock milk samples were generated by sampling reads with replacement from these genomes. Sequencing depth was modeled using a Poisson distribution, while mixed-strain DNA samples were simulated by including 1, 3, 6, or 9 GSVs per sample. Enrichment proportions were set at 0.3, 0.5, 0.7, and 0.9. Two classification tools, Kraken2 and Themisto/mSWEEP, were evaluated for their ability to detect and classify the simulated TE reads. Themisto/mSWEEP consistently outperformed Kraken2, achieving an average read classification accuracy of 84.9% compared with 1.4% for Kraken2. Sensitivity for Themisto/mSWEEP was 100% with a single spiked GSV and declined slightly to 97.0% with nine GSVs, whereas Kraken2 achieved sensitivities of only 17.3% and 4.7%, respectively. Positive predictive value (PPV) showed a similar pattern: 98% for Themisto/mSWEEP vs. 4.7% for Kraken2 with a single GSV, and 65.5% vs. 10% with nine GSVs. While Kraken2's PPV increased slightly with additional GSVs, Themisto/mSWEEP's PPV decreased. Both methods maintained high specificity and negative predictive value (>91%) across all scenarios. Enrichment proportion had no measurable effect on performance. Overall, Themisto/mSWEEP demonstrated superior accuracy for GSV-level identification of M. bovis strains. Enrichment to at least 30% of total reads was sufficient to recover strain-level data. Further work is needed to assess the biological relevance and practical applications of these genomic clusters.}, }
@article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Periodontitis/therapy/microbiology ; Longitudinal Studies ; Male ; *Mouth/microbiology ; Female ; Middle Aged ; *Lung/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Adult ; Dental Plaque/microbiology ; Respiratory Function Tests ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, }
@article {pmid41929455, year = {2026}, author = {Geng, Y and Yuan, Y and Lin, X and Wei, J and Zhang, Q and Mao, X and Zhang, X and Zhang, X and Zhang, Y and Zhao, J and Guo, F and Zheng, P}, title = {Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1653022}, pmid = {41929455}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/virology/epidemiology/microbiology ; China/epidemiology ; *Coinfection/microbiology/virology/epidemiology ; Female ; *SARS-CoV-2/genetics/isolation &amp; purification ; Male ; Middle Aged ; Aged ; Adult ; Risk Factors ; Mycoplasma pneumoniae/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; Severity of Illness Index ; Pneumonia, Mycoplasma/epidemiology ; }, abstract = {BACKGROUND: Reports on mixed infection with different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in China remain scarce. In this study, we analyzed the clinical characteristics of mixed infections involving different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in central China.<br><br>METHODS: Nested polymerase chain reactions and metagenomic next-generation sequencing were employed to identify severe acute respiratory syndrome coronavirus 2 variants. Clinical data, including hospitalization days, severity classification, outcomes, and laboratory data, were collected and analyzed.<br><br>RESULTS: Seven patients had mixed infections with different severe acute respiratory syndrome coronavirus 2 variants in samples collected on different dates. Overall, 54.6% (83/152) of patients had co-existing respiratory pathogen infection. The most common co-existing respiratory pathogen was Mycoplasma pneumoniae. Longer hospital stays, intensive care unit admission, and prolonged duration from admission to positive severe acute respiratory syndrome coronavirus 2 sample detection were independent risk factors for acute coronavirus disease infection with different respiratory pathogens. Severity classification, mixed infection, cerebral fraction, and fever were independent risk factors for failed treatment. Early detection of white blood cell count, procalcitonin, and D-dimer concentrations can help predict mixed respiratory infections and treatment outcomes.<br><br>CONCLUSIONS: The phenomenon of mixed infection with different variants in patients with coronavirus disease may have been underestimated. Therefore, active surveillance of severe acute respiratory syndrome coronavirus 2 variants should be performed in older patients with comorbidities.}, }
@article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; Humans ; *Asthenozoospermia/metabolism/etiology/microbiology ; *Dysbiosis/complications/metabolism/microbiology ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Adult ; Fecal Microbiota Transplantation ; Case-Control Studies ; Sperm Motility ; Metabolomics ; Spermatozoa ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, }
@article {pmid41929693, year = {2026}, author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z}, title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729476}, pmid = {41929693}, issn = {1664-302X}, abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.<br><br>METHODS: Vaginal swabs (sPTB, n&#x202f;=&#x202f;37; term, n&#x202f;=&#x202f;62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.<br><br>RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p&#x202f;<&#x202f;0.05), and distinct community structure (PERMANOVA p&#x202f;<&#x202f;0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC&#x202f;=&#x202f;0.82), and a multi-metabolite model improved classification (AUROC&#x202f;=&#x202f;0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.<br><br>CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.}, }
@article {pmid41929767, year = {2026}, author = {Peng, W and Yang, W and Ma, L and Wang, Q and Yang, R and Ji, A and She, M and Wang, T and Gong, W and Yan, L}, title = {Flower vinegar prepared from Yunnan large-leaved tea tree prevents high-fat diet-induced obesity in mice by regulating gut microbiota.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1749951}, pmid = {41929767}, issn = {2296-861X}, abstract = {Obesity and its metabolic complications are major public health concerns. The gut microbiota plays a pivotal role in regulating host adiposity. Fermented products from Camellia sinensisvar. Assamica (Yunnan large-leaved tea) flowers, a novel food ingredient, may offer therapeutic potential, but their effects on obesity and gut microbiota remain unexplored. We investigated the anti-obesity effects of vinegar fermented from Camellia sinensisvar. Assamica flowers (TTFV) in a high-fat diet (HFD)-induced obese mouse model. Body weight, glucose and lipid metabolism, hepatic injury, steatosis, inflammation, and oxidative stress were assessed. Metabolomic analysis and metagenomic sequencing of gut microbiota were performed. Key metabolic pathways were analyzed. TTFV supplementation significantly attenuated HFD-induced body weight gain, improved glucose and lipid profiles, alleviated hepatic steatosis and injury, and reduced systemic inflammation and oxidative stress. TTFV modulated host metabolite profiles and related metabolic pathways. Crucially, TTFV reshaped the gut microbiota structure: it increased the relative abundance of Bacteroidota and decreased the Firmicutes/Bacteroidota ratio at the phylum level. At the family level, it promoted beneficial bacteria (Oscillospiraceae, Eubacteriaceae) and suppressed potentially harmful ones (Erysipelotrichaceae). Metabolic pathway analysis indicated TTFV's positive role in maintaining cellular homeostasis and regulating metabolic disturbances. Our findings demonstrate that TTFV exerts protective effects against HFD-induced obesity in mice. These benefits are closely associated with the remodeling of gut microbiota composition and the modulation of key metabolic pathways. This study is the first to report the anti-obesity potential and microbiota-regulating effects of TTFV, suggesting its promise as a functional food ingredient for promoting intestinal health and mitigating obesity-related metabolic disorders.}, }
@article {pmid41929953, year = {2026}, author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE}, title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261436287}, pmid = {41929953}, issn = {2542-4823}, abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.<br><br>OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.<br><br>METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.<br><br>RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (&#x3b5;4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.<br><br>CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.}, }
@article {pmid41930262, year = {2025}, author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C}, title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1757196}, pmid = {41930262}, issn = {1664-302X}, abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.}, }
@article {pmid41930266, year = {2026}, author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag041}, pmid = {41930266}, issn = {2730-6151}, abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.}, }
@article {pmid41930333, year = {2026}, author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T}, title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.}, journal = {MedComm}, volume = {7}, number = {4}, pages = {e70705}, pmid = {41930333}, issn = {2688-2663}, abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.}, }
@article {pmid41930475, year = {2026}, author = {Tan, Y and Zou, D and Ni, C and Zeng, Q and Li, M}, title = {From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {14}, pages = {10789-10803}, doi = {10.1021/acs.est.5c12277}, pmid = {41930475}, issn = {1520-5851}, mesh = {*Synechococcus/genetics ; Estuaries ; *Bacteriophages/genetics ; Mutation ; *Metagenome ; Ecosystem ; }, abstract = {Picocyanobacteria, represented by Prochlorococcus and Synechococcus, are major photosynthetic organisms in aquatic ecosystems, and their viruses (cyanophages) significantly impact cyanobacterial ecology and evolution. Here, we combined metagenomics of Synechococcus communities along four representative estuaries in China and whole-genome analyses of laboratory-evolved Synechococcus mutants to link viral diversity to host adaptation and evolution. We assembled 83 cyanophage genomes (mainly cyanomyoviruses), with expanded auxiliary metabolic genes encoding glycosyltransferases and radical S-adenosyl methionine proteins involved in amino acid and lipopolysaccharide metabolism. Metagenome-assembled cyanobacterial genomes revealed mutations predominantly in membrane-associated functions linked to phage infection. In parallel, we identified genetic pathways conferring phage resistance in 18 evolved Synechococcus mutant strains that are resistant to phage infection. Notably, mutations in carbohydrate (rfbA) and photosynthetic energy transfer (cpeT) of Synechococcus mutants recurred in both cultured isolates and recovered metagenomes. These results indicate that cyanophages in estuaries leverage broader metabolic toolkits, while Synechococcus repeatedly evolves resistance. Together, these findings outline a reciprocal adaptive landscape that helps explain the persistence and turnover of picocyanobacterial populations in estuarine environments.}, }
@article {pmid41930516, year = {2026}, author = {Wang, W and Li, M and Liu, X and Li, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Anaerobic antimony oxidation by mine groundwater bacteria: The energy-detoxification trade off governed by carbon source and Sb concentration.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141926}, doi = {10.1016/j.jhazmat.2026.141926}, pmid = {41930516}, issn = {1873-3336}, mesh = {*Antimony/metabolism ; Oxidation-Reduction ; *Groundwater/microbiology/chemistry ; *Carbon/metabolism ; Mining ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Anaerobiosis ; }, abstract = {Microorganisms drive anaerobic antimony (Sb) oxidation and detoxification in groundwater, how carbon source (organic vs. inorganic) regulates this process and shapes microbial adaptive strategies remains unclear. To fill this knowledge gap, microcosms were conducted with groundwater from Xikuangshan mining-area, integrating with hydrochemistry, genes quantification, and metagenomics. The results demonstrated efficient anaerobic Sb(III) oxidation coupled with NO3[-] reduction, regulated synergistically by Sb concentration and carbon sources. The concentration of 0.5 mM Sb(III) served as a critical threshold that triggered changes in bacterial diversity, composition, and Sb(III)-oxidation behavior. Below this, NaHCO3 promoted higher oxidation rates (P < 0.05), linked to enrichment of Hydrogenophaga, Aquabacterium, Acidovorax, and aioA genes (Sb-oxidizing gene). Above 0.7 mM Sb(III), Na-lactate activated aioA and narrowed the rate gap, accompanied by increases in both abundance and niche of Dechloromonas. In addition, elevated Sb stress reshaped the metabolic networks across microcosms. The communities prioritized energy allocation to nitrogen fixation (nifH) with multiple benefits over redundant carbon fixation (cbbL). This research expands the known range of Sb and carbon drive microbial metabolic remodeling, advancing our predictive understanding of Sb biogeochemical cycling in contaminated aquifers.}, }
@article {pmid41930813, year = {2026}, author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S}, title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158039}, doi = {10.1016/j.phymed.2026.158039}, pmid = {41930813}, issn = {1618-095X}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/metabolism ; *Diterpenes/pharmacology ; Humans ; Mice ; Male ; *Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; Signal Transduction/drug effects ; Dextran Sulfate ; Colon/drug effects ; Andrographis/chemistry ; }, abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.<br><br>PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.<br><br>METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-&#x3b3;-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.<br><br>RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1&#x3b2;, IL-6, TNF-&#x3b1;) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-&#x3ba;B signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-&#x3ba;B signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.<br><br>CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-&#x3ba;B signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.}, }
@article {pmid41931872, year = {2026}, author = {Ren, Z and Wen, Y and Ma, Y and Li, M and Wang, L and Yu, R and Wu, L}, title = {Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.}, journal = {Water research}, volume = {298}, number = {}, pages = {125791}, doi = {10.1016/j.watres.2026.125791}, pmid = {41931872}, issn = {1879-2448}, mesh = {*Wetlands ; Salinity ; *Methane/metabolism ; Oxidation-Reduction ; *Nitrites/metabolism ; Anaerobiosis ; Species Specificity ; Adaptation, Physiological ; }, abstract = {Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a key process regulating methane emissions from wetland ecosystems. However, the species-specific mechanisms that enable N-DAMO bacteria to adapt and occupy distinct niches along environmental gradients (such as salinity) remain largely unknown. This makes it difficult to predict the ecological function of these bacteria. In this study, the structure, functional diversity, and species-specific salinity adaptation mechanisms of N-DAMO bacterial community in the Ulansuhai Wetland along a natural salinity gradient were investigated. An integrated approach combining metagenomic sequencing, isotopic tracer experiment, quantitative PCR, and biogeochemical measurements was employed for this research. The results show that salinity significantly reshaped the community structure and diversity of N-DAMO bacteria, while their potential activity remained functionally stable. This functional resilience was underpinned by distinct niche partitioning among four dominant species of Candidatus Methylomirabilis, species. Each species exhibited unique genomic potential for exopolysaccharide biosynthesis, osmoregulation, and stress response. Furthermore, the N-DAMO process constituted a significant methane sink, representing 39.5% of the observed anaerobic methane oxidation activity. Path analysis further explained that salinity regulated N-DAMO bacterial communities directly and through indirect pathways mediated by soil carbon and nitrogen pools. This research provides the first mechanistic framework linking species-specific genomic traits of N-DAMO bacteria to salinity adaptation and niche partitioning. The study offers novel insights for predicting wetland methane emissions.}, }
@article {pmid41931886, year = {2026}, author = {Xiao, S and Han, Z and Tang, Y and Wu, X and Huang, J and Zeng, W}, title = {Dual roles of tetracycline-degrading bacteria in pollutant detoxification and resistome reshaping under tetracycline-copper co-contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141951}, doi = {10.1016/j.jhazmat.2026.141951}, pmid = {41931886}, issn = {1873-3336}, mesh = {*Copper/metabolism/toxicity ; *Tetracycline/metabolism ; *Soil Pollutants/metabolism/toxicity ; Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism ; Soil Microbiology ; *Bacteria/metabolism/genetics ; }, abstract = {Combined contamination of soils with antibiotics and heavy metals represents a growing environmental challenge, yet remediation strategies addressing their synergistic toxicity remain limited. In this study, the bioremediation potential of a tetracycline-degrading bacterial consortium (Raoultella sp. XY-1 and Pandoraea sp. XY-2) was evaluated in tetracycline-copper (TC-Cu) co-contaminated soils by integrating chemical, biological, and ecological assessments. Soil column experiments demonstrated that bioaugmentation significantly enhanced TC degradation (48.57-53.71% after 90 days) compared to uninoculated controls (<12%), while simultaneously reducing copper bioavailability by shifting acid-extractable and reducible fractions toward more stable oxidizable forms. Inoculation further alleviated the strong inhibition of soil enzymatic activities (sucrase, urease, phosphatase), reflecting improved soil functional recovery. Metagenomic sequencing revealed that TC-Cu co-contamination reshaped microbial community composition, particularly increasing the relative abundance of Actinomycetota and Campylobacterota. Bioaugmentation further facilitated the establishment of Raoultella and indirectly stimulated indigenous resistant taxa through community interactions. Correlation network analysis further revealed that Raoultella was a highly connected genus in co-occurrence networks of antibiotic resistance gene (ARG)- and metal resistance gene (MRG)-hosting genera. LC-MS detection of intermediate products during TC microbial degradation proposed three microbial degradation pathways and inferred microbial resistance mechanisms under TC-Cu coexistence. Collectively, these findings highlight that TC-degrading bacteria not only reduce pollutant toxicity but also reshape microbial and genetic landscapes in co-contaminated soils, potentially suppressing the diffusion risk of resistance genes at low TC-Cu level. This work provides novel insights into the ecological trade-offs of bioremediation and supports the development of targeted, sustainable strategies for complex antibiotic-metal pollution scenarios.}, }
@article {pmid41931897, year = {2026}, author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y}, title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141890}, doi = {10.1016/j.jhazmat.2026.141890}, pmid = {41931897}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Wastewater/microbiology/analysis ; *Fluorocarbons/analysis/toxicity ; RNA, Ribosomal, 16S/genetics ; *Genes, Bacterial ; *Microbiota/drug effects/genetics ; Water Microbiology ; Bacteria/genetics ; }, abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.}, }
@article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, mesh = {*Olea/microbiology ; Fermentation ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Food Microbiology ; *Microbiota ; Fermented Foods/microbiology ; Italy ; }, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, }
@article {pmid41932427, year = {2026}, author = {Bao, C and Ren, Y and Tang, C and Su, Y and Yue, H and Chen, X}, title = {Viral isolation and genomic characteristics of the first bovine parainfluenza virus type 3 isolated from water buffaloes (Bubalus bubalis) in China.}, journal = {Veterinary journal (London, England : 1997)}, volume = {317}, number = {}, pages = {106655}, doi = {10.1016/j.tvjl.2026.106655}, pmid = {41932427}, issn = {1532-2971}, mesh = {Animals ; *Buffaloes/virology ; *Parainfluenza Virus 3, Bovine/genetics/isolation &amp; purification ; China ; Phylogeny ; *Respirovirus Infections/veterinary/virology ; *Genome, Viral ; Microscopy, Electron, Transmission/veterinary ; }, abstract = {Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease. In this study, we report the isolation and genomic characterization of BPIV3 from a water buffalo with respiratory symptoms in China. Virus isolation was performed using susceptible cell cultures, followed by identification via RT-qPCR, transmission electron microscopy, and indirect immunofluorescence. Metagenomic sequencing of the near-complete genome showed that the isolate shared 89.9%-91.1% nucleotide identity with BPIV3 genotype A strains. Notably, several distinct mutations were identified in the structural protein genes, and phylogenetic analysis demonstrated that the isolate formed a separate cluster within genotype A, suggesting that it may represent a novel subtype within this genotype. To our knowledge, this is the first report describing the isolation and genomic characterization of BPIV3 from water buffaloes in China. These findings provide baseline molecular data for further studies on the genetic diversity and evolution of BPIV3.}, }
@article {pmid41932524, year = {2026}, author = {Qian, J and Li, X and Xu, X and Zhang, D and Xiang, G and Wang, Z and Zhang, Z and Liu, M and Hao, W and Wu, D}, title = {Thiosulfate-Driven redox buffering enables efficient nitrogen removal and norfloxacin degradation in mixed denitrifying systems.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134550}, doi = {10.1016/j.biortech.2026.134550}, pmid = {41932524}, issn = {1873-2976}, mesh = {*Norfloxacin/metabolism/isolation &amp; purification ; *Denitrification/drug effects ; Oxidation-Reduction ; *Thiosulfates/pharmacology/chemistry ; *Nitrogen/isolation &amp; purification ; Biodegradation, Environmental/drug effects ; Bioreactors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Wastewaters often contain both conventional pollutants and recalcitrant antibiotics, posing challenges to biological treatment. This study investigated a mixed autotrophic-heterotrophic denitrification system driven by sodium acetate and sodium thiosulfate for simultaneous nitrate and norfloxacin removal. A sequencing batch reactor was operated in four stages, culminating in norfloxacin exposure (0.5 mg/L). Results showed stable nitrogen removal (>95%) and norfloxacin degradation (>90%) under sustained antibiotic stress. Batch tests confirmed that the co-presence of thiosulfate and acetate enhanced norfloxacin biodegradation via co-metabolic pathways, with negligible abiotic removal. Three-dimensional excitation-emission matrix spectroscopy revealed a shift toward humic-like extracellular polymeric substances under norfloxacin, supporting biofilm integrity. 16S rRNA sequencing and metagenomics indicated dynamic microbial restructuring, with persistent core taxa (Thauera, Desulfofustis) and enrichment of stress-tolerant groups (norank_o_SJA-15). Functional analysis showed upregulation of carbon metabolism (pta, ackA), denitrification (nirS, nosZ), and sulfur oxidation (SUOX, SoxX, SoxA) genes, alongside oxidative stress mitigation genes (catB, gst) and xenobiotic degradation genes (HGD, E1.13.11.4). Antibiotic resistance gene profiles shifted toward multidrug (>29%), peptide resistance (14.0%→15.4%), and glycopeptide resistance (7.0%→9.4%), dominated by multidrug efflux and target alteration mechanisms, enabling community resilience while minimizing energetically costly defenses. This work elucidates the synergistic roles of dual electron donors in pollutant co-removal and stress mitigation, offering a robust, sustainable strategy for treating antibiotic-laden wastewater.}, }
@article {pmid41932525, year = {2026}, author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J}, title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134546}, doi = {10.1016/j.biortech.2026.134546}, pmid = {41932525}, issn = {1873-2976}, mesh = {Oxidation-Reduction ; *Chromium/metabolism ; *Methane/metabolism ; Electron Transport ; Biodegradation, Environmental ; *Microbial Consortia/physiology ; }, abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-L-Proline, L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.}, }
@article {pmid41932647, year = {2026}, author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L}, title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2026.03.023}, pmid = {41932647}, issn = {1673-8527}, abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.}, }
@article {pmid41932883, year = {2026}, author = {Silva, RMB and Slyvka, A and Lee, YJ and Guan, C and Lund, SR and Raleigh, EA and Skowronek, K and Kuska, MS and Bochtler, M and Weigele, PR}, title = {A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41932883}, issn = {2041-1723}, support = {FNP, POIR.04.04.00-00-5D81/17-00//Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)/ ; }, mesh = {*Adenine/metabolism/chemistry ; *RNA, Transfer/metabolism ; *Bacteriophage mu/enzymology/genetics ; *Viral Proteins/metabolism/genetics/chemistry ; *DNA, Viral/metabolism/chemistry/genetics ; *Deoxyadenosines/biosynthesis/chemistry/metabolism ; Models, Molecular ; }, abstract = {Nucleic acid modifying enzymes drive diverse defense and counter-defense measures in the evolutionary arms race between viruses and their cellular hosts. Abundant and widespread bacterial viruses (bacteriophage or phage) encode for biosynthetic pathways that install elaborate DNA hypermodifications which protect their genomic DNA from host endonucleases. Here, we establish the molecular basis for the multistep biosynthesis of 6-aminocarboxymethyl-2'-deoxyadenosine (6-NcmdA), a nucleobase hypermodification found in the virion DNA of bacteriophage Mu that leads to restriction evasion in the context of phage-host conflicts. In the first step, we show that Mu-encoded Mom enzyme catalyzes the formation of 6-NcmdA by transferring glycine from charged tRNA[Gly] to the N6 position of adenine within double-stranded DNA. We uncover a second step where the glycyl-dA intermediate undergoes an on-base rearrangement to form 6-NcmdA. Examination of the proposed reaction pathways by quantum chemical calculations confirms the instability of acyl exocyclic groups at N6-adenine and reveals an energetically favorable orientation of 6-NcmdA that restores canonical base pairing. An X-ray structure confirms Mom is a member of the GNAT superfamily and suggests binding sites for both tRNA and DNA. Guided by the Mom structure and patterns of sequence conservation across metagenomic space, we show residues R111 and S124 are essential for catalysis. This work demonstrates that the Mom enzyme defines a new category of acetyltransferases utilizing charged tRNA to modify DNA.}, }
@article {pmid41932890, year = {2026}, author = {Zhao, L and Zheng, J and Shen, Y and Xu, X and Liu, X and Yu, J and Li, J and Yang, B and Chen, L and Wang, F and Liu, S and Peng, X and Du, J and Dong, R}, title = {Composite polyphenols mitigate microplastic exposure-related immune disturbances: a two-phase population trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71167-8}, pmid = {41932890}, issn = {2041-1723}, abstract = {Microplastics (MPs) are widespread, making it urgent to elucidate their toxicity and identify intervention strategies. Here, we designed a two-phase population trial, comprising a baseline pilot population (n = 151) and a 28-day randomized, double-blind, placebo-controlled trial (n = 98). Primary outcomes include fecal MP concentration and blood parameters (complete blood count, glycemic and lipid, and cytokines), with exploratory outcomes comprising fecal metagenomics and plasma metabolomics. The median MP concentration in 151 participants' fecal samples is 158.28 μg/g dry weight, correlating with levels of 7 inflammatory indexes, 4 cytokines, and 2 lipid indicators. Composite polyphenols (CP) significantly reduced plasma levels of IL-1β (P = 0.045, effect sizes = -0.463), IL-6 (P = 0.023, effect sizes = -0.576) and IL-8 (P = 0.022, effect sizes = -0.529). 507 differentially expressed microbiotas (DEMs; P < 0.05) and 144 significantly different metabolites (SDMs; P-FDR < 0.25, VIP ≥ 1) are observed between the high and low MP exposure groups; 108 DEMs and 85 SDMs are identified following CP intervention. Notably, CP could mitigate the pro-inflammatory effects of high MP exposure by modulating gut microbiota and up-regulating glycerophospholipid metabolism and arginine biosynthesis. The gut bacteria Staphylococcus and the plasma metabolite PC (22:5/0:0) are identified as potential mediators in this protective effect. Trial registration: ClinicalTrials.gov: NCT06437119.}, }
@article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41932913}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Bacteriocins/pharmacology/metabolism/biosynthesis ; Homeostasis ; *Mouth/microbiology ; Phosphorylation ; Streptococcus salivarius/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects ; Porphyromonas gingivalis/drug effects ; Biofilms/drug effects ; Streptococcus pneumoniae/drug effects ; Metagenomics ; Symbiosis ; Antimicrobial Peptides ; }, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, }
@article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41933095}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; *Pneumonia/microbiology/diagnosis/genetics ; *Lung/microbiology ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Multiomics ; Prospective Studies ; Sputum/microbiology ; Transcriptome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, }
@article {pmid41933201, year = {2026}, author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB}, title = {Unbinned contigs expand known diversity in the global microbiome.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1437-1449}, pmid = {41933201}, issn = {2058-5276}, support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Metagenome ; Phylogeny ; Genetic Variation ; *Biodiversity ; Soil Microbiology ; }, abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.}, }
@article {pmid41933302, year = {2026}, author = {Wu, L and Pu, J and Xi, X and Bao, Y and Luo, L}, title = {Streptomyces morookaense spinal suppurative infection: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41933302}, issn = {1471-2334}, support = {2025M781412//The China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; Female ; Aged ; *Streptomyces/isolation &amp; purification/genetics ; Anti-Bacterial Agents/therapeutic use ; Magnetic Resonance Imaging ; Thoracic Vertebrae/microbiology/diagnostic imaging/pathology ; Tomography, X-Ray Computed ; Suppuration/microbiology ; }, abstract = {PURPOSE: Streptomyces species are ubiquitous soil actinomycetes and a major source of antibiotics, but invasive human infection with spinal involvement is exceedingly rare and may mimic tuberculous or fungal spondylodiscitis. We report a thoracic suppurative vertebral infection caused by Streptomyces morookaense and highlight an integrated diagnostic approach.<br><br>METHODS: A 66-year-old woman with no known immunodeficiency developed progressive thoracic back pain one month after severe trauma with open wounds. CT/MRI showed osteolytic endplate destruction at T3-T4 with paravertebral abscess formation. Fluoroscopy-guided percutaneous biopsy of the T4 vertebral body was performed for histopathology, culture, and metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Histopathology demonstrated fibrinous exudate, necrosis, and inflammatory granulation tissue with fragmented trabeculae, without granuloma or caseous necrosis; acid-fast staining was negative. Vertebral tissue culture grew Streptomyces spp, and mNGS identified high-abundance sequences matching S. morookaense. Intravenous piperacillin/tazobactam led to rapid pain relief and normalization of inflammatory markers within one week, and no recurrence was observed during follow-up.<br><br>CONCLUSION: This case suggests that Streptomyces morookaense has the potential to involve the thoracic spine in immunocompetent individuals. For unexplained spinal infections with negative routine tests, percutaneous vertebral sampling with integrated interpretation of pathology, culture, and mNGS can improve detection of rare pathogens and help avoid inappropriate empirical therapy.}, }
@article {pmid41933424, year = {2026}, author = {Zhao, Y and Wang, Z and Fan, D and Zhang, J and Tu, Y and Diao, Q and Cui, K}, title = {Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41933424}, issn = {1674-9782}, support = {2024YFD1300204//National Key Research and Development Program of China/ ; 32172764//National Natural Science Foundation of China/ ; 25036//Agricultural Science Technology Project of Shijiazhuang/ ; }, abstract = {BACKGROUND: Early weaning is a key strategy to improve lamb production efficiency; however, it inevitably compromises intestinal barrier integrity and function. This study aimed to investigate the effects of epigallocatechin (EGC) on growth performance and intestinal barrier function in weaned lambs, using metagenomics, metabolomics, and intestinal transcriptomics to elucidate the underlying mechanisms.<br><br>RESULTS: Weaning induced oxidative stress, inflammation, and metabolic disruptions in the jejunum. Supplementation with 12.5&#xa0;mg/kg EGC (LE) significantly improved growth performance, reduced diarrhea incidence (P&#x2009;<&#x2009;0.05), enhanced mucosal antioxidant capacity (P&#x2009;<&#x2009;0.001), and strengthened anti-inflammatory ability (P&#x2009;<&#x2009;0.001). Metagenomic analysis showed that the LE intervention enriched Ruminococcus spp. and reduced the abundance of Slackia. This microbial shift was associated with elevated luminal concentrations of valeric acid and microbial metabolites derived from EGC. Transcriptomic profiling revealed that the intervention upregulated the PPAR signaling pathway, which supports nutrient metabolism and barrier repair. Concurrently, it attenuated aberrant IL-17 signaling and promoted the restoration of mucosal immune homeostasis, indicating a resolution of excessive inflammatory responses.<br><br>CONCLUSIONS: Supplementation with 12.5&#xa0;mg/kg EGC alleviates weaning stress by fostering a beneficial gut microbiota and promoting the production of specific metabolites. These changes reactivate PPAR mediated epithelial repair and dampen pathological immune activation. Low-dose EGC is an effective nutritional strategy to improve intestinal health and growth in weaned ruminants.}, }
@article {pmid41933601, year = {2026}, author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y}, title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134536}, doi = {10.1016/j.biortech.2026.134536}, pmid = {41933601}, issn = {1873-2976}, mesh = {Food Loss and Waste ; Methane/biosynthesis ; *Temperature ; Anaerobiosis ; Hydrolysis ; *Microbial Consortia/physiology ; Archaea/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism ; *Refuse Disposal/methods ; }, abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.}, }
@article {pmid41933710, year = {2026}, author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {140}, number = {}, pages = {105932}, doi = {10.1016/j.meegid.2026.105932}, pmid = {41933710}, issn = {1567-7257}, mesh = {Animals ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Tibet ; Phylogeny ; Genome, Viral ; *Mammals/virology ; Metagenome ; Virome ; }, abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.}, }
@article {pmid41933826, year = {2026}, author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D}, title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128041}, doi = {10.1016/j.envpol.2026.128041}, pmid = {41933826}, issn = {1873-6424}, mesh = {Animals ; *Animals, Wild ; *Soil Microbiology ; Ecosystem ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Soil/chemistry ; Metabolomics ; Colobinae ; Bacteria/genetics ; }, abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.}, }
@article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.005}, pmid = {41934012}, issn = {1878-4380}, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, }
@article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {7}, pages = {e70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Multiomics ; Metagenomics ; *Microbiota ; Feces/microbiology ; Bacteria/genetics/classification ; Male ; Adult ; Fungi/genetics/classification ; Female ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, }
@article {pmid41934511, year = {2026}, author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM}, title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41934511}, issn = {1572-9699}, mesh = {Animals ; *Chitosan/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Dietary Supplements ; Biodiversity ; Diet ; Prebiotics ; *Fishes/microbiology ; }, abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.}, }
@article {pmid41934651, year = {2026}, author = {Zhang, N and Li, L and Chen, F and Kang, X and Liu, L and Kuang, D}, title = {Rapid Cavitary Pneumonia and Reversible Hepatic Injury in Burkholderia pseudomallei ST271 Infection.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951729}, pmid = {41934651}, issn = {1941-5923}, mesh = {Humans ; Male ; *Melioidosis/diagnosis/complications/drug therapy ; Middle Aged ; *Burkholderia pseudomallei/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/microbiology/diagnosis/drug therapy ; *Liver Diseases/microbiology/diagnosis ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease endemic to tropical and subtropical regions that displays highly variable clinical presentations, ranging from localized abscesses to severe septicemia. Sequence type (ST) 271 has been rarely reported; data concerning its clinical and epidemiological characteristics remain limited. This report describes a rare case of ST271 infection presenting with rapidly progressive cavitary pneumonia and reversible hepatic injury. CASE REPORT A previously healthy 50-year-old male construction worker from Haikou, China, presented with a 2-week history of intermittent fever, hemoptysis, and persistent cough. Chest computed tomography revealed a thick-walled cavitary mass in the right upper lobe. Laboratory findings demonstrated substantially elevated liver enzymes, indicating acute hepatic injury. Metagenomic sequencing of bronchoalveolar lavage fluid identified B. pseudomallei, and whole-genome sequencing classified the isolate as ST271. The strain was sensitive to imipenem, ceftazidime, and trimethoprim-sulfamethoxazole; preliminary in vitro bacteriophage susceptibility also was observed. After initiation of intravenous ceftazidime followed by oral trimethoprim-sulfamethoxazole, the patient showed rapid clinical improvement that included robust resolution of the pulmonary lesion and normalization of liver enzymes, consistent with reversible hepatic injury. CONCLUSIONS This case highlights the aggressive clinical course of the rare B. pseudomallei ST271 strain, characterized by rapidly progressive cavitary pneumonia and concurrent hepatic injury in an immunocompetent host. Early identification using sequencing techniques facilitated timely targeted therapy and a favorable recovery. The observed in vitro phage susceptibility may provide preliminary insight for future research into alternative management strategies for resistant strains.}, }
@article {pmid41934839, year = {2026}, author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B}, title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141959}, doi = {10.1016/j.jhazmat.2026.141959}, pmid = {41934839}, issn = {1873-3336}, mesh = {*Seafood/microbiology/analysis ; Animals ; *Dietary Exposure ; Food Chain ; *Drug Resistance, Microbial/genetics ; Metagenome ; Genes, Bacterial ; Humans ; }, abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.}, }
@article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, mesh = {*Drinking Water ; Animals ; *Chlorine/toxicity ; Halogenation ; *Gastrointestinal Microbiome/drug effects ; Humans ; Mice ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, }
@article {pmid41935036, year = {2026}, author = {Larsson, DGJ and Flach, CF and Kristiansson, E}, title = {Antibiotic resistance gene analyses in microbial communities: challenges and opportunities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41935036}, issn = {2041-1723}, support = {2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, abstract = {Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain.}, }
@article {pmid41935109, year = {2026}, author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J}, title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41935109}, issn = {2045-2322}, support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; }, mesh = {*Caves/microbiology ; China ; Humans ; Geologic Sediments/microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; *Human Activities ; Nitrogen/metabolism ; Phosphorus/metabolism ; Metagenomics ; }, abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.}, }
@article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41935274}, issn = {1743-422X}, mesh = {Animals ; Swine ; England/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Swine Diseases/virology/epidemiology ; *Virome ; Feces/virology ; *Viruses/classification/isolation &amp; purification/genetics ; Weaning ; Metagenomics ; Gastrointestinal Tract/virology ; Phylogeny ; *Virus Diseases/veterinary/virology ; }, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.<br><br>METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.<br><br>RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.<br><br>CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, }
@article {pmid41935328, year = {2026}, author = {Li, XX and Li, BY and Fu, GW and Zhao, H and Li, J and Zhou, YH and Zhang, X and Zhao, YC}, title = {Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41935328}, issn = {1471-2334}, abstract = {BACKGROUND: Timely pathogen identification is crucial for guiding antimicrobial therapy in severe pneumonia requiring veno-venous extracorporeal membrane oxygenation (vv-ECMO). Compared with slow and often insensitive conventional culture, metagenomic next-generation sequencing (mNGS) enables more rapid and comprehensive pathogen detection and may improve clinical management. This study aimed to evaluate the clinical impact of mNGS compared with conventional culture in non-immunocompromised patients undergoing vv-ECMO for severe pneumonia. METHODS: The retrospective study explored non-immunocompromised patients with severe pneumonia who received vv-ECMO support between January 2017 and June 2023. A total of 151 patients were categorized into the mNGS group and the non-mNGS group, based on whether they underwent mNGS testing. Furthermore, they were stratified into the Death group and Survive group according to their survival status at day 30. Demographics, laboratory test results, pathogens, antibiotic treatment, and clinical outcomes data were recorded and analyzed. RESULTS: The positivity rate identified through the mNGS method (73.3%) was notably higher than that obtained through conventional culture (43.1%, P < 0.001). mNGS exhibited superior capabilities in identifying co-infections compared to conventional culture (70.9% vs. 30.1%, P < 0.001). Furthermore, the 30-day mortality rate within the mNGS group demonstrated a significant decrease compared to the no-mNGS group (P = 0.045). Additionally, Kaplan-Meier survival analysis yielded comparable outcomes in both groups (P = 0.035). Factors protecting against adverse outcomes encompassed prolonged hospital stay time, extended ECMO duration, lower Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, successful ECMO weaning, and the application of mNGS. Antibiotic adjustments were implemented in 29 patients (58%) in the mNGS group and 39 patients (38.6%) in the no-mNGS group, with a markedly higher adjustment ratio in the former, demonstrating statistical significance (P = 0.024). Following adjustment of the treatment plan, the mNGS group demonstrated reduced APACHE II scores compared to the no-mNGS group after 5 days of treatment (P = 0.006). CONCLUSIONS: The mNGS technique, with its superior pathogen detection rate, emerges as a promising tool for microbiological diagnosis and antibiotic management, ultimately contributing to enhanced patient outcomes.}, }
@article {pmid41935339, year = {2026}, author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R}, title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41935339}, issn = {2524-6372}, abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.<br><br>RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.<br><br>CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.}, }
@article {pmid41935438, year = {2026}, author = {Bai, Y and Zhao, J and Wang, Z and Zheng, J and Zhu, X and Shao, Y and Zhang, X}, title = {A case of Rickettsia felis caused pneumonia and diagnosed by clinical analysis and Targeted Next-Generation Sequencing (tNGS) using Bronchoalveolar Lavage Fluid (BALF): A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {5}, pages = {103217}, doi = {10.1016/j.jiph.2026.103217}, pmid = {41935438}, issn = {1876-035X}, mesh = {Male ; Humans ; *Rickettsia felis/genetics/isolation &amp; purification ; *Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Animals ; *Rickettsia Infections/diagnosis/drug therapy/microbiology/veterinary ; Anti-Bacterial Agents/therapeutic use ; Cats ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; *Pneumonia, Bacterial/diagnosis/microbiology/drug therapy/veterinary ; }, abstract = {Feline rickettsia pneumonia is a rare lung disease caused by feline R. felis infection, which is mainly transmitted by feline fleas. A 57-year-old male patient was hospitalized with pain in the back of the sternum. Chest CT showed bilateral diffuse interstitial lung disease with multiple nodules. After the empirical anti-infection treatment was ineffective, the second-generation meta-genome sequencing (mNGS) of bronchoalveolar lavage (BALF) was diagnosed as feline rickettsia infection. In terms of treatment, inject tegacycline intravenously and then sequentially take minocycline. The patient's symptoms were relieved quickly, and the imaging improved significantly. This report summarizes the clinical and imaging characteristics and diagnosis and treatment experience of the case, aiming to provide reference for the early identification and treatment of such rare infections.}, }
@article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {7}, pages = {101848}, pmid = {41935631}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.<br><br>METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n = 462), alongside matched healthy controls (n = 148), and validated key findings in two independent ALD cohorts (n = 34 and n = 52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.<br><br>RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F = 69.9, p = 8.6e-66) and feces (inprimis, cholic acid: F = 5.5, p = 1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multistep dehydroxylation pathway (including baiB) increased, whereas those in the reduction arm (baiN) were depleted. In patients with ALD, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.<br><br>CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.<br><br>IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive ALD progression. Additionally, our study identifies specific bacterial species influencing BA concentrations in ALD using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating ALD.}, }
@article {pmid41935814, year = {2026}, author = {Sambucci, KM and Samaš, P and Ssebide, B and Petrželková, KJ and Okello, RO and Nizeyimana, F and Bukamba, N and Smiley-Evans, T and Gilardi, K and Pafčo, B and Červená, B}, title = {Shifts in strongylid communities associated with chronic wasting in mountain gorillas.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {104848}, doi = {10.1016/j.ijpara.2026.104848}, pmid = {41935814}, issn = {1879-0135}, abstract = {Host-parasite relationships are typically maintained in a dynamic equilibrium, but disruptions to this balance can lead to clinical disease and population-level health impacts. Chronic wasting, characterized by chronic loss of body condition, alopecia, a browning hair coat and pot belly, is an emerging health concern in mountain gorillas of Bwindi Impenetrable National Park, Uganda. Deworming of suspected cases has led to marked short-term health improvements, implicating intestinal helminths. To investigate, we analysed faecal samples from human-habituated gorillas collected in 2018 and 2021, and unhabituated gorillas in 2018, using high-throughput sequencing of strongylid nematodes (ITS-2) and gut bacteria (16S). Strongylid community composition varied with chronic wasting occurrence, with Oesophagostomum emerging as a key taxon driving this difference, while bacterial communities remained relatively stable. Strongylid diversity increased between 2018 and 2021, and habituated gorillas exhibited reduced strongylid genetic diversity, higher relative abundance of Oesophagostomum and lower relative abundance of Murshidia compared to unhabituated gorillas. These results suggest that a higher abundance of Oesophagostomum is associated with chronic wasting in mountain gorillas due to either a causative association or other genetic, immunological or environmental causes allowing Oesophagostomum, a common member of the gut eukaryote community of the Bwindi gorillas, to overpopulate.}, }
@article {pmid41935918, year = {2026}, author = {Lazarevic, V and Ruppé, E and Schrenzel, J}, title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.}, journal = {Trends in microbiology}, volume = {34}, number = {5}, pages = {449-453}, doi = {10.1016/j.tim.2026.03.008}, pmid = {41935918}, issn = {1878-4380}, mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; }, abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.}, }
@article {pmid41936200, year = {2026}, author = {Uematsu, S}, title = {Programming systemic and mucosal immunity through co-adjuvant-based prime-boost vaccination.}, journal = {Current opinion in virology}, volume = {76}, number = {}, pages = {101525}, doi = {10.1016/j.coviro.2026.101525}, pmid = {41936200}, issn = {1879-6265}, abstract = {The development of effective mucosal vaccines has been limited by the limited availability of mucosal adjuvant approaches with established clinical track records and an incomplete understanding of how systemic and mucosal immunity are coordinated. Recent studies indicate that the priming phase of vaccination plays a decisive role in programming the quality, durability, and anatomical distribution of subsequent immune responses. This review discusses emerging evidence that co-adjuvant-based priming strategies can establish long-lasting immune programs that enable adjuvant-free mucosal boosting. Focusing on the combination of CpG DNA and curdlan as a prototypical example, this review highlights how coordinated activation of innate immune receptors during priming imprints dendritic cells, B cells, and T cells to support robust mucosal IgA and tissue-resident immunity. This review further discusses translational advances demonstrating that this immune programming paradigm can be maintained using translationally oriented formulations designed with clinical development in mind and validated in non-human primates. Independent studies using mRNA and protein-based vaccines support the general principle that the quality of priming, rather than the boosting modality, determines successful mucosal immunity. Together, these findings redefine vaccine adjuvants as tools for immune programming and provide a conceptual framework for next-generation vaccine design.}, }
@article {pmid41936930, year = {2026}, author = {Zhou, Z and Song, Y and Zhou, Y}, title = {Metagenomic next-generation sequencing profiling of primary versus iatrogenic osteoarticular infections: Unveiling distinct pathogen spectra and diagnostic implications.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {168}, number = {}, pages = {108688}, doi = {10.1016/j.ijid.2026.108688}, pmid = {41936930}, issn = {1878-3511}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Male ; Iatrogenic Disease ; Retrospective Studies ; Middle Aged ; Aged ; Staphylococcus aureus/genetics/isolation &amp; purification ; Osteomyelitis/microbiology/diagnosis ; *Bacteria/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; Coinfection/microbiology/diagnosis ; Osteoarthritis/microbiology/diagnosis ; Staphylococcal Infections/diagnosis/microbiology ; }, abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus microbial culture in primary osteoarticular infection (POI) and iatrogenic osteoarticular infection (IOI), and to analyze pathogen spectrum differences and clinical implications.<br><br>METHODS: Ninety-two patients with confirmed osteoarticular infection (POI, n = 42; IOI, n = 50) were retrospectively analyzed. All specimens were tested using both mNGS and conventional culture. The pathogen detection rates, pathogen spectrum composition, detection of mixed infections, and concordance of results between the two methods were compared.<br><br>RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (72.83% vs 43.48%; P < 0.001), particularly in IOI (78.00% vs 34.00%; P < 0.001). Pathogen profiling showed predominance of Staphylococcus aureus in POI, whereas IOI exhibited greater microbial diversity with increased detection of Staphylococcus epidermidis (31.03%) and anaerobes (13.79%). Polymicrobial infections were more frequently identified by mNGS (14.13% vs 4.35% by culture; P = 0.024), primarily in the IOI group. Concordance between mNGS and culture was substantial in POI (&#x3ba; = 0.66; 95% CI: 0.42-0.89) but only slight in IOI (&#x3ba; = 0.12; 95% CI: -0.12 to 0.35), largely attributable to the high rate of mNGS-exclusive positives in IOI (48.00%).<br><br>CONCLUSION: mNGS improves pathogen detection in osteoarticular infections, especially in IOI where it identifies complex and polymicrobial infections more effectively than culture, providing critical support for guiding antimicrobial therapy.}, }
@article {pmid41936935, year = {2026}, author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F}, title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134553}, doi = {10.1016/j.biortech.2026.134553}, pmid = {41936935}, issn = {1873-2976}, mesh = {*Wetlands ; *Nitrogen/isolation &amp; purification/metabolism ; *Poaceae/growth &amp; development/metabolism ; Biomass ; Biodegradation, Environmental ; Bacteria/metabolism ; Nitrates ; }, abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.}, }
@article {pmid41936957, year = {2026}, author = {Ghaly, TM and Shah, BS and Coleman, NV and Elbourne, LDH and Le Roux, JJ and Gillings, MR and Paulsen, IT and Tetu, SG}, title = {Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.}, journal = {Environmental research}, volume = {300}, number = {}, pages = {124428}, doi = {10.1016/j.envres.2026.124428}, pmid = {41936957}, issn = {1096-0953}, mesh = {Soil Microbiology ; *Nitrate Reductase/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Agriculture ; Evolution, Molecular ; }, abstract = {Humans are a major evolutionary force, yet our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase (Nar) were specific to Burkholderiales, a major group of denitrifying bacteria. Nar protein regions under positive selection flanked the enzyme's substrate channel, favouring smaller amino acids, likely resulting in the widening of the channel entrance. We present a novel hypothesis that this channel widening could increase rates of substrate turnover, which we propose would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant nitrate reducers globally, such evolutionary consequences of agriculture on this lineage could have cascading environmental impacts, including increased nitrous oxide emissions. These findings indicate that anthropogenic selection might be altering protein-level evolution of vital microbial biogeochemical processes.}, }
@article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {71}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, mesh = {*Doxycycline/therapeutic use/pharmacology ; Humans ; *Military Personnel ; *Antimalarials/therapeutic use ; Case-Control Studies ; Male ; Germany ; *Gastrointestinal Microbiome/drug effects/genetics ; Adult ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; Young Adult ; Feces/microbiology ; Female ; Malaria/prevention &amp; control ; *Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.<br><br>METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.<br><br>RESULTS: In total, 3770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).<br><br>CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, }
@article {pmid41937144, year = {2026}, author = {Bočaj, V and Pongrac, P and Likar, M}, title = {Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41937144}, issn = {2524-6372}, support = {P1-0212//The Slovenian Research and Innovation Agency/ ; }, abstract = {BACKGROUND: Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.<br><br>RESULTS: The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log2 fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.<br><br>CONCLUSION: Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.}, }
@article {pmid41937169, year = {2026}, author = {Mullin, CE and Louca, S}, title = {Effects of heat-assisted sample desiccation on microbiome surveys.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41937169}, issn = {2524-6372}, abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.}, }
@article {pmid41937465, year = {2026}, author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT}, title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2508050}, pmid = {41937465}, issn = {1738-8872}, mesh = {*Petroleum/metabolism/microbiology ; Biodegradation, Environmental ; Soil Microbiology ; *Salinity ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification/growth &amp; development ; *Metagenomics ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; Culture Media/chemistry ; Phylogeny ; Metagenome ; Metabolic Networks and Pathways ; }, abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.}, }
@article {pmid41937665, year = {2026}, author = {Sizikova, TE and Lebedev, VN and Borisevich, SV}, title = {The Mengla virus (Filoviridae: Dianlovirus).}, journal = {Voprosy virusologii}, volume = {71}, number = {1}, pages = {7-12}, doi = {10.36233/0507-4088-356}, pmid = {41937665}, issn = {2411-2097}, mesh = {Animals ; *Chiroptera/virology ; *Filoviridae/genetics/classification/pathogenicity/isolation &amp; purification ; *Filoviridae Infections/virology/epidemiology/genetics ; *Genome, Viral ; Phylogeny ; Humans ; Genetic Variation ; Asia, Southeastern/epidemiology ; }, abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.<br><br>MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.<br><br>RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.<br><br>CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.}, }
@article {pmid41937718, year = {2026}, author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X}, title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {19}, pages = {14120-14136}, doi = {10.1021/acs.est.5c17817}, pmid = {41937718}, issn = {1520-5851}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; *Horseshoe Crabs/microbiology ; *Drug Resistance, Microbial/genetics ; Diet ; }, abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.}, }
@article {pmid41937905, year = {2026}, author = {Cheng, Y and Peng, L and Liu, D and Zhong, L and Liu, Y and Yang, T}, title = {Case Report: A rare culprit of severe pulmonary infection in children: prevotella.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1782202}, pmid = {41937905}, issn = {2296-2360}, abstract = {BACKGROUND: To characterize the clinical features, diagnostic pitfalls, and treatment of severe pediatric pulmonary infection caused by Prevotella species.<br><br>METHODS: We retrospectively reviewed clinical data, the diagnostic workflow, antimicrobial regimens, and outcomes of two children with severe Prevotella pulmonary infection.<br><br>RESULTS: Case 1 was an 11-year-old boy with necrotizing pneumonia, and Case 2 was a 13-year-old boy with retained foreign-body aspiration. Both patients responded poorly to initial cephalosporin-based therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid identified Prevotella nanceiensis (sequence count 299,022; relative abundance 92.24%) and Prevotella oralis (210,449; 67.98%) within 24&#x2005;h, whereas anaerobic culture (Case 1) became positive after 4 days. Based on mNGS results antibiotics were adjusted to metronidazole plus a carbapenem (meropenem for Case 1; imipenem-cilastatin for Case 2), and both children received adjunctive pulmonary rehabilitation before discharge. They subsequently recovered and were discharged.<br><br>CONCLUSION: Severe Prevotella pulmonary infection in children has non-specific manifestations and may respond poorly to conventional beta-lactam therapy, leading to delayed diagnosis. mNGS enables rapid pathogen identification and supports targeted anti-anaerobic treatment. For severe or complicated cases refractory to empirical therapy, metronidazole combined with a carbapenem may be an effective option.}, }
@article {pmid41937991, year = {2026}, author = {Halphen, J and Ahmadzade, M and Mankidy, B and Berenji, A and Ghasemi-Rad, M}, title = {Letter to the Editor: Evidence for a two-step species-level pulmonary nocardiosis diagnostic approach.}, journal = {World journal of radiology}, volume = {18}, number = {3}, pages = {118126}, pmid = {41937991}, issn = {1949-8470}, abstract = {Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The authors also compared traditional cultures to mNGS, finding that traditional cultures and mNGS were concordantly positive in only 3.3% of cases. This letter supports a combined radiologic and molecular diagnostic approach, enabling earlier and more accurate species identification in pulmonary nocardiosis, thereby informing treatment decisions, and enhancing epidemiologic understanding.}, }
@article {pmid41938562, year = {2026}, author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F}, title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {864-876}, pmid = {41938562}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.<br><br>MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), &#x3b1;- and &#x3b2;-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.<br><br>RESULTS: &#x3b1;-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, &#x3b2;-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.<br><br>CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.}, }
@article {pmid41938867, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R}, title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779554}, pmid = {41938867}, issn = {2235-2988}, mesh = {Humans ; Female ; Phylogeny ; Genome, Viral ; *Candidiasis, Vulvovaginal/virology/microbiology ; Vagina/virology ; Sequence Analysis, DNA ; RNA-Dependent RNA Polymerase/genetics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; Metagenomics ; *Double Stranded RNA Viruses/isolation &amp; purification/genetics/classification ; }, abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.<br><br>METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.<br><br>RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.<br><br>DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.}, }
@article {pmid41939082, year = {2026}, author = {Turner, ML and Nguyen, MT and Kung, Y and Doan, T and Seitzman, GD}, title = {Rhizopus angle abscess, scleritis and endophthalmitis following Kahook Dual Blade goniotomy and phacoemulsification.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102572}, pmid = {41939082}, issn = {2451-9936}, abstract = {PURPOSE: To describe a rare case of Rhizopus angle abscess progressing to scleritis and endophthalmitis after routine cataract surgery with Kahook Dual Blade (KDB) goniotomy in an immunocompetent patient.<br><br>OBSERVATION: A 79-year-old male developed hyphema and anterior chamber fibrin three days after uncomplicated phacoemulsification with KDB. Despite intravitreal vancomycin and ceftazidime, inflammation worsened, and by postoperative day nine vision was count fingers with intraocular pressure of 29&#xa0;mmHg. Slit-lamp exam showed an inferonasal corneal infiltrate with a purulent angle abscess at the goniotomy site and dense vitritis. Intravitreal and oral voriconazole were started for presumed fungal infection. Standard cultures and PCR were negative, but metagenomic RNA deep sequencing of aqueous fluid detected Rhizopus stolonifer. After two months of systemic and intravitreal voriconazole, the infection resolved and visual acuity improved to 20/70, leaving localized limbal thinning.<br><br>CONCLUSION AND IMPORTANCE: This case illustrates that Rhizopus angle abscess can occur in an immunocompetent host following anterior segment surgery and may masquerade as bacterial endophthalmitis. Early suspicion of fungal infection and use of metagenomic deep sequencing were critical for diagnosis and successful treatment, emphasizing the need to consider invasive fungal pathogens and advanced molecular diagnostics in culture-negative postoperative ocular infections.}, }
@article {pmid41939697, year = {2026}, author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M}, title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786817}, pmid = {41939697}, issn = {1664-302X}, abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.}, }
@article {pmid41939705, year = {2026}, author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP}, title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768977}, pmid = {41939705}, issn = {1664-302X}, abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.}, }
@article {pmid41939707, year = {2026}, author = {Li, X and Jin, S and Hu, H and Lan, Y and Ni, B and Su, J and Luo, S and Tan, L and Zhang, Y and Huang, H and Xu, Y and Yang, J and Zhou, C and Chen, K and Li, S and Liang, B and Bai, S and Zhang, K and Pan, H and Dong, X and Yan, D}, title = {Feeding Diqing Tibetan pigs with 50% of soybean meal replaced by walnut meal can reduce subcutaneous fat deposition and promote intramuscular fat accumulation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794046}, pmid = {41939707}, issn = {1664-302X}, abstract = {BACKGROUND: Protein feed resource shortage is a major constraint to the sustainable development of the livestock industry and a bottleneck problem hindering the growth of the Tibetan pig industry in China's Qinghai-Tibet Plateau region. Walnut meal, rich in protein, holds promise as a substitute for soybean meal. However, the effects and underlying mechanisms of walnut meal substitution on Tibetan pigs in Diqing remain unclear.<br><br>RESULTS: The study showed that substituting 50% of soybean meal with walnut meal in the diet of Diqing Tibetan pigs significantly reduced backfat thickness and increased intramuscular fat content (P < 0.05). Integrated multi-omics analyses, including metagenomics, transcriptomics, and lipidomics, revealed that walnut meal substitution significantly reduced the abundance of Clostridium butyricum in the cecum of Diqing Tibetan pigs. The reduction in Clostridium butyricum was linked to the lipolytic capacity of subcutaneous adipose tissue, potentially facilitating the breakdown of triglycerides into free fatty acids (FFAs), which are then released into the bloodstream. When these free fatty acids are transported to muscle tissue, the muscle exhibited inhibited oxidative metabolism (e.g., a decrease in acylcarnitine metabolites), while showing an upregulation in the expression of genes related to adipocyte differentiation (e.g., MEDAG, VDR) and triglyceride synthesis (e.g., PPARGC1A, ANGPTL4). Ultimately, these processes may contribute to the synthesis and storage of triglycerides in muscle, thereby facilitating intramuscular fat deposition.<br><br>CONCLUSION: This study reveals that walnut meal can serve as a substitute for soybean meal, and a 50% substitution ratio is conducive to intramuscular fat deposition in Diqing Tibetan pigs. The findings provide valuable insights for the development and application of unconventional protein feed resources, and offer new perspectives for the production of marbled pork.}, }
@article {pmid41939710, year = {2026}, author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J}, title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741638}, pmid = {41939710}, issn = {1664-302X}, abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.}, }
@article {pmid41939717, year = {2026}, author = {Navarro-Nieva, A and Martínez-Checa, F and Delgado, R and Párraga, J and Francino, MP and Jiménez-Hernández, N and Del Moral, A}, title = {Airborne microorganisms in muddy rain: microbe-mineral interactions and their ecosystem impact.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772201}, pmid = {41939717}, issn = {1664-302X}, abstract = {The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.}, }
@article {pmid41940150, year = {2026}, author = {Luo, H and Wang, Y and Hou, H and Yang, J and Liu, YX}, title = {Advances and applications in sequencing-based pathogen surveillance.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100004}, pmid = {41940150}, issn = {2662-1738}, abstract = {The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.}, }
@article {pmid41940273, year = {2026}, author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X}, title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.}, journal = {Current zoology}, volume = {72}, number = {1}, pages = {14-29}, pmid = {41940273}, issn = {1674-5507}, abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.}, }
@article {pmid41940285, year = {2025}, author = {Jeong, GH and Lim, KS}, title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.}, journal = {Journal of animal science and technology}, volume = {67}, number = {6}, pages = {1207-1214}, pmid = {41940285}, issn = {2055-0391}, abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.}, }
@article {pmid41940335, year = {2026}, author = {Buysse, M and Ballinger, MJ and Bruley, M and Amoros, J and Grillet, J and Farassat, N and Serr, A and Lagrèze, WA and Wennerås, C and Grankvist, A and Schön, T and Berglund, J and Bell-Sakyi, L and Sprong, H and Duron, O}, title = {A human-associated Spiroplasma ixodetis lineage responsible for infantile cataracts and adult febrile illness.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115233}, pmid = {41940335}, issn = {2589-0042}, abstract = {Bacteria of the Spiroplasma ixodetis clade are well characterized as reproductive parasites and defensive endosymbionts of arthropods. Nevertheless, clinical evidence indicates that they can also infect humans, causing neonatal ocular disease and acute febrile illness in adults. Using metagenomic assembly and phylogenomic analyses of Spiroplasma ixodetis-related human infections (SiRHIs), combined with a systematic meta-analysis of public datasets, we identified 25 human cases across ten European countries. Despite the frequent detection of multiple S. ixodetis strains in ticks, our data provide no evidence implicating tick-associated strains in human infections. Instead, SiRHI constitute a distinct monophyletic lineage within the S. ixodetis clade, consistent with a shared evolutionary origin with arthropod-associated relatives. Notably, SiRHI genomes harbor horizontally acquired chaperone genes absent from most arthropod-associated Spiroplasma, while retaining conserved effector genes typical of endosymbionts, suggesting the preservation of ancestral symbiotic traits alongside newly acquired molecular adaptations.}, }
@article {pmid41940665, year = {2026}, author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X}, title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0191125}, pmid = {41940665}, issn = {2165-0497}, abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.<br><br>IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.}, }
@article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0190325}, pmid = {41940696}, issn = {1098-5336}, support = {21TQ1400210//the Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 32071271//National Natural Science Foundation of China/ ; 32371332//National Natural Science Foundation of China/ ; 92478203//National Natural Science Foundation of China/ ; IPP30140//College Student Innovation and Practice Program of Shanghai Jiao Tong University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenome ; *Colorectal Neoplasms/microbiology ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; *Polysaccharide-Lyases/genetics/metabolism ; Mucins/metabolism ; Female ; Male ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, }
@article {pmid41940802, year = {2026}, author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , }, title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653550}, doi = {10.1080/19490976.2026.2653550}, pmid = {41940802}, issn = {1949-0984}, mesh = {Humans ; *Mouth/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Child, Preschool ; Saliva/microbiology ; Feces/microbiology ; *Growth Disorders/microbiology ; Male ; Cross-Sectional Studies ; Central African Republic ; Female ; Infant ; *Bacterial Translocation ; *Gastrointestinal Tract/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.}, }
@article {pmid41940852, year = {2026}, author = {Jin, Z and Yuan, Q and Wang, J and Liao, H and Bol, R and Wu, D and Wu, Q and Tang, Y and Guo, W and Liu, Y and Chen, J}, title = {Recycling of Sedimentary Phosphorus Pools in Two Yunnan-Guizhou Plateau Lakes, Southwest China.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {15}, pages = {11519-11528}, doi = {10.1021/acs.est.6c00162}, pmid = {41940852}, issn = {1520-5851}, mesh = {*Geologic Sediments/chemistry ; *Lakes ; China ; *Phosphorus ; Oxygen Isotopes ; Phosphates ; }, abstract = {Applying phosphate oxygen isotopes (δ[18]OP) to identify sediment phosphorus (P) sources and its recycling is still challenging due to poor understanding in δ[18]OP variations of sediment P pools and their driving mechanisms. Here, we analyzed the δ[18]OP in inorganic P (Pi) pools of sediment cores and varied P sources from Lake Dianchi and Lake Erhai in the Yunnan-Guizhou Plateau, Southwest China. The δ[18]OP values of sediment detrital Pi (Det-Pi, nonbioavailable P) were consistent with those of watershed soils (within ∼0.4-0.6‰), indicating that the δ[18]OP of sediment Det-Pi inherits the δ[18]OP of soil Det-Pi. The δ[18]OP values of aluminum-bound Pi (Al-Pi) and authigenic Pi (Auth-Pi) in sediment were close to or within the δ[18]OP equilibrium (δ[18]OP-eq) ranges, implying oxygen isotopic exchange equilibrium between phosphate and ambient water prior to the formation of sediment Al-Pi and Auth-Pi. However, the δ[18]OP of iron oxide-bound Pi (Fe-Pi) in sediment was lighter (∼3‰) than δ[18]OP-eq, retaining the negative isotopic signal of organic P (Po) remineralization. Furthermore, [31]P NMR and metagenomic analysis indicated that microbial-mediated Po mineralization and Pi recycling are the driving factors for δ[18]OP changes in sediment Fe-Pi, Al-Pi, and Auth-Pi. These integrated insights deepen our understanding of the biogeochemical cycling for sedimentary P.}, }
@article {pmid41940893, year = {2026}, author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S}, title = {Establishment of the chromid database and analysis of evolutionary research.}, journal = {Molecular genetics and genomics : MGG}, volume = {301}, number = {1}, pages = {}, pmid = {41940893}, issn = {1617-4623}, mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics ; *Replicon/genetics ; Metagenomics/methods ; Computational Biology/methods ; Polymorphism, Single Nucleotide ; }, abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.}, }
@article {pmid41941835, year = {2026}, author = {Hennen, J and Ifrach, J and Morse, C and Charcos, I and Godil, SS and Mossop, CM}, title = {First reported case of Lawsonella clevelandensis brain abscess in the setting of invasive cutaneous squamous cell carcinoma identified via bedside stereotactic aspiration: illustrative case.}, journal = {Journal of neurosurgery. Case lessons}, volume = {11}, number = {14}, pages = {}, pmid = {41941835}, issn = {2694-1902}, abstract = {BACKGROUND: Brain abscesses associated with malignant skull base invasion pose unique diagnostic and management challenges for neurosurgeons, particularly when routine cultures remain negative. The authors report the first documented intracranial infection caused by Lawsonella clevelandensis, a recently described anaerobe that mimics Nocardia or Mycobacterium sp., diagnosed using bedside stereotactic biopsy as well as metagenomic next-generation sequencing.<br><br>OBSERVATIONS: A 74-year-old woman with recurrent, locally invasive facial squamous cell carcinoma presented with recent-onset shaking of her lower extremity and a large right frontal mass extending through the calvarium and orbit. Imaging revealed ring-enhancing lesions consistent with abscess. Bedside stereotactic biopsy and drainage were performed, and metagenomic sequencing identified L. clevelandensis. Antibiotics were narrowed to ceftriaxone and metronidazole, stabilizing her condition, although repeat drainage was required for radiographic progression. She subsequently underwent multidisciplinary skull base resection and reconstruction, with operative cultures isolating Enterococcus faecium but no further Lawsonella sp.<br><br>LESSONS: This case represents the first documented intracranial L. clevelandensis infection and demonstrates the diagnostic value of molecular sequencing in culture-negative brain abscesses. It also highlights bedside stereotactic biopsy and drainage as a safe, minimally invasive strategy for managing intracranial infection in medically complex patients. https://thejns.org/doi/10.3171/CASE25887.}, }
@article {pmid41942049, year = {2026}, author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J}, title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.004}, pmid = {41942049}, issn = {2090-1224}, abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.<br><br>OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.<br><br>METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.<br><br>RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.<br><br>CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.}, }
@article {pmid41942192, year = {2026}, author = {Xia, Y and Kuda, T and Zhou, Q and He, Q}, title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118924}, doi = {10.1016/j.foodres.2026.118924}, pmid = {41942192}, issn = {1873-7145}, mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; Animals ; Antioxidants/pharmacology ; *Microbiota/drug effects ; Metabolomics ; Food, Processed ; Biogenic Amines/analysis ; Swine ; }, abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.}, }
@article {pmid41942205, year = {2026}, author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H}, title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118955}, doi = {10.1016/j.foodres.2026.118955}, pmid = {41942205}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Prunus avium/microbiology ; *Food Storage/methods ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/classification/genetics ; *Fruit/microbiology ; }, abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.}, }
@article {pmid41942425, year = {2026}, author = {Peña-Valencia, MF and Robaina-Estévez, S and Custer, GF and Turak, O and Sierra, F and Mendes, LW and Rubiano-Labrador, C and Gutiérrez, J and Vaksmaa, A and Dini-Andreote, F and Rosado, AS and Reyes, A and Jiménez, DJ}, title = {Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41942425}, issn = {2041-1723}, mesh = {*Lignin/metabolism ; *Soil Microbiology ; *Polyethylene Terephthalates/metabolism ; Phylogeny ; Bacteria/genetics/enzymology/classification ; Seawater ; Soil/chemistry ; Archaea/genetics/enzymology ; Metagenomics ; Salinity ; }, abstract = {Mangroves are ecosystems located at land-sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.}, }
@article {pmid41942854, year = {2026}, author = {Salengros, A and Dechamps, E and Meunier, L and George, IF}, title = {Uncovering the ecophysiological potential of Motilimonas through genomic profiling analysis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41942854}, issn = {1471-2164}, abstract = {BACKGROUND: The Motilimonas genus was proposed in 2017 and presently include three recognized species isolated from various environments. This genus is still poorly characterized, and its ability to degrade chitin has recently been reported. A genomic profiling analysis was conducted on the seven Motilimonas genomes (family Psychromonadaceae) available in the NCBI database.<br><br>RESULTS: The phylogenetic study suggests that Motilimonas sp. E26, Motilimonas sp. 1_MG-2023 G1M02 and Motilimonas sp. Spo1_1 could form a new clade distinct from other already existing clades within the Motilimonas genus (i.e. M. cestriensis, M. pumila and M. eburnea). The genomic features of all Motilimonas genomes are consistent with a moderately copiotrophic lifestyle. For instance, they encode proteins involved in chemotaxis, motility, type IV pili biosynthesis, sugar phosphotransferase systems (PTS) and chitin degradation. Additional shared traits include aerobic respiration, a preference for sugars over organic acids as carbon sources, the use of a &#x201c;compatible solute&#x201d; strategy to tolerate osmotic stress in saline environments, and, except for M. cestriensis MKS20[T], the ability to perform nitrate reduction. Furthermore, all Motilimonas genomes encode a diversity of secretion systems. For example, each genome contains one or several complete type I secretion systems (T1SS), one complete T2SS, and four genomes (Motilimonas sp. Spo1_1, M. sp. E26, M. sp. 1_MG-2023 G1M02 and Motilimonas sp. KMU-193) harbor a complete type VI secretion system (T6SS). Notably, only M. pumila PLHSC7-2[T] possesses genes encoding a complete type III secretion system (T3SS).<br><br>CONCLUSIONS: These findings provide new insights into the ecological versatility and adaptive strategies of the Motilimonas genus. The next step will involve genome-resolved analyses of metagenomic datasets with the objective to investigate the functional ecology of Motilimonas in a broader range of environments contributing to the better understanding of their ecological distribution.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12781-0.}, }
@article {pmid41942856, year = {2026}, author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT}, title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41942856}, issn = {1471-2180}, support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; }, abstract = {BACKGROUND: To explore the differences in intestinal microbiota between patients with ankylosing spondylitis (AS) and healthy individuals (HC) in terms of genetic, species composition, and functional levels, and to reveal the role of intestinal microorganisms in the pathogenesis of AS.<br><br>METHODS: This study selected 17 AS patients (AS group) and 17 healthy subjects (HC group) from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine between August to October 2024. Basic clinical data, as well as the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Visual Analogue Scale (VAS) score, of the AS group, were collected. Fresh fecal samples were also collected for metagenomic sequencing. Differences in microbiota were analyzed using methods including Alpha diversity analysis, species abundance analysis, Principal Coordinates Analysis (PCoA), Non-metric Multidimensional Scaling (NMDS), DESeq2 analysis, Linear Discriminant Analysis Effect Size (LEfSe), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation.<br><br>RESULTS: The number of unique genes in the AS group (566,526) was higher than that in the HC group (406,609). At the species level, there were no significant differences in Alpha diversity or the overall microbial structure (revealed by PCoA and NMDS) between the two groups (p&#x2009;>&#x2009;0.05). However, significant differences in abundance were observed at the family, genus, and species levels. DESeq2 identified a total of 43 differential species, among which 22 species had increased abundance and 21 species had decreased abundance in the AS group. LEfSe analysis showed that the HC group had 16 dominant bacterial species, while the AS group had only Neoporus faecalis as the dominant species. There were differences in KEGG Level 3 functional pathways between the two groups, but no statistically significant difference was found in the overall functional structure (p&#x2009;=&#x2009;0.698). Functional enrichment analysis revealed that AS-specific genes were primarily enriched in neurodegenerative disease pathways, protein processing in the endoplasmic reticulum, and autophagy-related pathways, with substantial contributions from genera including Bacteroides, Streptococcus, Eubacterium, and Faecalibacterium. However, neither individual differential species nor their functional pathways showed significant correlations with clinical disease activity scores (BASDAI and VAS)&#x3002;.<br><br>CONCLUSION: The studies indicated that although there was no significant difference in the overall diversity of intestinal microbiota between AS patients and healthy individuals, there were obvious distinctions in genetic composition, specific bacterial species, and functional pathways, suggesting that intestinal microorganisms may be involved in the pathogenesis of AS.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04996-8.}, }
@article {pmid41942925, year = {2026}, author = {Maimaitiming, A}, title = {Metagenomic next-generation sequencing (mNGS) for severe cat bite infections with negative aerobic culture: a single-center retrospective study in a rabies vaccination center.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41942925}, issn = {1471-2334}, abstract = {BACKGROUND: Cat bite infections are common emergency settings and are characterized by small, deep puncture wounds that readily form an anaerobic microenvironment, leading to a high incidence of anaerobic bacterial infections. Conventional aerobic bacterial culture has extremely low detection efficiency for such infections and is prone to false-negative results and delayed treatment. As a designated regional rabies vaccination and treatment center, our hospital manages refractory and severe animal bite cases referred from primary medical institutions, with an annual volume of approximately 3000 animal bite consultations. METHODS: Clinical data were retrospectively collected for 17 patients with cat bite infections (13 mild, 4 severe) and negative traditional aerobic bacterial cultures admitted to the Emergency Department of our hospital from May 2025 to January 2026. All patients were treated with emergency debridement and empirical antibiotic therapy. For the 4 severe patients with no improvement after conventional treatment, metagenomic next-generation sequencing (mNGS) was recommended for etiological detection, with only 1 patient consenting to external testing at Beijing You’an Hospital due to economic constraints. RESULTS: All 17 patients had deep puncture wounds (depth > 0.5 cm), and the aerobic bacterial culture results were all negative after 72 h of incubation. In the single severe patient who underwent mNGS testing within 24 h of sample collection, multiple anaerobic or facultative anaerobic pathogens were identified (no viral, fungal or parasitic pathogens detected), with the specific species and their relative abundances shown in Table 1. The dominant pathogen was Bacteroides pyogenes (67.5%), followed by other oral anaerobes, including Fusobacterium russii and Porphyromonas gulae; the classic cat bite pathogen Pasteurella multocida (1.5%) was also detected in this mixed infection. The relative abundance distribution of all identified pathogens is presented in Figure 1, and the genome coverage plots for the key pathogenic bacteria are shown in Figure 2. The 4 severe patients all achieved effective infection control after adjustment based on antibiotic regimens with reference to the mNGS results. The average treatment cycle of 4 severe patients was 14.5 ± 2.3 days, and that of 13 mild patients was 18.7 ± 3.1 days; no statistical analysis was performed due to the small sample size. CONCLUSION: In this small single-center retrospective study, aerobic culture was negative in all 17 cat bite infection cases. In the single tested severe patient, mNGS identified multiple anaerobic and facultative anaerobic pathogens and facilitated targeted antibiotic adjustment, suggesting that mNGS may serve as a potential supplementary diagnostic tool for severe culture-negative cat bite infections in emergency settings. Given the limited sample size and the fact that only one mNGS test was performed, no broad conclusions can be drawn regarding the generalizability of mNGS. Regional rabies vaccination and treatment centers should establish standardized debridement procedures, strengthen physician‒patient risk communication, and improve the referral system to reduce the risk of severe complications and medical disputes. CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41943157, year = {2026}, author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M}, title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41943157}, issn = {2524-6372}, support = {2023-21230832//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1230084//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; Consolidator grant 865694/ERC_/European Research Council/International ; }, abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.<br><br>RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.<br><br>CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.}, }
@article {pmid41943240, year = {2026}, author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J}, title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70421}, pmid = {41943240}, issn = {2050-4527}, support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; }, mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid ; *SARS-CoV-2 ; *Area Postrema/pathology/virology ; Middle Aged ; Betacoronavirus ; Magnetic Resonance Imaging ; *Neuromyelitis Optica/cerebrospinal fluid ; Immunoglobulin G/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/cerebrospinal fluid ; Adult ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.<br><br>METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.<br><br>RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.<br><br>CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.}, }
@article {pmid41943413, year = {2026}, author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J}, title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {75-83}, pmid = {41943413}, issn = {2544-4646}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Retrospective Studies ; *Pneumonia/microbiology/blood/complications ; Male ; Bacteria/isolation &amp; purification/genetics/classification ; Aged ; Middle Aged ; Fungi/isolation &amp; purification/genetics/classification ; Sensitivity and Specificity ; }, abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.}, }
@article {pmid41943678, year = {2026}, author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J}, title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70843}, doi = {10.1111/gcb.70843}, pmid = {41943678}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; *Fungi/physiology ; *Soil/chemistry ; China ; Ecosystem ; *Sodium/analysis ; }, abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.}, }
@article {pmid41944124, year = {2026}, author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W}, title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {21}, pages = {15124-15138}, doi = {10.1021/acs.est.5c10074}, pmid = {41944124}, issn = {1520-5851}, mesh = {*Anaerobiosis/drug effects ; *Methane/metabolism ; *Amines/metabolism/toxicity ; *Sewage/analysis/microbiology ; Stress, Physiological/physiology ; Acetate Kinase/metabolism ; Methanobacterium/physiology ; *Water Pollutants, Chemical/toxicity ; Water Purification ; Wastewater/chemistry/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.}, }
@article {pmid41944276, year = {2026}, author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R}, title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {20}, pages = {14507-14521}, doi = {10.1021/acs.est.5c13821}, pmid = {41944276}, issn = {1520-5851}, mesh = {*Mining ; Oxidation-Reduction ; Metals ; Soil Microbiology ; Humidity ; Soil ; }, abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.}, }
@article {pmid41944309, year = {2026}, author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L}, title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {34}, pages = {e17245}, doi = {10.1002/advs.202517245}, pmid = {41944309}, issn = {2198-3844}, support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; }, mesh = {*Colorectal Neoplasms/microbiology/metabolism/genetics/pathology ; Animals ; Humans ; *Tumor Suppressor Protein p53/metabolism/genetics ; Mice ; Signal Transduction ; *Carcinogenesis/genetics/metabolism ; *ras Proteins/metabolism/genetics ; }, abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.}, }
@article {pmid41944841, year = {2026}, author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME}, title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41944841}, issn = {1432-072X}, abstract = {Tapping Panel Dryness (TPD) is a complex physiological disorder in Hevea brasiliensis that leads to the cessation of latex flow, causing significant economic loss, yet its underlying cause remains unclear. Anatomical investigation of bark samples collected from TPD-affected samples exhibited deformed latex vessels, blocked sieve tubes, and DNA-containing bodies within phloem elements. Metagenomic profiling indicated largely similar microbial composition and diversity between healthy and TPD-affected bark samples, except for the presence of low-abundance taxa such as phytoplasma only in affected samples. However, predicted metabolic pathways differed significantly between healthy and TPD samples. The combined anatomical, cytological, and molecular evidences in the current study supports the potential involvement of a biotic factor in the etiology of TPD.}, }
@article {pmid41946009, year = {2026}, author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P}, title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.}, journal = {Enzyme and microbial technology}, volume = {198}, number = {}, pages = {110869}, doi = {10.1016/j.enzmictec.2026.110869}, pmid = {41946009}, issn = {1879-0909}, mesh = {*Lipase/metabolism/chemistry/genetics ; *Bacteria/enzymology/genetics ; *Fungi/enzymology ; Biocatalysis ; Substrate Specificity ; Protein Engineering ; Biotechnology ; *Bacterial Proteins/metabolism/chemistry/genetics ; Industrial Microbiology ; Enzyme Stability ; }, abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.}, }
@article {pmid41946242, year = {2026}, author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L}, title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141986}, doi = {10.1016/j.jhazmat.2026.141986}, pmid = {41946242}, issn = {1873-3336}, mesh = {Temperature ; Waste Disposal Facilities ; Demethylation ; *Methane/metabolism ; *Arsenic/metabolism ; *Cacodylic Acid/metabolism ; *Carbon/metabolism ; *Water Pollutants, Chemical/metabolism ; *Arsenicals/metabolism ; }, abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.}, }
@article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, mesh = {*Chromium/toxicity ; *Wastewater/microbiology ; Reactive Oxygen Species/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Antioxidants/pharmacology ; *Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Plasmids ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, }
@article {pmid41946403, year = {2026}, author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y}, title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134561}, doi = {10.1016/j.biortech.2026.134561}, pmid = {41946403}, issn = {1873-2976}, mesh = {Ammonium Compounds ; Oxidation-Reduction ; *Cephalexin/toxicity ; *Bioreactors ; *Microbial Consortia/drug effects ; Molecular Docking Simulation ; Stress, Physiological ; *Water Purification ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.}, }
@article {pmid41946559, year = {2026}, author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S}, title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328867}, pmid = {41946559}, issn = {1468-2079}, abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.<br><br>METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.<br><br>RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; &#x3ba;=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; &#x3ba;=0.78), though accuracy remained below specialists (87-90%; &#x3ba;&#x2248;0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; &#x3ba;=0.95; GPT-5 91.7%; &#x3ba;=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.<br><br>CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.}, }
@article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; *Lactation/physiology ; Milk/chemistry/metabolism ; Multiomics ; Metagenomics/methods ; Postpartum Period ; Prevotella/isolation &amp; purification/genetics ; Fatty Acids, Volatile/metabolism ; Methanobrevibacter/genetics/isolation &amp; purification ; Metabolomics ; Succinivibrionaceae/isolation &amp; purification/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.<br><br>RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.<br><br>CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, }
@article {pmid41947478, year = {2026}, author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G}, title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {}, number = {}, pages = {}, doi = {10.1002/ptr.70205}, pmid = {41947478}, issn = {1099-1573}, support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; }, abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.}, }
@article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Virome/genetics ; Metagenomics ; Feces/microbiology/virology ; *Fungi/classification/genetics/isolation &amp; purification ; *Constipation/microbiology/virology ; Bacteria/classification/genetics/isolation &amp; purification ; *Mycobiome/genetics ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Metagenome ; Female ; Chronic Disease ; Viruses/classification/genetics/isolation &amp; purification ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, }
@article {pmid41948038, year = {2026}, author = {Howells, AEG and Santana, M and Cook, EM and Orrill, B and Boyer, G and Debes, RV and Fecteau, KM and Colman, DR and Boyd, ES and Shock, EL}, title = {Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736896}, pmid = {41948038}, issn = {1664-302X}, abstract = {Methane oxidation in terrestrial geothermal systems is an understudied process contributing to carbon cycling in extreme environments. We combined geochemical analyses, 16S rRNA gene amplicon sequencing, shotgun metagenome sequencing, and [14]CH4 microcosm assays across 61 Yellowstone hot springs spanning pH 1.9-9.0 and temperatures of 28.6-92.2 °C to survey hydrothermal systems for methanotrophy. Bacterial aerobic methanotroph phylotypes were detected at multiple sites, including Verrucomicrobia (order S-BQ2-57) and Alphaproteobacteria, with the family Methylocystaceae having the highest relative abundance among bacterial methanotroph phylotypes. No known archaeal anaerobic methanotrophs were observed. Biological methane oxidation was widespread, occurring at 14 of 17 experimental sites under both ambient and air-amended conditions. Rates were highest at CH4-rich, NH3-poor sites dominated by bacterial methanotrophs, consistent with energy supply predictions integrating CH4/O2 and CH4/NH3 concentration ratios. Conversely, NH3-rich, energy-rich sites exhibited lower methane oxidation rates (MOR) and were dominated by archaeal ammonia oxidizers, primarily Candidatus Nitrosocaldus, suggesting chemical competitive inhibition of NH3 on methanotrophy. Remarkably, significant methane oxidation occurred at eight sites where no known methanotrophs were detected, including a site at 89.9 °C-well above the previously reported upper growth temperature limit for methanotrophs from continental geothermal and hydrothermal systems-pointing to uncharacterized thermophilic lineages. These results suggest that biological methane oxidation in Yellowstone hot springs is influenced by the interplay of substrate availability and energy supply. By linking energy supply calculations with microbial distributions, we identify both known methanotrophs (Verrucomicrobia, Alphaproteobacteria) and archaeal ammonia oxidizers as potential active contributors, while highlighting the potential for novel thermophilic lineages, thereby expanding the ecological and thermal boundaries of methane oxidation in extreme terrestrial ecosystems.}, }
@article {pmid41948759, year = {2026}, author = {Zhu, G and Zou, Z and Fang, Z and Xu, B}, title = {Rare but Critical: Severe Tropheryma Whipplei Pneumonia-Induced Cardiopulmonary Failure in a Young Immunocompromised Adult-A Case Report and Literature Review.}, journal = {Clinical case reports}, volume = {14}, number = {4}, pages = {e72448}, pmid = {41948759}, issn = {2050-0904}, abstract = {Tropheryma whipplei, traditionally linked to classic Whipple's disease with gastrointestinal involvement, is increasingly recognized as a cause of pneumonia. Reports of T. whipplei-associated pneumonia progressing to respiratory failure with concurrent acute cardiac failure remain extremely rare. A 38-year-old man with poorly controlled diabetes presented to the emergency department with acute chest tightness, dyspnea, and impaired consciousness. Laboratory findings indicated type II respiratory failure and elevated inflammatory markers. Imaging revealed scattered patchy hazy opacities and increased density bilaterally, prompting emergent intubation and transfer to the intensive care unit. Despite empirical antibiotics for severe pneumonia, he developed acute cardiac failure on day 3, manifesting as bloody sputum and diffuse moist rales with rhonchi on auscultation, alongside an LVEF of 49% and a markedly elevated serum BNP level of 3100 pg/mL. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected abundant T. whipplei sequences. He was administered targeted therapy with meropenem, supported by mechanical ventilation, diuresis, and glycemic control. Cardiopulmonary function improved, and he was discharged on oral doxycycline plus hydroxychloroquine. Follow-up endoscopy and biopsy showed no gastrointestinal involvement (Periodic Acid-Schiff negative), restored cardiac function (LVEF 58.6%), and no recurrence. This case underscores T. whipplei as a potential cause of isolated pneumonia with cardiopulmonary failure in functionally immunocompromised hosts and highlights the critical role of mNGS in guiding timely targeted therapy to improve outcomes.}, }
@article {pmid41949195, year = {2026}, author = {Saini, G and Yadav, R and Bagga, R and Sharma, N and Sethi, S}, title = {Cervicovaginal microbiota in female sex workers with bacterial vaginosis: A metagenomic perspective.}, journal = {Indian journal of dermatology, venereology and leprology}, volume = {}, number = {}, pages = {1-3}, doi = {10.25259/IJDVL_1199_2025}, pmid = {41949195}, issn = {0973-3922}, }
@article {pmid41949263, year = {2026}, author = {Marriott, L and Martinez-Lopez, A and Liga, A and Horiba, K and Warr, A and Phulusa, JN and Kumar, RS and Carey, L and Ito, Y and Parcell, BJ and Leslie, NR and Feasey, NA and Jacob, ST and Rylance, J and Kersaudy-Kerhoas, M}, title = {An automated and portable platform for rapid cell-free DNA isolation and its application in microbial DNA metagenomic sequencing from human blood samples.}, journal = {Lab on a chip}, volume = {26}, number = {9}, pages = {2849-2860}, doi = {10.1039/d5lc00876j}, pmid = {41949263}, issn = {1473-0189}, mesh = {Humans ; *Cell-Free Nucleic Acids/blood/isolation &amp; purification/genetics ; *DNA, Bacterial/blood/genetics/isolation &amp; purification ; Automation ; *Metagenomics/instrumentation ; *Sequence Analysis, DNA/instrumentation ; Rapid Diagnostic Tests ; }, abstract = {The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days and is positive in less than 15% of cases, with many prevalent pathogens difficult or impossible to culture. While microbial cfDNA in blood could facilitate the diagnosis of sepsis, febrile and infectious conditions, sample preparation for cell-free DNA (cfDNA) analysis in decentralised settings presents challenges due to its complexity and the low concentration and fragmented nature of cfDNA in blood plasma. We developed a portable and automated platform and a consumable (CNASafe) for cfDNA isolation from human plasma samples. The platform-device performance was evaluated by comparing relative cfDNA yield against a reference (QIAGEN QIAamp Circulating Nucleic Acid Kit). cfDNA eluates from ten non-cultured blood samples from hospital patients were sequenced on a nanopore sequencer, and results compared to blood cultures. Extraction of cfDNA using the CNASafe device was completed in 40 minutes, compared to the 1 hour 15 min reference protocol. The device achieved an average relative cfDNA recovery of 100.5% over 333 unique extractions encompassing all parameter variations, demonstrating a performance equivalent to the reference kit. From the patient samples, a sufficient quantity of microbial cfDNA was extracted to either identify pathogens missed by blood cultures or confirm negative cultures. The CNASafe platform and real-time nanopore sequencing offer a promising solution for the rapid deployment of metagenomic diagnostics, enabling pathogen identification within a few hours in decentralised clinical environments.}, }
@article {pmid41949675, year = {2026}, author = {Chen, Y and Sun, N and Gan, B and He, Y and Luo, J and Pan, K and Zeng, Y and Jing, B and Zeng, D and Ni, X}, title = {Targeting Bifidobacterium animalis alleviates high-fluoride exposure-induced kidney injury in mice.}, journal = {AMB Express}, volume = {16}, number = {1}, pages = {}, pmid = {41949675}, issn = {2191-0855}, support = {2025YFHZ0278//Sichuan Science and Technology Program/ ; }, abstract = {In areas with high fluoride concentrations in drinking water, residents may consume excessive fluoride, which may increase the risk of renal impairment. Although accumulating evidence suggests that probiotics may exert renoprotective effects, support for probiotic interventions against fluoride-associated renal injury remains limited, and the effects appear to be strain dependent. In a prolonged exposure model, mice received sodium fluoride in drinking water (25 or 50 ppm) for 56 weeks, after which renal function was assessed and metagenomic profiling was performed. Mice exposed to varying fluoride concentrations developed renal injury, and the relative abundance of Bifidobacterium animalis was significantly correlated with markers of renal function. A short-term fluoride-exposure model (sodium fluoride, 24 mg/kg/day for 8 weeks, by gavage) was used to evaluate the renal protective effect of Bifidobacterium animalis GY007. Supplementation with GY007 significantly reduced renal injury markers, including β2-microglobulin (β2-MG) and lipocalin 2 (LCN2). GY007 reduced pro-inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), increased anti-inflammatory interleukin-10 (IL-10), and alleviated oxidative stress. Transmission electron microscopy (TEM) analysis indicated that GY007 improved mitochondrial morphology in damaged renal tissue. Further analyses showed that GY007 improved mitochondrial membrane potential, attenuated the upregulation of dynamin-related protein 1 (Drp1) and fission 1 (Fis1), and normalized altered mitochondrial DNA (mtDNA) copy number. The mRNA levels of mtDNA-encoded genes (mtND3, mtCO2, and mtcyb) and the nuclear-encoded gene Sdhb were altered. Kidney metabolomic analysis revealed metabolic alterations associated with GY007 supplementation in fluoride-exposed mice, identifying eight significantly altered metabolites. This study provides evidence supporting the development of probiotic interventions to mitigate fluoride-associated renal injury in settings with elevated fluoride concentrations in drinking water.}, }
@article {pmid41949810, year = {2026}, author = {Adolph, JE and Pentek, C and Bauch, T and Held, C and Brenner, T and Felderhoff-Müser, U and Grumaz, S and Horvatek, P and Steindor, M and Asar, L and Voigt, S and Dziobaka, J and Dohna-Schwake, C and Goretzki, SC}, title = {Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.}, journal = {Molecular and cellular pediatrics}, volume = {13}, number = {1}, pages = {}, pmid = {41949810}, issn = {2194-7791}, abstract = {BACKGROUND: Rapid and accurate pathogen detection is critical for optimizing outcomes in pediatric sepsis. Next-generation sequencing (NGS) of cell-free DNA (cfDNA) from blood enables culture-independent identification of microbial DNA from bacteria, viruses, fungi, and parasites. We evaluated the diagnostic yield and clinical impact of cfDNA-based NGS in critically ill and predominantly immunocompromised pediatric patients (≤ 18 years) with suspected infection. This retrospective single-center study included pediatric patients who underwent plasma cfDNA-NGS at a tertiary care hospital in Germany. Following computational removal of human DNA, remaining sequences were aligned to curated microbial reference databases. Diagnostic performance was compared with blood cultures and viral PCR, and clinical relevance was assessed by pediatric infectious disease specialists.<br><br>RESULTS: 111 tests in 78 pediatric patients, mostly with systemic inflammatory response syndrome of unknown etiology, were performed. Overall, 61 tests (54.5%) were positive for pathogenic cfDNA. Compared with conventional microbiological diagnostics, NGS demonstrated a sensitivity of 64.7% and specificity of 88.2% when blood cultures and viral PCR served as the reference standard. NGS identified additional pathogens in a substantial proportion (41.1%) of cases that remained negative by standard testing. Of those pathogens only found by NGS, over 60% were deemed clinically relevant. In 14.8% of positive NGS results, a pathogen-specific therapy was started, while 40.2% of tests led to a discontinuation of therapy (51.0% of negative tests). Out of all positive NGS, 38 (62.3%) were classified as clinically relevant. NGS testing also detected rare infections with fungi and parasites in four cases each.<br><br>CONCLUSION: Detection of pathogenic cfDNA through NGS from blood shows promising results as an additional diagnostic tool in critically ill pediatric patients with suspected infections. Clinical utility is currently still limited by its high cost, undetermined diagnostic validity and limitations in testing for resistances and restricted availability of raw sequencing data due to data-protection constraints.}, }
@article {pmid41949970, year = {2025}, author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A}, title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.}, journal = {La Tunisie medicale}, volume = {103}, number = {11}, pages = {1707-1717}, doi = {10.62438/tunismed.v103i11.6101}, pmid = {41949970}, issn = {2724-7031}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/therapy/microbiology ; *Dysbiosis/therapy/etiology/microbiology ; Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology/drug effects ; Prebiotics/administration &amp; dosage ; Diet, Mediterranean ; }, abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.}, }
@article {pmid41950191, year = {2026}, author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT}, title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0344367}, pmid = {41950191}, issn = {1932-6203}, mesh = {Animals ; *Chickens/microbiology ; Bangladesh ; RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Aquaculture ; Anti-Bacterial Agents/pharmacology ; Genomics ; *Drug Resistance, Bacterial ; Metagenomics ; Biodiversity ; }, abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.}, }
@article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/drug therapy ; Multiomics ; *Gastrointestinal Microbiome/genetics ; Drug Monitoring/methods ; Dysbiosis/microbiology ; Feces/microbiology ; Metagenomics ; Metabolomics ; Proteomics ; }, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, }
@article {pmid41950684, year = {2026}, author = {Cao, S and Liu, X and Tao, Y and Ren, J and Zhou, Z and Du, R}, title = {EPS-mediated mineralization drives granule densification and enhances denitratation-anammox coupling under alkaline conditions.}, journal = {Water research}, volume = {299}, number = {}, pages = {125888}, doi = {10.1016/j.watres.2026.125888}, pmid = {41950684}, issn = {1879-2448}, mesh = {Bioreactors/microbiology ; Hydrogen-Ion Concentration ; Nitrogen/metabolism ; *Extracellular Polymeric Substance Matrix/chemistry/metabolism ; *Denitrification ; Sewage/microbiology/chemistry ; *Waste Disposal, Fluid/methods ; Nitrates/metabolism ; }, abstract = {The granular-based CANDAN (Complete Ammonium and Nitrate removal via Denitratation-Anammox over Nitrite) process offers a promising low-carbon and high-rate strategy for nitrogen removal; yet the mechanisms by which alkaline conditions regulate granule structure and functional coupling remain insufficiently understood. Here, a 9-L sequencing batch reactor (SBR) was operated for 130 days with stepwise pH elevation from 7.31 ± 0.03 to 8.52 ± 0.08 to elucidate alkaline condition-driven structural and functional adaptations in CANDAN granules. Moderate alkaline conditions significantly improved nitrogen removal, with total nitrogen removal efficiency increasing to 91.4 ± 0.1 %, accompanied by pronounced improvement in sludge settleability (sludge volume index after 30 min of settling, SVI30, decreased from 76.4 to 19.4 mL g[-1] SS) and stabilization of dominant granule sizes at 0.5-1 mm, accounting for approximately 69.8 % of the total granules, indicating progressive granule densification. Mineralogical analyses revealed that hydroxyapatite dominated the inorganic matrix, with co-precipitation of calcium carbonate (CaCO3) and transient magnesium ammonium phosphate formation reinforcing granule structure. Elevated pH also remodeled extracellular polymeric substances (EPS), increasing loosely bound EPS, raising the protein-to-polysaccharide ratio, and enriching tryptophan-like proteins that facilitated EPS-mediated mineral nucleation. Metagenomic analysis revealed streamlined carbon metabolism and enrichment of key nitrogen-cycling genes (napA, nosZ, hzsA), while downregulation of Ca[2+], Mg[2+], and phosphate transport genes favored extracellular mineral accumulation. Overall, moderately alkaline conditions drive EPS-mediated mineralization that densifies granules and stabilizes Denitratation-Anammox coupling, providing mechanistic insight for optimizing low-carbon nitrogen removal under alkaline wastewater conditions.}, }
@article {pmid41950685, year = {2026}, author = {Zuo, Z and Xing, Y and Qiao, L and Yang, S and Ren, D and Guo, M and Liu, Y and Huang, X}, title = {Unveiling in-pipe carbon-sulfur transformation and microbial function during urine transport for centralized management.}, journal = {Water research}, volume = {299}, number = {}, pages = {125840}, doi = {10.1016/j.watres.2026.125840}, pmid = {41950685}, issn = {1879-2448}, mesh = {Bioreactors/microbiology ; *Carbon/metabolism ; *Sulfur/metabolism ; *Urine/chemistry ; Sewage/microbiology ; Bacteria/metabolism ; Waste Disposal, Fluid ; }, abstract = {Source-separated urine collection and centralized nutrient recovery at city-scale hold great potential for advancing sustainable resource management. As the critical link between urine collection systems and nutrient recovery facilities, urine-transporting sewer systems have recently been incorporated into life cycle assessments (LCA), yet their potential for biochemical transformations has not been explored. Here, for the first time, we experimentally unveil key pollutant transformations and microbial functions in a urine-fed bioreactor (representing urine transport), with a sewage-fed bioreactor serving as a control. Major urine nutrients (N, P, and K) remained largely stable during transport, whereas organic carbon and sulfate decreased markedly. Methane production was negligible over 160 days, while sulfide production initially declined but fully recovered by day 80, accompanied by elevated microbial activity and substantial sulfide accumulation in sediments. Microbial community analyses revealed that urine exposure reduced community richness and led to a pronounced community, with methanogenic archaea strongly inhibited and sulfate-reducing bacteria (SRB) becoming dominant under prolonged urine stress. A Desulfomicrobium-like SRB species was progressively enriched (∼35% of total metagenome-assembled genomes (MAGs)) and likely responsible for the sulfide rebound. Spatial heterogeneity of microbial communities in sediments further explains depth-specific sulfide accumulation. Overall, this study provides important insights into carbon-sulfur transformations and microbial adaptation in urine transport systems, informing improved system design, operation, and further LCA.}, }
@article {pmid41950966, year = {2026}, author = {Yan, S and Han, Q and Chen, L and Jin, D and Lu, Y and Zhou, J and Zhang, X}, title = {Simultaneous removal of Se(IV) and Cr(VI) from acidic wastewater using a Se(IV)-reducing internal circulation reactor: performance and microbial resistance mechanisms.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134537}, doi = {10.1016/j.biortech.2026.134537}, pmid = {41950966}, issn = {1873-2976}, mesh = {*Chromium/isolation &amp; purification ; *Wastewater/chemistry ; Hydrogen-Ion Concentration ; *Bioreactors/microbiology ; *Selenium/isolation &amp; purification ; *Water Purification/methods/instrumentation ; *Water Pollutants, Chemical/isolation &amp; purification ; Oxidation-Reduction ; Biodegradation, Environmental ; Bacteria/metabolism ; Sewage/microbiology ; }, abstract = {Acidic wastewater contaminated with selenite (Se(IV)) and chromate (Cr(VI)) poses elevated environmental risks due to the combined toxicity of metal(liod) and acidity. Metal(loid)-resistant consortia, such as Se(IV)-reducing sludge (SeRS), provide a promising strategy for treating such wastewater by converting Se(IV) and Cr(VI) into less toxic Se(0) and Cr(III), respectively. In this study, an internal circulation (IC) reactor packed with SeRS and granular activated carbon was constructed to evaluate its performance in treating such wastewater. In the absence of Cr(VI), the reactor achieved Se(IV) removal efficiencies of 94.6-98.5% at influent pH values of 4.5-8.0 and Se(IV) concentrations of 1-3 mM. At an optimal pH 5.5, nearly complete removal of both oxyanions was achieved at Se(IV)/Cr(VI) molar ratios of 5.2-10.4. Alkalinity generated from acetate oxidation buffered the influent acidity at influent pH values of 4.5-5.5, thereby sustaining microbial activity. Cr(VI) stress selectively enriched Brucella, Trichlorobacter, and Seleniivibrio for Cr(VI) reduction, while Pseudomonas accounted for Se(IV) and Cr(VI) reduction. Integrated extracellular polymeric substances (EPS), glutathione reductase (GOR), and metagenomic analyses revealed that microbial resistance to Cr(VI) stress likely relied on intracellular glutathione-related detoxification, enzymatic Se(IV)/Cr(VI) reduction and antioxidant defenses, while extracellular EPS protection declined. Overall, it was demonstrated that the developed IC reactor process enabled robust and efficient removal of both Se(IV) and Cr(VI) from acidic wastewater.}, }
@article {pmid41951175, year = {2026}, author = {Rana, N and Tiewsoh, K and Ray, P and Angrup, A}, title = {Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease.}, journal = {Indian journal of medical microbiology}, volume = {61}, number = {}, pages = {101110}, doi = {10.1016/j.ijmmb.2026.101110}, pmid = {41951175}, issn = {1998-3646}, mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Workflow ; Phylogeny ; Computational Biology/methods ; Bacteria/classification/genetics ; Software ; }, abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.<br><br>METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.<br><br>RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.<br><br>CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.}, }
@article {pmid41951362, year = {2026}, author = {Kariya, E and Tirard-Collet, P and Boulagnon-Rombi, C and Destras, G and Wallon, M and Menotti, J and Lapendry, A and Kaidi, N and Rabodonirina, M and Lievre, L and Depaquit, J and Villena, I and Trecourt, A and Huguenin, A}, title = {Integrated histomolecular diagnosis of mesenteric anisakiasis.}, journal = {Journal of clinical pathology}, volume = {79}, number = {6}, pages = {427-430}, doi = {10.1136/jcp-2026-210635}, pmid = {41951362}, issn = {1472-4146}, mesh = {Humans ; Female ; Middle Aged ; *Anisakiasis/diagnosis/parasitology/pathology/surgery ; Animals ; *Anisakis/genetics/isolation &amp; purification ; *Mesentery/parasitology/pathology ; Metagenomics ; *Mesenteric Ischemia/parasitology/surgery/diagnosis ; Larva ; }, abstract = {A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.}, }
@article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41951635}, issn = {2052-4463}, mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Sus scrofa/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Archaea/genetics/classification ; Bacteria/genetics/classification ; }, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, }
@article {pmid41951715, year = {2026}, author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL}, title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41951715}, issn = {2399-3642}, mesh = {*Mycobiome/genetics ; Transcriptome ; Metagenome ; *Fungi/classification/genetics ; *Metagenomics/methods ; Genetic Markers ; }, abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.}, }
@article {pmid41951791, year = {2026}, author = {Somerville, TF and Kaye, SB}, title = {Comment on: 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections'.}, journal = {Eye (London, England)}, volume = {40}, number = {9}, pages = {1421}, pmid = {41951791}, issn = {1476-5454}, }
@article {pmid41951875, year = {2026}, author = {Wang, Y and Li, Y and Fang, J and Huang, Z and Zhang, C and Xu, B}, title = {A Novel Broad pH-Adaptive Bile Salt Hydrolase from Nomascus concolor Fecal Microbial Metagenome Facilitates the Cholesterol-Lowering Ability of Escherichia coli Nissle 1917.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41951875}, issn = {1867-1314}, support = {32360034//National Natural Science Foundation of China/ ; }, abstract = {High serum cholesterol levels are among the key risk factors for atherosclerosis cardiovascular disease. The utilization of probiotics to lower cholesterol is a relatively safe and efficient therapy, and the bile salt hydrolase gene serves a key function in this process. We aim to identify novel bile salt hydrolase genes from the wild western black crested gibbon (Nomascus concolor) faecal metagenome. Additionally, we intend to develop a new generation of probiotics with cholesterol-lowering properties. Our study amplified and heterologously expressed novel bile salt hydrolases from the faecal metagenome of western black crested gibbons and investigated their enzymatic properties. The recombinant probiotic was constructed using Escherichia coli Nissle 1917 (EcN), and its physiological characteristics and cholesterol-lowering ability were evaluated. We screened uncharacterized bile salt hydrolase genes (NCbsh3 and NCbsh5) from Eubacterium and Roseburia. NCbsh3 exhibited broad pH adaptability and stability; its optimal pH range was 4–7, and the relative enzyme activity was maintained at 80% after 60 min at pH 3–9. The recombinant probiotic EcN/NCbsh3 was constructed, and its bile salt tolerance and cholesterol-lowering ability significantly increased (P < 0.05). These results indicated that NCbsh3 may adapt to the complex pH environment of the intestine and that the NCbsh3 gene is expected to increase the colonization capacity of the EcN strain in the gastrointestinal tract and reduce host serum cholesterol levels. EcN/NCbsh3 has favourable application potential and may contribute positively to the treatment of diseases caused by bile acid metabolism disorders.}, }
@article {pmid41952168, year = {2026}, author = {Shen, Y and Qu, S}, title = {Ganciclovir for severe neonatal varicella pneumonia when acyclovir is unavailable: a case report.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41952168}, issn = {1743-422X}, mesh = {Humans ; Female ; *Antiviral Agents/therapeutic use/administration &amp; dosage ; *Ganciclovir/therapeutic use/administration &amp; dosage ; Infant, Newborn ; *Pneumonia, Viral/drug therapy/diagnosis ; Herpesvirus 3, Human/isolation &amp; purification/genetics ; *Chickenpox/drug therapy/diagnosis ; Treatment Outcome ; Acyclovir/therapeutic use ; Pregnancy ; DNA, Viral/blood ; }, abstract = {BACKGROUND: Perinatal varicella is a rare and severe condition with a high mortality rate, particularly when it leads to complications such as pneumonia in neonates. Acyclovir is the standard treatment for varicella-zoster virus (VZV) infections; however, limited options exist when it is unavailable. This case report describes the successful treatment of neonatal varicella pneumonia with ganciclovir and provides insights into its potential as an alternative therapy. A female Asian neonate was admitted to our hospital on the 9th day of life with a rash, fever, and respiratory distress. Her mother developed varicella at 39 weeks of pregnancy, four days before delivery. The infant was diagnosed with VZV pneumonia based on clinical presentation and confirmed by detection of VZV DNA in blood(metagenomic next-generation sequencing detected 109,491 sequences with 100% relative abundance and 99% confidence).<br><br>INTERVENTION: Ganciclovir 5&#xa0;mg/kg every 12&#xa0;h for 8 days; intravenous immunoglobulin 400&#xa0;mg/kg once daily for 3 days.<br><br>OUTCOME: The infant was successfully weaned off mechanical ventilation, with normalized blood gas parameters (PaO&#x2082;/FiO&#x2082; ratio 346) and inflammatory markers (CRP decreased from 29.44&#xa0;mg/L to 2.87&#xa0;mg/L). She was discharged home with stable breathing and crusted skin lesions. Telephone follow-up at 2 and 4 weeks post-discharge confirmed the infant remained well with no respiratory symptoms or developmental concerns.<br><br>CONCLUSION: Ganciclovir may serve as a life-saving alternative for severe neonatal VZV pneumonia when acyclovir is unavailable. This case highlights the need for further research to establish its safety, optimal dosing, and efficacy in this population.}, }
@article {pmid41953110, year = {2026}, author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J}, title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101380}, pmid = {41953110}, issn = {2352-7714}, abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.}, }
@article {pmid41953529, year = {2026}, author = {Brown, JR and Ross, CS and Worth, A and Merve, A and Storey, N and Hacohen, Y and Mankad, K and Kaliakatsos, M and Shendi, HM and Atkinson, L and Gilmour, K and Hatcher, J and Lennon, A and Bamford, A and Kusters, M and Elfeky, R and Núñe, A and Brown, IH and Reid, SM and Cooper, J and Byrne, AMP and James, J and Lean, FZ and Banyard, AC and Breuer, J}, title = {Identifying virulent avian paramyxovirus type-1: A paediatric case of progressive encephalitis diagnosed by clinical metagenomics with case series review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02555}, pmid = {41953529}, issn = {2214-2509}, abstract = {BACKGROUND: Immunocompromised patients presenting with encephalitis can present a diagnostic conundrum as infection can be caused by a broad range of pathogens, many of which are not detected by standard of care testing pathways. Untargeted metagenomics has proven utility in the diagnosis of such infections, particularly for immunocompromised patients.<br><br>METHODS: An immunosuppressed adolescent presented with idiopathic progressive muscle weakness resulting in respiratory failure, 16 years after haematopoeitic stem cell transplant for familial haemophagocytic lymphohistiocytosis type 5. Clinical and radiological findings suggested a diagnosis of isolated central nervous system haemophagocytic lymphohistiocytosis, however the patient demonstrated no improvement on immunosuppressive therapy. Untargeted metagenomics was performed on brain biopsy tissue.<br><br>RESULTS: Clinical metagenomics detected avian paramyxovirus 1 (APMV-1) in the brain tissue 12 days after biopsy, confirmed by targeted PCR and immunohistochemistry. The metagenomics results guided treatment; immunosuppression was stopped and medication with potential activity against RNA viruses started. The patient died 8 months after symptom onset.<br><br>CONCLUSIONS: We describe the third published case of fatal encephalitis caused by APMV-1, detectable only in brain parenchyma and only by clinical metagenomics, demonstrating the utility of brain biopsy and metagenomics when investigating encephalitis in immunocompromised patients. Case series review suggests profoundly immunocompromised patients are at risk of severe infection caused by AMPV-1.}, }
@article {pmid41953658, year = {2026}, author = {Song, J and Li, Y and Wang, L and Zhang, J and Shi, C and Zhong, L and Liu, C and Song, M and Yu, X and Zhang, W and Wen, P}, title = {Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103771}, pmid = {41953658}, issn = {2590-1575}, abstract = {This study aimed to elucidate differences between the commercial starter culture (CK) and traditional starters from different Tibetan regions (Gannan (GN), Qinghai (QH), Tibet (XZ)) in fermenting yak yogurt by physicochemical properties, flavor, and bacterial community. Results indicated acidity, proline, arginine, alanine, and C6:0 contents were significantly higher in the traditional starter culture than CK (P < 0.05). Gas chromatography-ion mobility spectrometry analysis found the traditional starter culture group was dominated by alcohols and esters, whereas CK exhibited richer ketones. Metagenomic analysis revealed Lactobacillus delbrueckii (49.56% in XZ, 24.86% in GN) and Streptococcus spp. (18.30% in CK, 17.21% in QH) as the dominant. Moreover, pH and titratable acidity were primary factors affecting microbial diversity. Meanwhile, glutamic acid modulated ester biosynthesis like ethyl acetate, while C16:0 fatty acids inhibited off-odor ketones such as 2-pentanone. This study offers valuable insights into developing specialized fermentation agents and standardizing the quality of yak yogurt.}, }
@article {pmid41953764, year = {2026}, author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF}, title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41953764}, issn = {2312-0541}, abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.<br><br>METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.<br><br>RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in &#x3b1;- and &#x3b2;-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.<br><br>CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.}, }
@article {pmid41954112, year = {2026}, author = {Banerjee, M and Lahiri, A and Basak, S and DAS, S and Mukhopadhyay, S and Banerjee, R and Basak, K}, title = {StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {41954112}, issn = {0973-7138}, mesh = {Autoencoder ; Humans ; Long Short Term Memory ; *Cross Infection/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Algorithms ; *Drug Resistance, Bacterial/genetics ; Enterococcus faecium/pathogenicity/genetics/drug effects ; Deep Learning ; }, abstract = {As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for Enterococcus faecium using 4-mer data, with similar results for other organisms using various k-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.}, }
@article {pmid41954388, year = {2026}, author = {Zhao, P and Liu, H and Dong, J and Su, H and Jin, Q and Yang, F}, title = {From hepatitis misdiagnosis to zoonotic false alarms: a metagenomic blacklist framework for the parvo-like hybrid viral group.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0015726}, pmid = {41954388}, issn = {2165-0497}, }
@article {pmid41954393, year = {2026}, author = {Shukla, N and Budhbhatti, U and Puvar, A and Raval, I and Pandit, R and Chavda, P and Chauhan, A and Jhala, D and Shah, D and Shah, T and Raval, J and Prajapati, H and Patel, N and Upadhyay, K and Joshi, M and Patel, AK and Bondre, V and Kumar, N and Joshi, C}, title = {Genomic and evolutionary characterization of Chandipura virus: a cause of the 2024 outbreak in Gujarat, India.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0157825}, pmid = {41954393}, issn = {2165-0497}, abstract = {UNLABELLED: Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its transmission dynamics and evolutionary behavior. CHPV is endemic in India, with previous outbreaks (2003-2004) reported case fatality rates (CFRs) ranging from 56% to 75%. In the current (2024) outbreak, the CFR declined to 46%, with an overall test-positivity rate of 18.6%, possibly reflecting improvements in supportive care. Despite advances in genomics and sequencing technologies, only a limited number of CHPV genomes are publicly available. To address this gap, we performed whole-genome sequencing of CHPV isolated from a pediatric patient aged 12 years from Patan, Gujarat. Comparative genomic analysis with previously reported Indian strain revealed approximately 293 mutations, including 24 non-synonymous. The estimated evolutionary rate of CHPV was ~1.62 × 10[-2] substitutions/site/year. Furthermore, the selective pressure analysis showed that, despite the virus being under strong purifying (negative) selection, several non-synonymous changes were identified. Nonetheless, as the present analysis is based on the single genome, further sequencing, validation, and broader comparative analysis are required to draw a definitive inference. However, these findings suggest that even under purifying selection pressure, CHPV retains the ability to infect and cause severe disease in children. This highlights the continued need to investigate virus-host interactions, particularly host immune responses, to better understand CHPV pathogenesis and its ability to cause disease in children.<br><br>IMPORTANCE: Chandipura virus (CHPV) is an etiological agent of acute encephalitis syndrome (AES) in children, characterized by rapid neurological decline; yet the viral and host factors governing its neuropathogenesis and sudden outbreak dynamics remain poorly defined. Despite minimal genomic variation indicative of strong purifying selection, which supports the continued efficacy of existing molecular diagnostics and candidate therapeutics, CHPV re-emerges unpredictably in human populations, as exemplified by the 2024 AES cluster in Gujarat. This outbreak underscores the importance of continuous genomic surveillance to elucidate viral behavior and immune-evasion mechanisms. Moreover, it highlights the utility of both amplicon-based and metagenomic next-generation sequencing approaches for future CHPV detection and comprehensive genome characterization.}, }
@article {pmid41954722, year = {2026}, author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C}, title = {Correction: Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next‑generation sequencing.}, journal = {Infection}, volume = {}, number = {}, pages = {}, doi = {10.1007/s15010-026-02771-5}, pmid = {41954722}, issn = {1439-0973}, }
@article {pmid41954798, year = {2026}, author = {Liu, P and Zhang, J and Liu, X and Li, B and Peng, Y and Li, B and Lyu, X and Tan, L and Guo, Z and Li, Z and Hu, M}, title = {Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41954798}, issn = {1435-4373}, support = {Grant No.2023XQLH173//Central Universities of Central South University/ ; No. 82102499//National Natural Science Foundation of China/ ; No. 82270658//National Natural Science Foundation of China/ ; No. 2021JJ40840//the Hunan Natural Science Foundation/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; }, }
@article {pmid41954996, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Krittikaviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {4}, pages = {}, doi = {10.1099/jgv.0.002239}, pmid = {41954996}, issn = {1465-2099}, mesh = {Genome, Viral ; Phylogeny ; Virion/ultrastructure/genetics ; *Archaeal Viruses/classification/genetics/isolation &amp; purification/ultrastructure ; Virus Replication ; DNA, Viral/genetics ; *DNA Viruses/classification/genetics/isolation &amp; purification ; *Archaea/virology ; }, abstract = {The family Krittikaviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. These viruses have been identified through metagenomic analysis of brackish estuarine samples and are closely related to other 'magroviruses'. The family belongs to the order Magrovirales and includes the genus Velanvirus and the species Velanvirus brisbanense. Viruses in the family have a genome of about 80 kbp that includes modules for DNA replication and virion morphogenesis. Krittikavirids are predicted to form virions with an icosahedral capsid and helical tail, characteristic of viruses belonging to the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Krittikaviridae, which is available at ictv.global/report/krittikaviridae.}, }
@article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.<br><br>METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.<br><br>RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n&#x2009;=&#x2009;18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.<br><br>CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, }
@article {pmid41955710, year = {2026}, author = {Sahu, TK and Rathored, J and Patil, P}, title = {Tri-layer microbiology for LMIC Hospitals: linking syndromic panels with reflex culture and targeted sequencing for real world care - a narrative review.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {30}, number = {3}, pages = {105808}, pmid = {41955710}, issn = {1678-4391}, mesh = {Humans ; Antimicrobial Stewardship ; *High-Throughput Nucleotide Sequencing/methods ; Molecular Diagnostic Techniques/methods ; Resource-Limited Settings ; }, abstract = {Rapid, syndromic molecular panels and high throughput sequencing have transformed the diagnostic landscape for sepsis, respiratory, gastrointestinal, and central nervous system infections, but their value in routine practice depends on how they are integrated with conventional microbiology and antimicrobial stewardship. This review synthesises recent high-quality evidence to propose a pragmatic three-tier hybrid framework. Tier 1 comprises syndrome specific rapid panels that provide organism and selected resistance markers within hours, primarily to accelerate early escalation or de-escalation rather than to replace culture. Tier 2 positions reflex culture and targeted adjunct tests as the non-negotiable specificity anchor, confirming molecular hits, distinguishing infection from colonisation or contamination, generating phenotypic susceptibility data and supplying isolates for infection prevention and public health surveillance. Tier 3 reserves targeted or metagenomic sequencing for a small, clinically critical subset of high suspicion, panel negative and culture negative cases, where additional breadth can realistically change management. Across sepsis/BSI, pneumonia, gastrointestinal infection and CNS disease, available data indicate that clinical benefit is driven less by any individual technology and more by disciplined implementation: clear indications, explicit reflex rules, close linkage to antimicrobial stewardship and systematic audit of key performance indicators such as time-to-targeted therapy, spectrum of antimicrobial use and cost per additional actionable diagnosis. The proposed tiered, syndrome wise algorithms provide a transferable conceptual scaffold that can be adapted to local resources, allowing laboratories in both high and low resource settings to introduce advanced diagnostics without abandoning culture-based anchors or stewardship accountability.}, }
@article {pmid41955799, year = {2026}, author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G}, title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141956}, doi = {10.1016/j.jhazmat.2026.141956}, pmid = {41955799}, issn = {1873-3336}, mesh = {*Cadmium/metabolism ; Mining ; *Sulfates/metabolism ; Biodegradation, Environmental ; Metagenomics ; Bioreactors ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; Sewage/microbiology ; Microbial Consortia ; Oxidation-Reduction ; Wastewater ; }, abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.}, }
@article {pmid41955854, year = {2026}, author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H}, title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128089}, doi = {10.1016/j.envpol.2026.128089}, pmid = {41955854}, issn = {1873-6424}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Sulfur/metabolism ; *Microplastics/analysis ; Bacteria/metabolism ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.}, }
@article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology ; *Inhalation Exposure/adverse effects ; *Air Pollutants/adverse effects ; }, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.<br><br>METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.<br><br>RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.<br><br>CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, }
@article {pmid41955982, year = {2026}, author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D}, title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.}, journal = {Water research}, volume = {299}, number = {}, pages = {125876}, doi = {10.1016/j.watres.2026.125876}, pmid = {41955982}, issn = {1879-2448}, mesh = {*Ciprofloxacin/pharmacology ; *Sewage/microbiology ; Anaerobiosis ; *Microalgae/metabolism ; Bioreactors ; Methane/metabolism ; Metagenomics ; Anti-Bacterial Agents ; Waste Disposal, Fluid ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.}, }
@article {pmid41955988, year = {2026}, author = {Wang, X and Xue, T and Li, J and Zhang, C and Hao, G and Xing, Y and Tao, R and Guo, L and Zhang, H and Chai, S and Zheng, L}, title = {Novel photoelectron-driven nitrate reduction in anammox granules using photosensitive semiconductor iron mineral for wastewater treatment.}, journal = {Water research}, volume = {299}, number = {}, pages = {125862}, doi = {10.1016/j.watres.2026.125862}, pmid = {41955988}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Nitrates/chemistry ; Wastewater ; Semiconductors ; Iron/chemistry ; Electrons ; Ferric Compounds/chemistry ; }, abstract = {The accumulation of nitrate byproducts and limited electron availability fundamentally constrain the efficacy of anaerobic ammonium oxidation (anammox) processes. While iron minerals regulate electron transfer, their potential to drive anammox via semiconductive photoexcitation remains underexplored. Here, we establish a novel "Photo-Chemo-Bio" strategy to overcome these thermodynamic bottlenecks using light-excited hematite (α-Fe2O3). Among tested minerals, hematite exhibited superior band-structure suitability, achieving a 3.65-fold photocurrent enhancement (4.06 μA·cm[-2]) upon bio-hybridization, facilitated by the active recruitment of photo-electrons via upregulated outer-membrane c-type cytochromes. Crucially, this photo-enhanced electron supply boosted the total nitrogen removal rate by 27.4% while suppressing nitrate yield by 42.8%. Kinetic analysis revealed a precise metabolic decoupling: solar irradiation did not accelerate ammonia oxidation but specifically diverted electron flow toward nitrate reduction pathways. Genome-resolved metagenomics unraveled the molecular basis of this synergy, identifying a "hardwired" cooperative network: flanking Desulfobacillus-like species, characterized by a specific metabolic truncation (absence of nor genes), act as obligate "net NO providers" to fuel the anammox core; concurrently, heterotrophic Casimicrobiaceae unexpectedly encode Photosystem II (psbA), functioning as auxiliary "energy antennas" to harvest photons. These findings demonstrate how mineral-microbe hybrids can orchestrate electron flux to close the nitrogen loop, offering a sustainable, carbon-free strategy for high-efficiency wastewater treatment.}, }
@article {pmid41956026, year = {2026}, author = {Sorgato, AC and Kim, B and Papillon, J and Nivala, J and Silveira, DD and Lapolli, FR and Forquet, N}, title = {Microbial fuel cells inoculated with French vertical flow treatment wetland sludge: A step towards clogging biodetector development.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {171}, number = {}, pages = {109297}, doi = {10.1016/j.bioelechem.2026.109297}, pmid = {41956026}, issn = {1878-562X}, mesh = {*Bioelectric Energy Sources/microbiology ; *Wetlands ; *Sewage/microbiology ; Biofilms ; Electrodes ; Bacteria/genetics/metabolism ; France ; }, abstract = {Clogging is considered an operational challenge in French vertical flow treatment wetlands (VFTWs), causing hydraulics and aeration problems. The available monitoring methods are labor intensive. Microbial fuel cells (MFCs) have emerged as real-time biosensors, including for treatment wetlands (TW) systems. In this study, French VFTW sludge was investigated as inoculum in MFCs, to assessing its adaptation into electrochemical environment as a step for clogging MFC-based biodetector implementation in such systems. The results show that the inoculum was successfully adapted, with stable current generation at 0.4 mA. The electrochemical impedance spectroscopy (EIS) demonstrated the establishment of a biofilm with electroactive characteristics and non-limiting anode. Metagenomic analysis showed that the French VFTW harbor electroactive species, and the MFC created a selective pressure on the VFTW sludge inoculum and significantly shaped the microbial community and function, stimulating the enrichment of electroactive bacteria (EAB), such Geobacterales (4.11% to 5.83%), with potential expression of cytochrome-c for extracellular electron transference (EET). This study illustrates the feasibility of developing electroactive biofilms from French VFTW and suggests its use as an inoculum, improving the integration of TW-MFC systems. Considering these results, the well-adapted anodic biofilm could enable the detection of aeration limitations via cathodic reactions in future studies.}, }
@article {pmid41956515, year = {2026}, author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH}, title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70300}, pmid = {41956515}, issn = {1462-2920}, support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; }, mesh = {*Biofilms/growth &amp; development ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/physiology ; *Biodiversity ; Cyanobacteria/genetics/physiology/classification ; Droughts ; Floods ; Groundwater/microbiology/chemistry ; Hydrology ; }, abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.}, }
@article {pmid41956535, year = {2026}, author = {Cui, T and Huang, M}, title = {Tuberculous Peritonitis Diagnosed by Metagenomic Next-Generation Sequencing Progressing to Fatal Encapsulating Peritoneal Sclerosis in a Peritoneal Dialysis Patient: A Case Report.}, journal = {Seminars in dialysis}, volume = {39}, number = {1-2}, pages = {53-56}, doi = {10.1111/sdi.70022}, pmid = {41956535}, issn = {1525-139X}, support = {SZSM202411016//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Humans ; Female ; *Peritonitis, Tuberculous/diagnosis/complications ; *Peritoneal Dialysis/adverse effects ; Adult ; *Peritoneal Fibrosis/etiology/diagnosis/microbiology ; Fatal Outcome ; *Kidney Failure, Chronic/therapy/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Metagenomics/methods ; }, abstract = {A 40-year-old woman on peritoneal dialysis for 3 years presented with febrile peritonitis. Metagenomic next-generation sequencing (mNGS) confirmed Mycobacterium tuberculosis complex in ascitic fluid, leading to prompt anti-tuberculosis therapy. She initially improved but developed ultrafiltration failure 15 months later and transitioned to hemodialysis. At 18 months, she developed bowel obstruction, bloody ascites, and characteristic imaging and laparoscopic findings of encapsulating peritoneal sclerosis (EPS). Despite supportive care, she deteriorated and died 30 months after tuberculosis peritonitis diagnosis. This case highlights that mNGS enables rapid diagnosis of tuberculous peritonitis when conventional tests are inconclusive, and that tuberculosis peritonitis may serve as a potent inflammatory trigger for EPS even after peritoneal dialysis cessation. Early recognition and timely intervention may improve outcomes.}, }
@article {pmid41956809, year = {2026}, author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J}, title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336025}, pmid = {41956809}, issn = {1468-3288}, abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.<br><br>OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.<br><br>DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.<br><br>RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice&#x2009;and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice&#x2009;and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.<br><br>CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.}, }
@article {pmid41957175, year = {2026}, author = {Yang, S and Wang, X and Duan, J and Yang, S and He, J and Fang, C and Zhao, N and Huang, Y}, title = {Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41957175}, issn = {2045-2322}, support = {2022YFD1901500, 2022YFD1901505//National Key R&amp;D Program Project/ ; ZSYS[2025]035//Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform)/ ; grant number BQW[2024]009//Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province/ ; }, mesh = {*Soil/chemistry ; *Fertilizers/analysis ; *Carbon/metabolism/chemistry ; Soil Microbiology ; *Carbon Cycle/genetics ; Nitrogen ; Phosphorus ; Metagenomics ; }, abstract = {Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving "carbon-compensation" mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO3[-]-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a "stoichiometry-community diversity" cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.}, }
@article {pmid41957291, year = {2026}, author = {Yang, M and Fang, J and Liao, Q}, title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {41957291}, issn = {1434-9949}, }
@article {pmid41957365, year = {2026}, author = {Kan, J and Spotton, K and Morales-Amador, A and Hernandez, Y and Burian, J and Panfil, C and Ternei, MA and Boer, RE and Bhattacharjee, A and Brady, SF}, title = {Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41957365}, issn = {2041-1723}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; T32 GM136640/GM/NIGMS NIH HHS/United States ; R35GM122559//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NIH T32 GM136640//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Endopeptidase Clp/metabolism/genetics/chemistry ; *Biological Products/chemistry/metabolism/pharmacology ; Multigene Family ; Anti-Bacterial Agents/pharmacology/chemistry ; *Bacterial Proteins/metabolism/genetics ; *Metagenome ; Computational Biology ; Phenylalanine/analogs &amp; derivatives/chemistry ; }, abstract = {The discovery of natural products with specific modes of action from metagenomes remains challenging. Here, we present resistance-CONKAT-seq, a pipeline that links biosynthetic gene clusters (BGCs) to self-resistance genes, enabling identification of metabolites with desired molecular targets. Using clpP-directed resistance-CONKAT-seq, we identify the calprotamides, which activate native ClpP and enhance its activity. Cryo-EM and bioinformatic analyses reveal that the calprotamides' medium-chain N-acylphenylalanine substructure is a convergently evolved ClpP-targeting motif and identify additional BGCs predicted to encode this moiety, including some with co-localized clp genes. The synthesis of structures bioinformatically inspired by two such clp-linked BGCs, desmethyl jomthonic acid C and tuscamide, reveals that both enhance ClpP activity. Extending our bioinformatically guided synthesis study to additional BGCs lacking nearby clp genes shows that ClpP activity enhancement correlated with antibacterial activity, with the strongest enhancers exhibiting narrow-spectrum antibiotic activity. These findings establish N-acylphenylalanine as a previously unrecognized but common natural motif for targeting ClpP, which should help guide the discovery of both natural and synthetic ClpP modulators for antibiotic and anticancer development. Resistance-CONKAT-seq offers a scalable method for exploring biosynthetic dark matter for metabolites with desired modes of action.}, }
@article {pmid41957864, year = {2026}, author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F}, title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41957864}, issn = {2524-6372}, support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.<br><br>RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.<br><br>CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.}, }
@article {pmid41957950, year = {2026}, author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A}, title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.}, journal = {Oncoimmunology}, volume = {15}, number = {1}, pages = {2656514}, doi = {10.1080/2162402X.2026.2656514}, pmid = {41957950}, issn = {2162-402X}, mesh = {Animals ; Humans ; Mice ; *Oncolytic Virotherapy/methods ; *Adenoviridae/genetics ; *Oncolytic Viruses/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Female ; *Actinobacteria/genetics/metabolism ; Feces/microbiology ; *Neoplasms/therapy ; Male ; }, abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.}, }
@article {pmid41958036, year = {2026}, author = {Shin, H and Jeon, MK and Hur, HG}, title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70327}, pmid = {41958036}, issn = {1758-2229}, support = {RS-2023-NR076613//National Research Foundation of Korea/ ; }, mesh = {*beta-Lactamases/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/enzymology/drug effects ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Metagenome ; *Bacterial Proteins/genetics ; }, abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.}, }
@article {pmid41958322, year = {2026}, author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B}, title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.}, journal = {American journal of primatology}, volume = {88}, number = {4}, pages = {e70148}, doi = {10.1002/ajp.70148}, pmid = {41958322}, issn = {1098-2345}, support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Virome ; *Macaca/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Tibet ; Animals, Wild/virology ; Animals, Zoo/virology ; }, abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.}, }
@article {pmid41958469, year = {2026}, author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A}, title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.}, journal = {Alzheimer's &amp; dementia (New York, N. Y.)}, volume = {12}, number = {2}, pages = {e70239}, pmid = {41958469}, issn = {2352-8737}, abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.<br><br>METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.<br><br>RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).<br><br>DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.}, }
@article {pmid41958710, year = {2026}, author = {Nakamichi, K and Manandhar, A and Shrestha, S and Sundararajan, M and Poudel, MP and Karmacharya, BM and Bade, A and Banjara, P and Shrestha, A and Sandt, A and Turski, G and Buhr, ED and Chowdhary, A and Van Gelder, RN}, title = {Association of Seasonal Hyperacute Panuveitis Syndrome with S. pneumoniae Endophthalmitis.}, journal = {Ophthalmology science}, volume = {6}, number = {5}, pages = {101128}, pmid = {41958710}, issn = {2666-9145}, abstract = {PURPOSE: To identify potential infectious agents in cases of seasonal hyperacute panuveitis syndrome (SHAPU) from vitreous biopsies of patients with this disorder.<br><br>DESIGN: A retrospective cohort analysis.<br><br>SUBJECTS: Vitreous biopsies were obtained during the course of care from 53 subjects with SHAPU.<br><br>METHODS: DNA extraction and whole genome shotgun sequencing was performed using Oxford Nanopore long read sequencing. Sequences were matched against microbial and human databases. Visual outcomes at presentation and at 6 months were recorded.<br><br>MAIN OUTCOME MEASURES: Identification and characterization of metagenomic sequences in vitreous isolates from subjects with SHAPU.<br><br>RESULTS: Adequate DNA for sequencing was obtained from 32 SHAPU subjects. Fifteen samples yielded bacteria on culture, with 14 S. pneumoniae and 1 S. aureus isolate recovered. Bacterial DNA was detected by whole genome sequencing in 29 of 32 cases. S. pneumoniae was the predominant organism recovered. Bacterial genomic loads ranged up to 10&#x2009;000 bacteria/human cell, indicating active infection. No pathogens were detected in control samples. Reconstruction of bacterial genome was possible in 7 SHAPU cases and indicated diverse S. pneumoniae subtypes associated with individual cases. Sufficient DNA remained for analysis of torque teno virus by qualitative polymerase chain reaction in 17 cases, of which 13 were positive. Visual outcomes were mixed, with 7 patients having hypotonous eyes at 6 months, but 8 patients having better than 20/200 vision. No relationship could be discerned between presenting bacterial load and visual outcome.<br><br>CONCLUSIONS: The majority of SHAPU cases show molecular evidence for concurrent S. pneumoniae infection. Good visual results are possible in treating SHAPU as endophthalmitis.<br><br>FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.}, }
@article {pmid41959051, year = {2026}, author = {Weng, Y and Moyne, O and Walker, C and Haddad, E and Lieng, C and Chin, L and Rahman, G and McDonald, D and Knight, R and Zengler, K}, title = {A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959051}, issn = {2692-8205}, abstract = {Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.}, }
@article {pmid41959053, year = {2026}, author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA}, title = {Infant gut microbiomes contribute to metabolic states that impact brain function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959053}, issn = {2692-8205}, abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.}, }
@article {pmid41959121, year = {2026}, author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A}, title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959121}, issn = {2692-8205}, abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.<br><br>OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.<br><br>METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.<br><br>MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.<br><br>CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.}, }
@article {pmid41959210, year = {2026}, author = {Muller, E and Baum, S and Borenstein, E}, title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959210}, issn = {2692-8205}, abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.<br><br>RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.<br><br>AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL.}, }
@article {pmid41959308, year = {2026}, author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ}, title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959308}, issn = {2692-8205}, abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.}, }
@article {pmid41959338, year = {2026}, author = {Kramer, AM and Zhang, A and Ayala, N and de Sanctis, B and Karim, L and Hinrichs, AS and Walia, S and Turakhia, Y and Corbett-Detig, R}, title = {Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959338}, issn = {2692-8205}, abstract = {Pangenomes capture population-level variation but remain computationally challenging at scale. We present Panmap, a tool that leverages evolutionary structure to place, align, and genotype sequencing reads against mutation-annotated pangenomes containing up to millions of genomes. Panmap introduces a phylogenetically compressed k-mer index that stores only sequence differences along branches, enabling efficient comparison of reads to both sampled genomes and inferred ancestors. This approach reduces index size by up to 600-fold and construction time by over three orders of magnitude relative to existing tools. Panmap places a 100× coverage SARS-CoV-2 sample onto 20,000 genomes in 0.4 seconds and onto 8 million genomes in under two minutes. Furthermore, it enables accurate haplotype identification and abundance estimation in metagenomic samples and sensitive placement of ancient environmental DNA without prior alignment. Our approach makes large-scale pangenomes directly amenable to read mapping, genome assembly, alignment-free phylogenetic placement, and metagenomic analysis.}, }
@article {pmid41959403, year = {2026}, author = {Maier, J and Gin, C and Rabasco, J and Bass, A and Spencer, W and Duerkop, BA and Callahan, B and Kleiner, M}, title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959403}, issn = {2692-8205}, support = {R01 AI171046/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.<br><br>RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.<br><br>CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.}, }
@article {pmid41959459, year = {2026}, author = {Kim, M and Ardell, SM and Kryazhimskiy, S}, title = {Module-Selection Balance in the Evolution of Modular Organisms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959459}, issn = {2692-8205}, abstract = {The architecture of the genotype-phenotype-fitness map (GPFM) is a key determinant of evolutionary dynamics. One salient feature of biological GPFMs is variational modularity, where each mutation affects only a small subset of functional traits. Variational modularity may constrain the dynamics of trait evolution, but these constraints are not well understood. Here, we use several extensions of the Fisher's geometric model with two functional traits to investigate these constrains. We find that on GPFMs with universal pleiotropy, populations evolve along the fitness gradient, which implies that the trait under stronger selection is optimized exponentially faster than the trait under weaker selection. In contrast, on modular GPFMs, populations approach a quasi-steady state that we term a "module-selection balance" where both traits improve at the same rate and their ratio remains constant. We demonstrate that the existence of a module-selection balance is robust with respect to the details of evolutionary dynamics and GPFMs themselves, as long as they are variationally modular. Our theory predicts that variationally modular organisms should exhibit stereotypical bi-phasic dynamics of genome evolution, especially in the strong clonal interference regime, and we find support for this prediction in metagenomic data from Lenski's long-term evolution experiment in bacterium Escherichia coli. We propose that module-selection balance is an inherent feature of variationally modular GPFMs, which imposes an important constraint on long-term trait evolution.}, }
@article {pmid41959466, year = {2026}, author = {Sapoval, N and Treangen, TJ and Nakhleh, L}, title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959466}, issn = {2692-8205}, abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.<br><br>RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.<br><br>https://github.com/nsapoval/bd-gsl.}, }
@article {pmid41959535, year = {2026}, author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG}, title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715631}, pmid = {41959535}, issn = {2692-8205}, abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.}, }
@article {pmid41959658, year = {2026}, author = {Funauchi, A and Hashimoto, K and Fukushima, K and Matsumoto, Y and Hamada, N and Hara, R and Niitsu, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Gastric Aspirate Isolate Demonstrates Strain-Level Concordance With Sputum Isolate in Nontuberculous Mycobacterial Pulmonary Disease.}, journal = {Open forum infectious diseases}, volume = {13}, number = {4}, pages = {ofag175}, pmid = {41959658}, issn = {2328-8957}, abstract = {The nontuberculous mycobacteria (NTM) isolated from gastric aspirate have demonstrated >85% strain concordance with those from the sputum, suggesting that they originate from the lungs rather than the environment. Gastric aspirate, although not yet internationally recognized, may be a useful supplementary specimen for diagnosing NTM pulmonary disease.}, }
@article {pmid41960427, year = {2026}, author = {Nuanmuang, N and Leekitcharoenphon, P and Njage, PMK and Jirakkakul, J and Dulsawat, S and Tachaleat, A and Svendsen, CA and Møller, FD and Otani, S and Cheevadhanarak, S and Aarestrup, FM}, title = {Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790551}, pmid = {41960427}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a significant public health threat and is associated with millions of deaths worldwide each year. Besides antimicrobial usage, different socioeconomic factors have recently gained attention as being associated with increased AMR. Bangkok, a city with diverse income levels, provided a unique setting for this study, which aimed to explore the possible within-city association between income-level areas and the diversity and abundance of AMR. Twenty-seven toilet waste samples were collected from nine different sites (low-, middle-, and high-income) during March-April 2023, and metagenomic sequencing was performed. The sequencing data were quality checked, and sequences that passed quality control were mapped to antimicrobial, metal, and disinfectant resistance gene databases as well as bacterial taxonomy databases. We observed higher antibiotic resistance genes (ARGs), metal resistance, and disinfectant resistance abundance (fragments per kilobase per million mapped reads, FPKM) in low-income groups compared to middle- and high-income groups. This included both acquired ARGs and presumed intrinsic ARGs, including genes associated with completely novel antibiotics that have so far only been identified through functional cloning. Significant differences in individual ARGs were also observed between sites. Our study highlights the relative abundance of ARGs across different income groups, emphasizing how the development of resistance mechanisms revealed through metagenomic analysis can serve as a valuable tool for city-level surveillance of AMR from toilet waste, particularly in low-income settings.}, }
@article {pmid41960429, year = {2026}, author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL}, title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691133}, pmid = {41960429}, issn = {1664-302X}, abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.<br><br>METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.<br><br>RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.<br><br>DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.}, }
@article {pmid41960438, year = {2026}, author = {Zhao, Z and Xiang, L and Liu, Y and Xu, S and Chen, Y and Yu, M}, title = {Rare fungal keratitis caused by plant pathogens: report of two cases and review of the literature.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1785252}, pmid = {41960438}, issn = {2673-6128}, abstract = {Macrophomina phaseolina and Colletotrichum fructicola are notable plant pathogens, yet cases of keratitis from these fungi are rarely reported. Limited awareness of this keratitis etiology among ophthalmic professionals reduces the likelihood of accurate diagnosis and timely treatment. This report aims to improve the understanding of these rare infections in eye care. We present two cases of keratitis: one caused by M. phaseolina and another by C. fructicola, both of whom experienced a complicated treatment course. Traditional fungal exams yielded negative results, which limited disease identification and focused therapy. To determine the cause, we used metagenomic next-generation sequencing (mNGS) on clinical samples obtained from corneal scrapings. The mNGS report was received during therapy and quickly identified the pathogen. Based on this, we looked for treatment regimens for this kind of infection in previous literature, altered and implemented appropriate antifungal drug therapy, and the patient's condition improved. We review the literature from 1970 to 2025 on M. phaseolina and Colletotrichum spp. keratitis. We identified 10 cases of M. phaseolina keratitis from four studies and 72 cases of Colletotrichum spp. keratitis, including five of C. fructicola, in 43 articles. Misdiagnosis was common due to limited clinical and microbiologic suspicion. The rise of infections by rare pathogens highlights diagnostic challenges. Traditional methods often delay accurate diagnosis, while mNGS enables rapid identification of pathogen, crucial for effective treatment and vision preservation.}, }
@article {pmid41960830, year = {2026}, author = {Sun, S and Zhou, Y and Deng, F and Meng, Y and Zhu, X and Wang, H and Wei, D}, title = {Engineering an l-Threonine Aldolase from Staphylococcus epidermidis for Enhanced Diastereoselectivity in the Synthesis of a Chloramphenicol Intermediate.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {15}, pages = {12271-12279}, doi = {10.1021/acs.jafc.6c01578}, pmid = {41960830}, issn = {1520-5118}, mesh = {*Chloramphenicol/chemistry/metabolism ; Stereoisomerism ; *Staphylococcus epidermidis/enzymology/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Glycine Hydroxymethyltransferase/genetics/chemistry/metabolism ; Biocatalysis ; Protein Engineering ; Substrate Specificity ; }, abstract = {l-Threonine aldolase (LTA) is an attractive biocatalyst for the synthesis of l-syn-p-nitrophenylserine (l-syn-1b), a key intermediate in chloramphenicol synthesis. However, low diastereoselectivity has limited its broader application in stereospecific C-C bond formation. To overcome this limitation, a metagenomic library constructed from non-natural amino acid-enriched environments was screened, leading to the identification of an LTA from Staphylococcus epidermidis (SeLTA) that exhibits the highest diastereoselectivity toward l-syn-1b among naturally occurring LTAs reported to date. To further enhance its diastereoselectivity, structural comparison, alanine scanning, and tunnel analysis were employed to identify hotspots that modulate the diastereoselectivity of SeLTA. Subsequent saturation mutagenesis and iterative saturation mutagenesis at these positions yielded the quadruple variant A176G/Y202S/N7C/F129E (Mut4), which increased the diastereoselectivity from 32.5%syn to 92.7%syn. Furthermore, Mut4 exhibits markedly improved diastereoselectivity toward para- and meta-substituted benzaldehyde derivatives. Molecular dynamics (MD) simulations further elucidated the molecular basis underlying the enhanced diastereoselectivity of Mut4. This study provides a potential biocatalyst for the sustainable and efficient synthesis of a chloramphenicol intermediate.}, }
@article {pmid41961352, year = {2026}, author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H}, title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41961352}, issn = {1573-6903}, abstract = {Depression is a highly prevalent mental disorder in which dysfunction of the gut microbiota is implicated as a significant factor in its pathogenesis. Puerarin has been suggested to alleviate depression via the microbe-gut-brain axis (MGBA), although the precise mechanisms remain elusive. This study aimed to elucidate the association between the antidepressant effects of puerarin and its role in regulating intestinal flora imbalance and inhibiting subsequent activation of the LPS/TLR4 inflammatory pathway from metabolomics and metagenomics perspectives. A rat model of depression was established using a 6-week chronic unpredictable mild stress (CUMS) protocol. Depressive-like behaviors were assessed through the sucrose preference test (SPT), forced swim test (FST), and open field test (OFT). Inflammatory cytokines (TNF-α, IL-1β, IL-6), LPS, corticosterone, and 5-HT were measured via ELISA. Hippocampal and colonic protein expression of TLR4, MyD88, IκBα, and NF-κB was analyzed by western blot. Colon tissue integrity was evaluated using H&amp;E staining, PAS staining, and transmission electron microscopy. Immunofluorescence was employed to detect Iba-1+ microglia, TLR4+ cells, and ZO-1 expression. Fecal metabolomics and metagenomics were conducted to identify differential metabolites and microbial composition, followed by KEGG and KO enrichment analyses to predict relevant pathways. Spearman correlation analysis was used to explore relationships among gut microbiota, metabolites, and behavioral indices. Puerarin markedly ameliorated depression-like behaviors in CUMS rats. Concurrently, puerarin inhibited the LPS/TLR4 signaling pathway and its downstream pro-inflammatory mediators in both the hippocampus and colon, resulting in a significant reduction in inflammatory responses across these regions, as well as in the serum. Metagenomic sequencing revealed that puerarin suppressed inflammation-associated bacteria, enhanced the abundance of Firmicutes, and induced alterations in the microbial community structure and composition. Metabolomic analysis demonstrated that puerarin could counteract dysregulated fecal metabolism, identifying 17 metabolites as potential key mediators in restoring metabolic homeostasis in CUMS rats. These biomarkers were implicated in several metabolic pathways, including Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, Alanine, Aspartate, and Glutamate metabolism. Puerarin may exert its antidepressant effects by modulating the gut microbial structure and metabolite profiles, thereby alleviating inflammatory stress in the colon, bloodstream, and hippocampus, potentially through inhibition of the LPS/TLR4 signaling pathway.}, }
@article {pmid41961522, year = {2026}, author = {Song, W and Li, M and Yue, X and Meng, Y and Xie, Y and Zhang, Y and Hu, Y and Zheng, Y and Yue, X}, title = {Microbial succession and metabolic mechanisms driving flavor evolution in Northeast Chinese dajiang: a comprehensive review integrating insights from East Asian fermented soybean pastes.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/10408398.2026.2644602}, pmid = {41961522}, issn = {1549-7852}, abstract = {This review systematically explores the spatiotemporal microbial succession and flavor evolution during the fermentation of northeast Chinese soybean paste (dajiang), with a focus on the jiangpei (solid-state starter) and jianglao (brine fermentation) stages. By integrating metagenomic, metabolomic, and sensory data, this review synthesizes evidence linking microbial community dynamics-featuring Lactobacillus spp., Zygosaccharomyces rouxii, and Aspergillus oryzae-to the biosynthesis of key flavor compounds. These include umami amino acids (e.g., glutamic acid, 1.5-2.0 g/kg), fruity esters (e.g., ethyl acetate, 124.67 μg/kg), and phenolic antioxidants. Cross-feeding interactions (e.g., yeast utilization of lactic acid for ester synthesis) and environmental stressors (12%-18% NaCl, 25 °C-30 °C) are shown to enhance flavor complexity by modulating metabolic pathways like amino acid degradation and lipid β-oxidation. Unlike prior studies focusing on fragmented fermentation stages, this review systematically addresses the full fermentation continuum, highlighting how aerobic-to-anaerobic transitions drive functional metabolite accumulation. The review concludes by outlining a roadmap to modernize dajiang production through standardized quality control, precision flavor modulation, and traditional process optimization, enabled by culturomics/MAGs, multi-omics integration, and AI-assisted fermentation monitoring and control.}, }
@article {pmid41961886, year = {2026}, author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T}, title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0345919}, pmid = {41961886}, issn = {1932-6203}, mesh = {*Computational Biology/methods ; Machine Learning ; *Models, Biological ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.}, }
@article {pmid41962241, year = {2026}, author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S}, title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.}, journal = {Water research}, volume = {299}, number = {}, pages = {125879}, doi = {10.1016/j.watres.2026.125879}, pmid = {41962241}, issn = {1879-2448}, mesh = {*Bacteria/metabolism/genetics ; *Nitrites/metabolism ; Seawater/microbiology ; Biofilms ; Phylogeny ; Ecosystem ; }, abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.}, }
@article {pmid41962374, year = {2026}, author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ}, title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141891}, doi = {10.1016/j.jhazmat.2026.141891}, pmid = {41962374}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; Fermentation ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Aerobiosis ; Anti-Bacterial Agents/metabolism ; Pilot Projects ; }, abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.}, }
@article {pmid41963033, year = {2026}, author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I}, title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105049}, doi = {10.1016/j.fm.2026.105049}, pmid = {41963033}, issn = {1095-9998}, mesh = {*Cheese/microbiology/classification ; Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; Milk/microbiology ; High-Throughput Nucleotide Sequencing ; Greece ; }, abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.}, }
@article {pmid41963036, year = {2026}, author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y}, title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105055}, doi = {10.1016/j.fm.2026.105055}, pmid = {41963036}, issn = {1095-9998}, mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Seeds/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Phylogeny ; Microbiota ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Soil Microbiology ; }, abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.}, }
@article {pmid41963043, year = {2026}, author = {Liu, G and Zhong, J and Yang, D and Zeng, Y and Cao, R and He, S and Bai, W and Qu, C}, title = {The mechanisms underlying ester enhancement and higher alcohol reduction in Chi-flavor base liquor brewing via Limosilactobacillus fermentum fortification: A multi-omics investigation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105070}, doi = {10.1016/j.fm.2026.105070}, pmid = {41963043}, issn = {1095-9998}, mesh = {Fermentation ; *Esters/metabolism/analysis ; *Alcoholic Beverages/microbiology/analysis ; *Ethanol/metabolism/analysis ; Flavoring Agents/metabolism ; Multiomics ; Taste ; Lactates/metabolism/analysis ; Saccharomyces cerevisiae/metabolism/genetics ; *Alcohols/metabolism/analysis ; Food Microbiology ; *Lactobacillaceae/metabolism/genetics ; }, abstract = {Chi-flavor Baijiu is a unique liquor in the Pearl River Delta region. Ethyl lactate is the key flavor with low content in base liquor, affecting qualities of Chi-flavor Baijiu. To address this issue, Limosilactobacillus fermentum Y8 (Y8) isolated from sour mash, was used to fortify the fermentation. Results showed that contents of ethyl acetate and ethyl lactate reached to 663.55 mg/L and 604.25 mg/L, increased by 334.97% and 331.26%, respectively, with that of ethanol unchanged and main higher alcohols reduced significantly. Metagenomic analysis revealed that Lactiplantibacillus, Limosilactobacillus, Pediococcus, Levilactobacillus, and Lactobacillus were the top five abundance species. Metatranscriptomic data indicated that Saccharomyces cerevisiae, Lactobacillus brevis and L. fermentum were the dominant active species, the succession of which was significantly influenced by Y8 addition. Correlation analysis revealed that L. fermentum was positively related to reducing sugar, total acid and esters, while negatively to higher alcohols. Based on metatranscriptomic analysis, a new pathway for lactate synthesis from lactaldehyde was found with Y8 fortification, along with acyl-CoA thioester hydrolase gene ybgC upregulated significantly, providing more precursors for ester synthesis. At the same time, enzymes related to ester synthesis were upregulated with that of higher alcohols downregulated. Collectively, Y8 fortification could affect the succession of microbiota and promote the synthesis of ester precursors and ester synthesis pathway, and decrease higher alcohols synthesis pathway. This study not only provides a strain to fortify Chi-Flavor Baijiu brewing with improved qualities but also reveals mechanisms of flavor modulation and microbial community succession during the brewing process.}, }
@article {pmid41963048, year = {2026}, author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M}, title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105075}, doi = {10.1016/j.fm.2026.105075}, pmid = {41963048}, issn = {1095-9998}, mesh = {Animals ; *Meat Products/microbiology/analysis ; Metagenomics ; Swine ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Food, Processed ; *Microbiota ; Cooking ; Food Microbiology ; Food Storage ; Food Handling ; }, abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.}, }
@article {pmid41963049, year = {2026}, author = {Zhai, WT and Zhao, H and Chai, LJ and Zhang, W and Zhang, XJ and Lu, ZM and Gao, CQ and Si, GR and Zhang, WQ and Wang, ST and Shen, CH and Xu, ZH}, title = {Microbial and environmental determinants of 1-propanol biosynthesis in Jiang-flavor Baijiu fermentation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105076}, doi = {10.1016/j.fm.2026.105076}, pmid = {41963049}, issn = {1095-9998}, mesh = {Fermentation ; *1-Propanol/metabolism/analysis ; *Flavoring Agents/metabolism ; *Wine/microbiology/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; *Yeasts/metabolism/genetics/classification ; Temperature ; Food Microbiology ; }, abstract = {1-Propanol is a crucial flavor compound in Jiang-flavor Baijiu, yet the key microbial pathways and environmental factors controlling its synthesis have not been systematically investigated. Using an integrated approach of metagenomics and culture-dependent techniques, this study identified the key microbes, pathways, and factors controlling 1-propanol synthesis. The highest 1-propanol level was detected in first-round base Baijiu, with rapid accumulation during early pit fermentation. Metagenomics revealed the propanoate pathway as the dominant route, primarily contributed by Limosilactobacillus, while Pichia and Saccharomyces were key providers of pyruvate decarboxylase in the citramalate and threonine pathways. Pure-culture validation confirmed that L. panis MR32 predominantly utilizes 1,2-propanediol as the precursor, while yeasts such as P. kudriavzevii 2J2 and S. cerevisiae LB7A prefer the 2-ketobutyrate pathway. Environmental tests revealed optimal 1-propanol production by L. panis MR32 at pH 5.5 and increasing yields with temperature (25-45 °C). In contrast, most yeasts produced the most 1-propanol at 30 °C, beyond which yields declined, with only P. kudriavzevii 2J2 and I. orientalis IO tolerating high lactic acid. Our findings clarify the microbial division of labor and environmental drivers of 1-propanol formation, enabling targeted fermentation control.}, }
@article {pmid41963512, year = {2026}, author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y}, title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41963512}, issn = {2045-2322}, mesh = {Humans ; *Stomach Neoplasms/microbiology/metabolism/pathology ; Male ; Aged ; *Gastrointestinal Microbiome ; Female ; *Metabolic Networks and Pathways ; Metagenome ; Middle Aged ; Bacteria/genetics/classification ; Aged, 80 and over ; Metagenomics ; }, abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.}, }
@article {pmid41963805, year = {2026}, author = {Roslan, MF and Saad, MFM and Pau, SSN and Basir, S and Aziz, H and Akbar, MA and Bunawan, H}, title = {Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41963805}, issn = {2730-6844}, abstract = {OBJECTIVES: Microbial communities in freshwater are pivotal for driving nutrient transformation, bioremediation, and maintaining the health balance of these ecosystems. However, microbial communities in freshwater ecosystems may undergo rapid shifts in composition in response to environmental changes. In some cases, these shifts may signal ecological imbalance. In the tropics like Malaysia, high humidity coupled with high temperatures and seasonal rainfalls creates an even hotter and highly variable environmental conditions that promote microbial proliferation and increase the risk of introducing potentially pathogenic microorganisms from surrounding anthropogenic sources via surface runoff. The current study offers a comprehensive characterisation of bacterial community composition in Malaysian freshwater drinking reservoirs using high throughput 16 S rRNA gene amplicon sequencing. This approach enables bacterial community profiling and supports initial microbial risk assessment in these vital freshwater ecosystems. DATA DESCRIPTION: State Authorities permitted the collection of water samples from eight freshwater reservoirs within Peninsular Malaysia’s protective zones. The 16 S rRNA gene’s V3-V4 hypervariable region was amplified for next generation sequencing. Raw DNA sequence data in FASTQ format were quality-filtered, adapter-trimmed and processed using a QIIME v1.9.1 based pipeline that integrated standard bioinformatics tools for OTU clustering and taxonomic assignment. Utilising R v3.3.1, statistical analyses and data visualisations were performed on this dataset. Characterising the community structure of bacteria in these important freshwater ecosystems is the first step to working with this dataset.}, }
@article {pmid41963968, year = {2026}, author = {Zhou, N and Liu, J and Zhang, X and Xiao, G and Zhang, M}, title = {Vitamin K2 emerges as the key mediator: Cetobacterium somerae ZNN-1 increases muscle protein deposition and improves liver health in Nile tilapia (Oreochromis niloticus).}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41963968}, issn = {1674-9782}, support = {32373145//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Cetobacterium somerae (C. somerae) is a common indigenous bacterium in the intestine of freshwater fish. Studies have shown that it has the potential to promote protein deposition, but the underlying mechanisms remain unclear.<br><br>RESULTS: Nile tilapia were fed with C. somerae ZNN-1 (10[8]&#xa0;CFU/g feed), which significantly increased the carcass ratio, reduced the hepatosomatic index, and decreased whole-body lipid content. Supplementation of C. somerae ZNN-1 significantly increased the crude protein content in muscle, promoted glucose uptake and utilization in muscle tissue, and activated the phosphorylation of S6K/S6 in muscle tissue. C. somerae ZNN-1 supplementation significantly decreased hepatic total lipid, triglyceride, and free fatty acid contents. Further analysis revealed that C. somerae ZNN-1 supplementation markedly activated the phosphorylation of hepatic AMPK and upregulated the expression of genes involved in hepatic lipolysis and fatty acid &#x3b2;-oxidation. Integrated serum metabolomic, bacterial genomic, and gut metagenomic analyses revealed that C. somerae ZNN-1 synthesized chorismate (CHA), which serves as a precursor for gut microbiota to produce vitamin K2 (VK2). In vitro experiments demonstrated that VK2 activated the S6K/S6 pathway to promote protein synthesis, while stimulating AMPK phosphorylation and activating lipid catabolism to reduce fat accumulation.<br><br>CONCLUSIONS: These findings provide a theoretical basis for the application of C. somerae ZNN-1 in enhancing edible protein content and reducing fat deposition of aquatic animals.}, }
@article {pmid41964024, year = {2026}, author = {Sosef, NP and Boxman, ILA and Dirks, RAM}, title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41964024}, issn = {1743-422X}, support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; }, mesh = {*Nucleic Acid Hybridization/methods ; *Food Safety/methods ; Animals ; Humans ; Ostreidae/virology ; *Virome ; Norovirus/genetics/isolation &amp; purification ; Food Microbiology ; *Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.}, }
@article {pmid41964077, year = {2026}, author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ}, title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41964077}, issn = {2049-2618}, support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; }, mesh = {*Soil Microbiology ; California ; *Carbon/analysis/metabolism ; *Grassland ; *Soil/chemistry ; *Rain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/growth &amp; development/metabolism ; Seasons ; *Microbiota ; Carbon Dioxide/analysis/metabolism ; Carbon Cycle ; Metagenome ; }, abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.<br><br>RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by&#x2009;~1 order of magnitude, yielding decreased community growth efficiency (CGE&#x2009;=&#x2009;new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.<br><br>CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.}, }
@article {pmid41964107, year = {2026}, author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W}, title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657047}, pmid = {41964107}, issn = {1949-0984}, mesh = {Humans ; *Aldosterone/metabolism/blood ; *Hyperaldosteronism/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Mice ; Ruminococcus/metabolism/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Eubacteriales/metabolism/isolation &amp; purification/genetics ; Essential Hypertension/microbiology ; Blood Pressure ; }, abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.}, }
@article {pmid41964456, year = {2026}, author = {Lefebvre, CS and Salmona, M and Hamane, S and Dellière, S and Charlier, V and Huguenin, A and Bonnal, C and Legoff, J and Feghoul, L and Dutkiewicz, M and Caméléna, F and Berçot, B and Charvet, E and Battistella, M and Alanio, A and Ghelfenstein-Ferreira, T}, title = {Shotgun metagenomic sequencing improves cross-kingdom diagnosis of mycetoma.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70450}, pmid = {41964456}, issn = {1468-3083}, }
@article {pmid41964564, year = {2026}, author = {Zhao, S and Lin, S and Chen, M and Yan, J and Yang, D and Guo, F and Qu, H and Chen, Y}, title = {Iron-Cycling-Constructed Wetland-Microbial Fuel Cell-Enhanced Removal of Sartans: The Overlooked Singlet Oxygen and Functional Microorganisms.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {16}, pages = {12539-12550}, doi = {10.1021/acs.est.6c00492}, pmid = {41964564}, issn = {1520-5851}, mesh = {*Wetlands ; *Bioelectric Energy Sources ; Iron ; Singlet Oxygen ; }, abstract = {The global challenge of population aging has led to an increase in the utilization of cardiovascular drugs such as sartans, which are frequently detected in aquatic environments and necessitate advanced treatment. Current sartan removal technologies are limited by their requirement for strict reaction conditions and the potential formation of toxic byproducts. This study presents a novel iron-cycling-constructed wetland-microbial fuel cell (Fe-CWMFC) that combines biotic and abiotic processes to effectively degrade sartans (94.4 ± 3.5%-95.9% ± 3.3%). Mass balance analysis revealed that direct microbial degradation pathways made the highest contribution (40.7-44.5%), followed by ROS-driven degradation (20.3-21.8%), substrate adsorption (26.1-29.7%), and plant uptake (2.3-2.5%). Iron cycling enhanced ROS-driven degradation, with 11.3-13.3% derived from biotic [1]O2 and 7.0-9.3% derived from abiotic [1]O2. Metagenomic binning analysis identified 60 MAGs (e.g., Thiobacillus, Nitrosomonas) with sartan degradation potential, which harbor genes encoding functional enzymes (e.g., decarboxylase, dehydroxylase, and demethylase). By combining biodegradation and ROS-driven degradation to target functional groups (e.g., -COOH, -OH, and -CH3) in sartans, the toxicity was significantly reduced. This research enhances our understanding of the combined role of ROS and microorganisms in micropollutant removal and highlights Fe-CWMFC as a high-efficiency, sustainable, and low-toxicity treatment technology for complex environmental applications.}, }
@article {pmid41964658, year = {2026}, author = {Liu, H and Wang, C and Huang, Z and Wang, J and Cai, F and Tian, C and Feng, J and Shen, J and Wang, X}, title = {Progressive Decomposition of Algal Organic Matter Decouples Nitrogen Transformations in Lake Sediments: Evidence from Short-Term Incubation.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {16}, pages = {12158-12169}, doi = {10.1021/acs.est.5c08386}, pmid = {41964658}, issn = {1520-5851}, mesh = {Lakes ; *Nitrogen ; Geologic Sediments ; Nitrification ; Eutrophication ; }, abstract = {Against the backdrop of global lake eutrophication, algal bloom decay is increasingly affecting ecosystems. Algal organic matter (AOM), a natural complex mixture, undergoes multiple release and transformation stages, yet its composition and pathways remain unclear. This study used spectroscopic, mass spectrometric, and metagenomic analyses to monitor a time-compressed algal decay experiment. Results showed that AOM release and transformation can be divided into three stages. Within 1 day, labile AOM consisting mainly of proteins (8.36%), lipids (8.22%), and unsaturated carbohydrates (7.72%) was rapidly released, reshaping nitrogen (N) cycling. Its high bioavailability promoted sediment mineralization and a positive priming effect, while anaerobic conditions reduced nitrification and denitrification rates by 88.7% and 34.5%. Within 3-7 days, semilabile AOM rich in tannins (19.2%) and carbohydrates (9.41%) was gradually decomposed, maintaining anaerobic conditions. The imbalance of excessive NH4[+] and depleted NO3[-] led to the decoupling of nitrification-denitrification. After 7 days, humic-like AOM dominated by lignins (56.8%) prevailed, reducing oxygen consumption and enabling rapid recovery of nitrification and slow rebound of denitrification. These findings clarify the phased transformations of AOM and their microbial interactions, providing mechanistic insights into the short-term fluctuations of lake water quality and microbial processes during bloom decay.}, }
@article {pmid41965517, year = {2026}, author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H}, title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41965517}, issn = {1471-2180}, support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Silicon Dioxide/adverse effects/toxicity ; *Arginine/metabolism ; Mice ; *Pulmonary Fibrosis/chemically induced/metabolism/microbiology ; *Dysbiosis/microbiology/metabolism ; Disease Models, Animal ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; Lung/pathology ; Akkermansia ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.<br><br>RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.<br><br>CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.}, }
@article {pmid41965542, year = {2026}, author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R}, title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.}, journal = {International journal of emergency medicine}, volume = {19}, number = {1}, pages = {}, pmid = {41965542}, issn = {1865-1372}, abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches. METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised. RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm. CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.}, }
@article {pmid41965741, year = {2026}, author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A}, title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.}, journal = {Biomedical engineering online}, volume = {25}, number = {1}, pages = {}, pmid = {41965741}, issn = {1475-925X}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; *Drug Resistance, Microbial/genetics ; *Microbiology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.}, }
@article {pmid41965996, year = {2026}, author = {Wang, C and Shen, J and Liu, H and Huang, Z and Wang, J and Tian, C and Cai, F and Feng, J and Sha, F and Wang, X}, title = {DNRA dominates over denitrification during algal blooms in a mesotrophic lake: Implications for nitrogen retention and eutrophication risk.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129621}, doi = {10.1016/j.jenvman.2026.129621}, pmid = {41965996}, issn = {1095-8630}, mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; *Denitrification ; *Nitrogen ; Nitrates ; }, abstract = {Nitrogen (N) overloading threatens global lake ecosystems. However, how algal blooms affect the N balance in mesotrophic lakes by shaping N-cycling biogeographic patterns remains a critical knowledge gap. This study systematically elucidated N cycling patterns and microbial mechanisms driving N retention during algal blooms in Erhai Lake by integrating field monitoring,[15]N isotope pairing technique ([15]N-IPT), and absolute quantitative metagenomics. Results revealed that algal blooms shaped a N-cycling functional pattern in Erhai Lake characterized by organic degradation and synthesis (ODAS) dominance and dissimilatory nitrate reduction (DNR) as a key process. Notably, algal blooms disrupted traditional nitrification-denitrification coupling, shifting N cycling towards a retention mode dominated by dissimilatory nitrate reduction to ammonium (DNRA). Sedimentary DNRA contributed 69% (14.69 ± 5.57 μmol N L[-1] h[-1]) of total dissimilatory nitrate reduction (DNR) process, supported by significantly elevated NrfA (602.49 ± 121.04 μmol d[-1] g[-1]) and NirBD (361.29 ± 138.39 μmol d[-1] g[-1]) enzyme activities. Partial Least Squares Path Modeling (PLS-PM) identified the nitrogen retention index (NRI) as co-regulated by water depth and algal-mediated microbial activity/rates. High-NRI sediments were dominated by Bacteroidota (mainly orders Marinilabiliales and families Prolixibacteraceae) and Myxococcota (primarily families Anaeromyxobacteraceae), while low-NRI sediments were characterized by enrichment of Pseudomonadota (Thioalkalivibrio nitratireducens and Gallionellaceae) and Campylobacterota (Campylobacter sp. BCW_8712). DNRA outcompeted denitrification, diverting nitrate to ammonium rather than N2 gas and resulting in an internal N loading that was an order of magnitude higher than external inputs. This work challenges the denitrification-centric paradigm, revealing the microbial mechanisms of endogenous N accumulation under algal bloom conditions and providing a theoretical basis for the management of plateau lakes.}, }
@article {pmid41966291, year = {2026}, author = {Ashango, ZA and Seyum, EG and Nwogha, JS}, title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {141}, number = {}, pages = {105941}, doi = {10.1016/j.meegid.2026.105941}, pmid = {41966291}, issn = {1567-7257}, mesh = {*Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Plant Breeding/methods ; *Microbiota ; }, abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.}, }
@article {pmid41966300, year = {2026}, author = {Bojko, J and Abd-Alla, A}, title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108623}, doi = {10.1016/j.jip.2026.108623}, pmid = {41966300}, issn = {1096-0805}, mesh = {Animals ; *Invertebrates/virology ; *Virome ; *Viruses/genetics ; }, abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.}, }
@article {pmid41966314, year = {2026}, author = {Liu, S and Qin, Y and Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Genomic characterization, antimicrobial resistance and virulence profiles of Klebsiella pneumoniae isolated from mink in Northern China.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108485}, doi = {10.1016/j.micpath.2026.108485}, pmid = {41966314}, issn = {1096-1208}, mesh = {Animals ; *Klebsiella pneumoniae/genetics/drug effects/pathogenicity/isolation &amp; purification ; China/epidemiology ; Anti-Bacterial Agents/pharmacology ; *Mink/microbiology ; Virulence/genetics ; *Klebsiella Infections/veterinary/microbiology/epidemiology ; Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Genome, Bacterial/genetics ; Feces/microbiology ; Plasmids/genetics ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Genomics ; Interspersed Repetitive Sequences ; }, abstract = {Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7259 ARGs and 6701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.}, }
@article {pmid41966472, year = {2026}, author = {Merkhan, K and Chaudhry, AS}, title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.}, journal = {Anaerobe}, volume = {98}, number = {}, pages = {103046}, doi = {10.1016/j.anaerobe.2026.103046}, pmid = {41966472}, issn = {1095-8274}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Methane/metabolism/biosynthesis ; Fermentation ; *Animal Feed/analysis ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; Archaea/metabolism ; Bacteria/classification/genetics/metabolism ; *Food Additives ; }, abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.<br><br>METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72&#xa0;h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20&#xa0;g&#xa0;kg[-1] DM) for each PFA.<br><br>RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20&#xa0;g&#xa0;kg[-1] DM, followed by GBL with a 28.5% reduction at 10&#xa0;g&#xa0;kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.<br><br>CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.}, }
@article {pmid41966559, year = {2026}, author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J}, title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142004}, doi = {10.1016/j.jhazmat.2026.142004}, pmid = {41966559}, issn = {1873-3336}, mesh = {*Soil Pollutants/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Acridines/metabolism ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Sphingomonadaceae/genetics/metabolism ; }, abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.}, }
@article {pmid41966829, year = {2026}, author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, S&#xc1; and Ferenczi, S and Szőke, Z}, title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104498}, pmid = {41966829}, issn = {2666-1667}, abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].}, }
@article {pmid41967167, year = {2026}, author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB}, title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101830}, doi = {10.1016/j.cbd.2026.101830}, pmid = {41967167}, issn = {1878-0407}, mesh = {Animals ; *Aquaculture/methods ; Metabolomics ; *Microbiota ; *Multiomics ; }, abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.}, }
@article {pmid41967206, year = {2026}, author = {Moletta-Denat, M and Azam, O and Pourcher, AM and Manno, M and Zennaro, B and Bonin, E and Bonnafous, A and Chenon, P and Leboucher, A and Alvarez-Fraga, L and Godon, JJ and Wéry, N}, title = {Fate of pathogenic bacteria in five full-scale biogas plants monitored using cultivation, dPCR, and shotgun metagenomics: Insights from each approach.}, journal = {Waste management (New York, N.Y.)}, volume = {218}, number = {}, pages = {115505}, doi = {10.1016/j.wasman.2026.115505}, pmid = {41967206}, issn = {1879-2456}, mesh = {*Metagenomics/methods ; *Biofuels/microbiology ; Polymerase Chain Reaction/methods ; *Bacteria/isolation &amp; purification/genetics ; Shotgun Sequencing ; }, abstract = {Current global standards for quantification of pathogenic or indicator bacteria in biogas plants primarily rely on culture-based methods using specific media. However, molecular techniques such as quantitative PCR, digital PCR (dPCR), and shotgun metagenomics are increasingly employed in research and may offer more effective pathogen monitoring for industrial applications. This study analyzed samples from five full-scale biogas plants using traditional culture-based methods, dPCR and shotgun metagenomics to monitor indicator bacteria (Escherichia coli, Enterococcus spp. and Clostridium perfringens) and pathogenic species (Salmonella enterica, Listeria monocytogenes, Staphylococcus aureus and Clostridium botulinum). The DNA extraction protocol was optimized to achieve quantification limits of 1.1 copies of gene g[-1] wet weight, compatible with regulatory thresholds. Comparing the three methods revealed that shotgun metagenomics detected a greater diversity of pathogenic species in biowaste, including S. aureus and C. botulinum. Acidophilic conditions in hydrolysis tank effectively hygienized the biowaste. In contrast, the four agricultural biogas plants showed limited effect on the three indicator bacteria, as indicated by dPCR. This study demonstrates, for the first time, the added value of combining dPCR and shotgun metagenomics to assess pathogen dynamics in biogas plants. Together, these methods provide a more comprehensive and specific view of microbial contaminants, as illustrated by the detection of Enterococcus cecorum in digestates.}, }
@article {pmid41967340, year = {2026}, author = {Li, M and Yao, K and Harindintwali, JD and Qian, M and Wu, N and Kan, Y and Song, Z and Xiao, X and Liu, P and Zhao, Y}, title = {Alkali-organic synergy rewires microbial acid tolerance to restore nitrogen cycling in acidic soils.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129619}, doi = {10.1016/j.jenvman.2026.129619}, pmid = {41967340}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Nitrogen Cycle ; Hydrogen-Ion Concentration ; Nitrogen ; Manure ; Alkalies ; }, abstract = {Soil acidification in global croplands is intensifying, yet the microbial mechanisms by which amendments restore soil nitrogen (N) cycling remain poorly understood. Here, we used a decade-long field experiment in strongly acidic soils to elucidate how alkali slag and organic manure, alone and in combination, regulate acid-tolerant microbial functions and N transformation processes. By integrating soil physicochemical analyses, 16 S rRNA gene sequencing, and shotgun metagenomics, we show that the combined application of organic manure and alkali slag (OM + AS) most effectively increased soil pH (from 4.18 to 5.42) and reduced inorganic N accumulation relative to single amendments (Ammonium nitrogen, nitrate nitrogen, and total organic nitrogen decreased by 15.66 mg/kg, 12.56 mg/kg, and 46.09 mg/kg respectively). Metagenomic profiling revealed that OM + AS consistently up-regulated acid-tolerance pathways (proton pump increased by 6.12%, alkali production increased by 9.75%, acid consumption increased by 5.12%) together with key N cycling genes, with the strongest enhancement observed for nitrification (increased by 84.54%). Network analysis demonstrated significant positive co-occurrence between acid-tolerance and nitrification genes across the microbial community. Correspondingly, bacterial taxa harboring these functions, including Sphingomonas and Nitrospira, were most abundant under OM + AS. We propose that alkali slag and organic manure act synergistically to elevate soil pH, relieve acid stress on microbes, and promote a community with dual capacities for acid tolerance and active N transformation. These findings mechanistically link soil acidity amelioration with enhanced microbial-mediated N cycling and offer a functional basis for designing targeted soil remediation strategies.}, }
@article {pmid41967439, year = {2026}, author = {Tang, C and Wan, C and Gan, J and He, Z and Wei, C and Tan, H and Wu, R and Yu, F and Li, Y}, title = {Rhizosphere phosphorus and iron cycling accelerates manganese phytoextraction by Polygonum lapathifolium.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142033}, doi = {10.1016/j.jhazmat.2026.142033}, pmid = {41967439}, issn = {1873-3336}, mesh = {*Rhizosphere ; Biodegradation, Environmental ; *Iron/metabolism ; *Phosphorus/metabolism ; *Manganese/metabolism ; *Soil Pollutants/metabolism ; *Polygonum/metabolism/growth &amp; development ; Enterobacter/metabolism ; }, abstract = {Manganese (Mn) contamination in mining soils poses persistent ecological risks due to its high mobility and potential accumulation in plants. Although exogenous microbial inoculation is increasingly used to improve phytoremediation, the mechanisms by which it regulates rhizosphere phosphorus (P) and iron (Fe) cycling, and thereby influences Mn bioavailability, remain poorly understood. We hypothesized that Enterobacter sp. inoculation would enhance Mn phytoextraction by stimulating rhizosphere P activation and Fe speciation transformation, thereby promoting nutrient acquisition and Mn mobilization. To test this hypothesis, we investigated the effects of Enterobacter sp. inoculation on rhizosphere P/Fe fractions, functional genes, and Mn phytoextraction. Enterobacter sp. significantly decreased rhizosphere soil pH and enhanced P-releasing enzyme activities, increasing available P by 26.7% under the C1.0 (3.8 ×10[7] CFU·g[-1] (soil)) treatment compared with the control (p < 0.05). Concurrently, Fe(II) and amorphous Fe increased by 11.9% and 15.1%, respectively (p < 0.05), indicating enhanced Fe transformation in the rhizosphere. These shifts facilitated plant P and Fe acquisition, promoted biomass production, enhanced Mn phytoextraction in Polygonum lapathifolium L. by strengthening rhizosphere redox conditions and mineral interfacial processes. Metagenomic analysis revealed that Enterobacter sp. inoculation increased the functional potential of genes related to P activation (e.g., gcd, phnP) and Fe biosynthesis/uptake (e.g., hemH, pchB), mainly associated with Pseudomonadota and Actinomycetota. Partial least squares path modeling further confirmed positive associations among P/Fe cycling genes, rhizosphere P/Fe fractions, enzymatic activities, and plant growth. Overall, microbial inoculation enhanced Mn phytoremediation by coordinating rhizosphere nutrient cycling processes, providing a promising strategy for the remediation of HMs-contaminated mining soils.}, }
@article {pmid41967476, year = {2026}, author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W}, title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.}, journal = {Tree physiology}, volume = {46}, number = {5}, pages = {}, doi = {10.1093/treephys/tpag042}, pmid = {41967476}, issn = {1758-4469}, mesh = {*Soil Microbiology ; *Forests ; *Soil/chemistry ; China ; *Trees/physiology ; }, abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a 6-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis Koidz. forest (QF), and Robinia pseudoacacia L. plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for ~70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.}, }
@article {pmid41967488, year = {2026}, author = {Du, M and Xue, P and Minasny, B and Jang, HJ and McBratney, A}, title = {Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41967488}, issn = {1751-7370}, support = {4-H4T0RYS//Department of Agriculture, Fisheries, and Forestry, Australian Government/ ; }, mesh = {*Soil Microbiology ; Australia ; Climate ; *Soil/chemistry ; *Anthropogenic Effects ; Metagenomics ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; }, abstract = {Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterized by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.}, }
@article {pmid41968394, year = {2026}, author = {Zhao, B and Yang, X and Feng, K and Wang, J and Liu, M and Wang, Y and Wang, D and Peng, X and He, Q and Lu, Y and Waseem, H and Wang, S and Deng, Y}, title = {Phylogenetic assembly of methanogenesis regulates methane yield in food-waste anaerobic digestion.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41968394}, issn = {1751-7370}, support = {42277104//National Nature Science Foundation of China/ ; 42577132//National Nature Science Foundation of China/ ; 2019YFC1905001//National Key Research and Development Program of China/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Phylogeny ; Anaerobiosis ; China ; Food Loss and Waste ; Biofuels ; *Archaea/classification/genetics/metabolism ; }, abstract = {Anaerobic digestion (AD) of food waste (FW) is a key waste-to-energy strategy, yet daily biogas yield is often challenging to sustain, partly due to a limited understanding of the internal methanogens and their functional divergence. Here, we investigated seven full-scale mesophilic FW-AD systems distributed across China along a broad latitudinal gradient (>2800 km), linking methane production variations (0.38-2.11 m3/m3•d-1) with the phylogenetic distributions of methanogens and their methanogenic genes. We found that hydrogenotrophic and aceticlastic pathways were ubiquitous, whereas methylotrophic methanogenesis showed regional enrichment in warmer regions, reflecting persistent influences of climate-associated upstream conditions on downstream methanogenic communities. Gene-level phylogeny of methanogenesis-related alleles, rather than species-level phylogeny, closely tracked biogas yield variation (Mantel's P < .05) and showed consistently stronger associations than gene-level compositions (mean standardized total effect: 0.491 vs. 0.298, P < .01). Higher methane yields (1.61 vs. 0.61 m3/m3•d-1 in high- vs. low-performing systems, P < .01) were significantly associated with reduced Faith's phylogenetic diversity (1.82 vs. 2.30, P < .01) and tighter clustering (mean pairwise phylogenetic distance: 0.25 vs. 0.30, P < .01) of methanogenic gene variants, suggesting that phylogenetic coherence may reflect ecological filtering favoring efficient methanogenesis, albeit at the expense of functional redundancy. These findings highlight gene-level trait phylogeny as a potential proxy for functional robustness, offering a framework for ecological design of AD microbiomes.}, }
@article {pmid41968748, year = {2026}, author = {Hilpert, K}, title = {Peptidomics: A New Dimension in Microbiome Research.}, journal = {Protein and peptide letters}, volume = {33}, number = {2}, pages = {488-496}, doi = {10.2174/0109298665436241260327111926}, pmid = {41968748}, issn = {1875-5305}, mesh = {Humans ; *Proteomics/methods ; *Peptides/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Microbiota ; Multiomics ; }, abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.}, }
@article {pmid41969349, year = {2026}, author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M}, title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {265-281}, pmid = {41969349}, issn = {2405-6383}, abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.}, }
@article {pmid41969354, year = {2026}, author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F}, title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {255-264}, pmid = {41969354}, issn = {2405-6383}, abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.}, }
@article {pmid41969371, year = {2026}, author = {Ramos Peña, DE and Boussetta-Charfi, O and Antezack, A and Amroune, N and Colson, P and Monnet-Corti, V and Saia, RS and Guillemot, J and Pozzetto, B and Pillet, S and La Scola, B and Bourlet, T and Fragoso Motta, AC}, title = {Interplay Between Oral Microbiota and Mouth Health in People Living With HIV Under Antiretroviral Therapy With or Without Periodontitis.}, journal = {International journal of dentistry}, volume = {2026}, number = {}, pages = {8794149}, pmid = {41969371}, issn = {1687-8728}, abstract = {People living with HIV (PLWH) in combined antiretroviral therapy (cART) face microbiota shifts linked to immune status, ART regimen, and periodontal diseases, which are capable of inducing local and systemic inflammation. This study aimed to analyze the oral microbial community composition in PLWH under cART with (n = 24) or without (n = 25) periodontitis using shotgun metagenomic sequence analysis, and describe the interaction between bacterial species, clinical and immunological parameters, and the response to nonsurgical periodontal therapy (NSPT). Saliva samples were collected at baseline for both groups, and 30 days after NSPT for the periodontitis group. Within the periodontitis group, all periodontal parameters presented highly significant improvement after NSPT when compared to baseline. The gingival microbiota did not differ significantly between patients with periodontitis and controls; however, a wider range of bacterial species was found in the microbiota of the periodontitis group compared to the control group, while post-treatment the periodontitis group presented an alpha diversity intermediate between the two former groups. Regarding the distribution of the different bacterial species, Porphyromonas gingivalis was found significantly enriched in the periodontitis group, along with different Treponema sp., Fretibacterium fastidiosum, Campylobacter rectus, Bacteroides zoogleoformans, Tannerella forsythia, and Porphyromonas endodontalis. Correlations between seven inflammatory markers and seven periodontitis-related bacterial taxa were found for saliva in the group of periodontitis patients, which was not the case in controls; interestingly, the profiles after NSPT showed intermediate results. By contrast to saliva, the inflammatory markers of periodontitis patients showed no marked differences in blood plasma, except for TNF-alpha and partly IL-4. In view of the fact that oral microbial imbalance may contribute not only to local disease but also to systemic immune activation in the course of HIV-1 infection, reinforcing the importance of maintaining periodontal health represents a part not to be neglected for an optimal management of PLWH.}, }
@article {pmid41969565, year = {2026}, author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH}, title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.}, journal = {PNAS nexus}, volume = {5}, number = {4}, pages = {pgag073}, pmid = {41969565}, issn = {2752-6542}, abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.}, }
@article {pmid41969652, year = {2026}, author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X}, title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826950}, doi = {10.3389/fcimb.2026.1826950}, pmid = {41969652}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].}, }
@article {pmid41969653, year = {2026}, author = {Dai, Z and Hu, Y and Tai, A and Lu, Y and Hu, S and Pan, J and Xiao, Y and Ma, X and Fu, Q and Zhao, H and Su, Z and Tong, P and Hao, Z and Yao, G and Wang, J}, title = {Characterization of a Klebsiella pneumoniae mutant strain wGF 1-2 with attenuated virulence, altered morphology, and reduced biofilm formation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761564}, pmid = {41969653}, issn = {2235-2988}, mesh = {Animals ; *Klebsiella pneumoniae/genetics/virology/pathogenicity/physiology/growth &amp; development ; *Biofilms/growth &amp; development ; Virulence ; Klebsiella Infections/microbiology/pathology ; Mice ; Disease Models, Animal ; Multiomics ; Gene Expression Profiling ; Host-Pathogen Interactions ; Bacteriophages ; Proteomics ; Mutation ; Female ; Proteome/analysis ; Survival Analysis ; Virulence Factors ; }, abstract = {INTRODUCTION: The global rise of antimicrobial resistance has positioned multidrug-resistant Klebsiella pneumoniae as a critical health threat, necessitating alternative therapeutic strategies such as phage therapy. However, the long-term evolutionary consequences of phage-bacteria interactions remain poorly understood. This study characterizes a unique attenuated mutant, wGF 1-2, derived from a hypervirulent K. pneumoniae strain (GF) during phage isolation efforts.<br><br>METHODS: The wGF 1-2 mutant was serendipitously isolated during attempts to obtain lytic phages against the parental GF strain. We performed an integrated multi-omics and phenotypic characterization, including genomic sequencing, proteomic profiling, and transcriptomic analysis. Host-pathogen interactions were assessed using a murine infection model (evaluating survival and tissue colonization), and the impact on the gut microbiota was analyzed via metagenomics.<br><br>RESULTS: Compared to the parental strain, wGF 1-2 exhibited a significant reduction in biofilm formation and distinct morphological alterations. In a murine model, the mutant was avirulent, resulting in 100% survival even at a high challenge dose (10&#x2076; CFU), with minimal tissue colonization. Multi-omics analysis revealed extensive genomic structural variations (81 insertions and 64 deletions). Proteomic shifts included the downregulation of proteins involved in metal ion binding and metabolic pathways. Furthermore, infection with wGF 1-2 led to host inflammatory suppression and a restructuring of the gut microbiota characterized by an increase in beneficial Bacteroidota.<br><br>DISCUSSION: This study provides a comprehensive characterization of an attenuated K. pneumoniae mutant, wGF 1-2. The extensive genomic and phenotypic alterations observed highlight the significant evolutionary potential of bacterial pathogens during phage interactions. These findings underscore the necessity of thorough safety assessments, including evolutionary risk evaluations, for the future development of phage-based therapies.}, }
@article {pmid41970373, year = {2026}, author = {Duan, Y and Wang, L and Cui, H and Fang, Z and Lu, Y and Sun, Z}, title = {The effect of elastic-band resistance training on fecal microbiota and derived metabolites of aged individuals with possible sarcopenia.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1762454}, pmid = {41970373}, issn = {2296-858X}, abstract = {BACKGROUND: Individuals with possible sarcopenia exhibit altered microbiota profiles and poor intestinal metabolism. Exercise training is linked to changes in gut microbiota and has been proposed to enhance the quality of aging skeletal muscle.<br><br>AIMS: In older adults with possible sarcopenia, the study aimed to determine if elastic-band resistance training modulates gut microbiota and its generated metabolites and investigate the underlying relationships with physical function.<br><br>METHODS: Thirty-one volunteers with possible sarcopenia were randomly assigned to either the control group (CG, n&#x202f;=&#x202f;17) or the intervention group (RG, n&#x202f;=&#x202f;14), which underwent 24&#x202f;weeks of elastic-band resistance training. Physical function, body composition, and blood and fecal samples were collected from each patient at baseline and 24&#x202f;weeks. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate protein metabolism regulatory factors, targeted metabolomics was used to quantify short-chain fatty acid (SCFA) levels, and metagenomic sequencing was used to analyze the composition of the fecal microbiota.<br><br>RESULTS: The gait speed (GS), arm curl test (ACT), 2-min step test (2MST), and timed up-and-go test (TUGT) all showed notable improvements in the RG. The RG also showed lower serum levels of tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and higher plasma concentrations of acetate and propionate. Following the intervention, the RG displayed decreased abundances of Eisenbergiella and Eggerthella and increased abundances of the genus Bacillus. Eggerthella abundance was inversely connected with 2MST performance, whereas the change in propionate level was positively correlated with 2MST, TUGT, GS, and appendicular skeletal muscle index (ASMI).<br><br>CONCLUSION: The elastic-band resistance training effectively improved physical function, modulates gut microbiota and SCFAs. The results revealed the physiological mechanisms by which gut microbiota and SCFAs regulate aging muscle health, providing scientific support for possible sarcopenia prevention and treatment via gut-muscle axis bidirectional crosstalk.<br><br>CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/index.html.}, }
@article {pmid41971320, year = {2026}, author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L}, title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1737792}, pmid = {41971320}, issn = {1664-302X}, abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.<br><br>METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.<br><br>RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.}, }
@article {pmid41971325, year = {2026}, author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L}, title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705784}, pmid = {41971325}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.<br><br>METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.<br><br>RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial &#x3b1;-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.<br><br>CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.}, }
@article {pmid41971343, year = {2026}, author = {Qiao, YC and Jiang, XX and Zhan, JP and Cheng, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG}, title = {Correction: Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1832275}, doi = {10.3389/fmicb.2026.1832275}, pmid = {41971343}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1691984.].}, }
@article {pmid41971525, year = {2026}, author = {Adekoya, AE and Boggs, TE and Ibberson, CB}, title = {Revealing community dynamics in polymicrobial infections through a quantitative framework.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag061}, pmid = {41971525}, issn = {2730-6151}, abstract = {Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.}, }
@article {pmid41971531, year = {2026}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag046}, pmid = {41971531}, issn = {2730-6151}, abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.}, }
@article {pmid41971738, year = {2026}, author = {Ji, HL and Liu, CH and Nie, CX and Luo, JF and Li, XR and Fu, AS and Ge, YL}, title = {Metagenomic next-generation sequencing unveils invasive aspergillosis masquerading as miliary tuberculosis in a neutropenic leukemia patient: a case report.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1751760}, pmid = {41971738}, issn = {2673-6128}, abstract = {BACKGROUND: Empirical anti-tuberculosis therapy is a common strategy when patients with acute leukemia chemotherapy-induced neutropenia develop diffuse pulmonary small nodular and subsolid lesions. However, the absence of pathogenetic verification may lead to catastrophic consequences.<br><br>METHODS: Following negative conventional microbiological cultures (bronchoalveolar lavage bacterial culture, Gram/Gram-negative test) and ineffective anti-infective therapy, a second bronchoscopy revealed caseous obstructive lesions in the right upper lobe bronchus. Metagenomic Next-Generation Sequencing (mNGS) analysis of lavage fluid ultimately confirmed invasive pulmonary fungal disease.<br><br>RESULTS: The mNGS analysis of the bronchoalveolar lavage fluid (BALF) reported 6,750 Aspergillus fumigatus sequences, 43 Aspergillus complex sequences, and 81 Candida albicans sequences (considered airway colonization with no pathogenic significance), confirming probable invasive pulmonary aspergillosis (IPA) in line with the 2023 revised EORTC/MSGERC consensus criteria for invasive fungal diseases. Following discontinuation of anti-tuberculosis therapy, targeted antifungal treatment with amphotericin B (40 mg daily) was initiated. Post-treatment, the patient's temperature normalized. Follow-up CT demonstrated improved absorption of lesions in the left lung and right lower lobe, with stable cavitary nodules in the right upper lobe.<br><br>CONCLUSION: This case demonstrates that invasive pulmonary fungal infection can perfectly mimic the typical radiographic features of hematogenous disseminated pulmonary tuberculosis, including diffuse small nodular and subsolid lesions with a miliary distribution pattern predominantly in the upper lobes and extrapulmonary manifestations such as erythema nodosum. For unexplained pulmonary infections in immunocompromised hosts where conventional diagnosis and empirical treatment fail, the timely application of bronchoscopy combined with mNGS technology represents a critical breakthrough for achieving precise diagnosis.}, }
@article {pmid41971837, year = {2026}, author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D}, title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.}, journal = {Fundamental research}, volume = {6}, number = {2}, pages = {837-846}, pmid = {41971837}, issn = {2667-3258}, abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.}, }
@article {pmid41971922, year = {2026}, author = {Zhu, W and Li, Y and Xu, Q and Lin, D and Zhou, T and Yang, F and Shi, M}, title = {Late-onset fungal infection of the bronchial stump post-lung resection: a report of two rare cases of Aspergillus flavus and mixed Candida/Cryptococcus coinfection diagnosed via metagenomic next-generation sequencing.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {63}, pmid = {41971922}, issn = {2523-1995}, abstract = {BACKGROUND: Fungal infection of the bronchial stump is rare, characterized by insidious clinical manifestations and often misdiagnosed as bacterial infection or tumor recurrence. Most reported cases involve Aspergillus fumigatus, with Aspergillus flavus encountered far less frequently. Importantly, fungal colonization of the bronchial stump by Cryptococcus species has not been previously documented, nor has a mixed infection involving Cryptococcus and other fungi at this site. These rare presentations highlight diagnostic blind spots in postoperative airway management and underscore the need for heightened clinical awareness.<br><br>CASE DESCRIPTION: Case 1: A 53-year-old man underwent left upper lobectomy for adenocarcinoma four years prior. In 2024, he presented with hoarseness and chest tightness. Positron emission tomography-computed tomography (PET-CT) revealed a metabolically active soft-tissue nodule adjacent to the surgical suture line. Bronchoscopic biopsy combined with metagenomic next-generation sequencing (mNGS) confirmed the diagnosis of bronchial stump aspergillosis (BSA). The patient received posaconazole therapy for 7 months. Case 2: A 77-year-old woman underwent right lower lobectomy for adenocarcinoma six years earlier. In 2025, she developed cough with sputum production. CT demonstrated bilateral pneumonia with focal consolidation/atelectasis and bilateral pleural effusions. Bronchoscopy and mNGS identified a mixed infection with Candida albicans and Cryptococcus neoformans at the bronchial stump. Following treatment with caspofungin and fluconazole, her clinical symptoms improved, and follow-up CT imaging showed resolution of inflammatory changes.<br><br>CONCLUSIONS: Although fungal infection of the bronchial stump is rare, it warrants early consideration when post-lobectomy patients develop persistent symptoms unresponsive to antibiotics. Early radiological clues-such as unexpected metabolic activity around suture granulomas or localized nodular thickening at the stump-should prompt further evaluation. When conventional cultures remain negative and clinical deterioration continues, early initiation of mNGS can facilitate timely pathogen identification and guide targeted antifungal therapy.}, }
@article {pmid41972094, year = {2026}, author = {Yoshioka, I and Hayashi, C and Endo, Y and Sawada, A and Mori, Y and Ban, S and Yaguchi, T}, title = {Detection of fungal contamination on museum books stored under controlled environmental conditions: A discrepancy between culture-based and metagenomic analysis approaches.}, journal = {Mycoscience}, volume = {67}, number = {1}, pages = {20-26}, pmid = {41972094}, issn = {1618-2545}, abstract = {Mold contamination in library and museum collections poses risks to both cultural heritage and human health. This study examined fungal flora on books stored under controlled environmental conditions (temperature <20 °C, relative humidity <50%) in The University Museum, The University of Tokyo. Both culture-dependent methods and DNA-based metabarcoding targeting the internal transcribed spacer 2 region were used. DNA analysis revealed that Aspergillus halophilicus accounted for over 90% of the sequences from six books. In contrast, culture-based methods using standard media (e.g., PDA, DG18, M40Y) primarily isolated species such as Aspergillus, Penicillium, and Cladosporium, but not A. halophilicus. However, cultivation on CzA supplemented with 70% sucrose at lower temperatures enabled successful isolation of A. halophilicus from one sample. The strain was identified based on morphological features and β-tubulin gene analysis. These findings demonstrate a notable discrepancy between molecular and culture-based results, underscoring the limitations of conventional media for detecting xerophilic fungi in dry environments. The study suggests that desiccation-tolerant species like A. halophilicus can thrive even under strict storage controls and may evade standard integrated pest management (IPM) protocols. To better assess fungal risks in preservation settings, combining improved media with DNA-based methods is essential.}, }
@article {pmid41972101, year = {2026}, author = {Tong, W and Qiao, L and Yang, Y and Li, X and Zhang, Y and Huang, Z and Luo, H and Zhao, L and Zhang, S}, title = {Cross-kingdom metabolic cooperation drives vanillic acid biosynthesis: A spatiotemporal dissection of microbial functional networks in solid-state fermentation.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101394}, pmid = {41972101}, issn = {2665-9271}, abstract = {Microbial self-organization into spatiotemporally structured consortia is key to metabolic specialization in natural environments, yet the principles governing this process in food fermentation are poorly understood. Here, we elucidate how cross-kingdom microbial cooperation drives the biosynthesis of vanillic acid (VA), a critical flavor and bioactive phenolic compound, during the solid-state fermentation of strong-flavor baijiu (SFB). Integrated metagenomic and network analyses across stratified pit layers and fermentation stages revealed a defined three-phase succession model. Early phase (D0-D12) was dominated by filamentous fungi (Aspergillus, Paecilomyces) in upper layers, initiating starch hydrolysis and phenylpropane precursor synthesis (e.g., contributing 22.6% to phenylalanine ammonia-lyase). A transitional bacterial-fungal consortium (Pichia, Klebsiella) then mediated intermediate conversion (D12-D45), with enzymatic hotspots shifting downward. The maturation phase (D45-D85) was defined by the dominance of acidophilic Acetilactobacillus (>80% relative abundance) in the lower layer, which executed the final synthesis steps (contributing 31.5% to caffeic acid O-methyltransferase) and concurrently suppressed vanillic acid degradation via downregulation of vanillate O-demethylase. Network analysis confirmed a spatial metabolic division of labor: fungi specialized in upper-layer lignin deconstruction, while bacteria dominated the completion of phenylpropanoid pathways in the lower layer. Critically, peak VA accumulation (0.375 mg/L at D45) coincided with synchronized enzyme expression across layers, demonstrating active metabolic coordination rather than passive environmental filtering. Our findings establish that functional succession and spatial compartmentalization are fundamental ecological principles enabling efficient biosynthesis in solid-state fermentation, demonstrating that flavor outcomes can be programmed through targeted microbial consortium design.}, }
@article {pmid41972180, year = {2026}, author = {Zhai, Y and Yu, M and Cheng, L and Liu, X and Yan, J}, title = {Orientia tsutsugamushi and Epstein-Barr Virus coinfection presenting with transient fluctuating hearing loss: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1750100}, pmid = {41972180}, issn = {1664-3224}, mesh = {Humans ; Female ; Middle Aged ; *Scrub Typhus/complications/diagnosis/drug therapy/microbiology ; *Coinfection ; *Orientia tsutsugamushi ; *Epstein-Barr Virus Infections/complications/diagnosis/drug therapy ; *Herpesvirus 4, Human ; *Hearing Loss/diagnosis/etiology ; }, abstract = {Scrub typhus, caused by the obligate intracellular bacterium Orientia tsutsugamushi(O. tsutsugamushi), is an acute febrile illness. While neurological complications are known, hearing loss is an uncommon manifestation, and coinfection with Epstein-Barr virus(EBV) presents unique diagnostic and pathophysiological challenges. A 58-year-old woman presented with a 5-day history of high fever, severe headache, and constitutional symptoms. She reported transient, fluctuating bilateral hearing loss. Examination revealed characteristic eschars on her legs. Laboratory findings indicated hepatic impairment and systemic inflammation. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid detected O. tsutsugamushi and EBV. EBV serology profile (VCA-IgG+, VCA-IgM-, EBNA-IgG+) suggested viral reactivation. The patient failed to respond to initial beta-lactam antibiotic therapy but showed rapid and complete resolution of symptoms, including hearing loss, after initiation of doxycycline. At the 1-month and 3-month follow-up, audiological assessment confirmed normal hearing. This case highlights a rare presentation of scrub typhus with EBV coinfection involving fluctuating hearing loss. The dramatic response to doxycycline suggests this auditory symptom may be a reversible, immune-mediated complication of O. tsutsugamushi infection. Physicians should be aware of this potential manifestation in endemic areas. The immunological interplay between these pathogens warrants further investigation.}, }
@article {pmid41972428, year = {2026}, author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG}, title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18849}, doi = {10.1002/advs.202518849}, pmid = {41972428}, issn = {2198-3844}, support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.}, }
@article {pmid41972755, year = {2026}, author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB}, title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.}, journal = {mSphere}, volume = {11}, number = {5}, pages = {e0011326}, pmid = {41972755}, issn = {2379-5042}, support = {//Flu Lab/ ; }, mesh = {Humans ; *Machine Learning ; *Biomarkers/analysis ; *Metagenome ; *Mouth/virology/microbiology ; *Viruses/genetics/isolation &amp; purification/classification ; *Environmental Monitoring/methods ; Microbiota ; *Nose/virology ; Saliva/virology ; Metagenomics ; }, abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.}, }
@article {pmid41972785, year = {2026}, author = {He, X and Liu, J and Cheng, H and Zhu, X and Lin, H and Li, D-W and Yang, Y and Liu, R and Song, D and Zheng, Y and Lea-Smith, DJ and Pedentchouk, N and Todd, JD and Zhao, M and Zhang, X-H}, title = {Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep.}, journal = {mBio}, volume = {17}, number = {5}, pages = {e0394325}, pmid = {41972785}, issn = {2150-7511}, support = {2025YFF0516900, 2025YFF0516903//National Key Research and Development Program of China/ ; LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; 32370118//National Natural Science Foundation of China/ ; ZR2022YQ38, ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; NE/X014428//Natural Environmental Research Council, United Kingdom/ ; }, mesh = {*Geologic Sediments/microbiology ; *Hydrocarbons/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Phylogeny ; Seawater/microbiology ; Metagenomics ; Metagenome ; }, abstract = {Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no <C18 n-alkanes at detectable levels were present, in contrast to proximal hadal seawater samples where these compounds were highly abundant. Metagenomic analysis identified diverse genes for aerobic and anaerobic degradation of n-alkanes and aromatic compounds, distributed across a wide range of taxa, dominated by Chloroflexota, Planctomycetes, Proteobacteria, and Actinobacteria, alongside six novel HYD phyla. Metabolic reconstruction of 120 HYD metagenome-assembled genomes (MAGs) suggests distinct hydrocarbon degradation preferences and metabolic strategies among different bacterial groups. Additionally, hadal bacterial isolates from Proteobacteria, Actinobacteria, and Firmicutes were able to degrade n-alkanes (C18-36), with Dietzia maris HXX048 removing ~50% of n-eicosane within 45 days under 5°C and 50 MPa. Predicted substrate binding of C10 and C20 with AhyA and heterologous expression of almA in Chloroflexota genomes supported their degradative capacity under anaerobic and aerobic conditions. The detection of putative hydrocarbon synthesis genes, specifically oleBC and oleC, suggests that hadal heterotrophic microorganisms may synthesize hydrocarbons. These findings provide evidence for microbial hydrocarbon production and thereby support a previously unrecognized sedimentary hydrocarbon cycle.IMPORTANCEOur findings suggest that hydrocarbon degradation may play an important role in organic matter decomposition and carbon cycling in the hadal subseafloor. This degradation capacity is likely distributed through diverse metabolic pathways across a wide range of phylogenetic taxa. The detection of genes likely encoding enzymes involved in aerobic and anaerobic hydrocarbon degradation, as well as the identification of novel hydrocarbon-degrading (HYD) phyla, highlights the complexity and significance of microbial processes in hadal subsurface sediment. The widespread distribution of hydrocarbon degradation capacity in different hadal sediments suggests hydrocarbons as a potential carbon source sustaining microbial life in this extreme environment. Moreover, the presence of genes associated with hydrocarbon synthesis suggests that hadal sediment microbes possess the genetic potential for both degrading and producing hydrocarbons, pointing to a dynamic and multifaceted hydrocarbon cycle within hadal subsurface sediment.}, }
@article {pmid41973308, year = {2026}, author = {Aydin, F and Çek, &#x15e;}, title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.}, journal = {Veterinary research communications}, volume = {50}, number = {4}, pages = {}, pmid = {41973308}, issn = {1573-7446}, abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.}, }
@article {pmid41973542, year = {2026}, author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S}, title = {Functional gut microbiomes enhance performance in house fly larvae.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0001126}, pmid = {41973542}, issn = {1098-5336}, support = {NNF21OC0070910//Novo Nordisk Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Houseflies/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.<br><br>IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.}, }
@article {pmid41973723, year = {2026}, author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB}, title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {229}, pages = {}, doi = {10.3791/70187}, pmid = {41973723}, issn = {1940-087X}, support = {U01 DE034198/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Feces/virology ; *DNA, Viral/genetics/isolation &amp; purification/chemistry ; *Metagenomics/methods ; *DNA Viruses/genetics/isolation &amp; purification ; }, abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.}, }
@article {pmid41974680, year = {2026}, author = {Valverde, G and Sarhan, MS and Cook, R and Rota-Stabelli, O and Adriaenssens, EM and Zink, A and Maixner, F}, title = {An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974680}, issn = {2041-1723}, mesh = {*Streptococcus pyogenes/genetics/isolation &amp; purification/classification/pathogenicity ; Humans ; *Genome, Bacterial/genetics ; Phylogeny ; *Mummies/microbiology ; Bolivia ; DNA, Mitochondrial/genetics ; *Streptococcal Infections/microbiology/history ; Bayes Theorem ; }, abstract = {Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen responsible for a range of diseases, from mild infections to severe illnesses. Despite its significance in modern clinical settings, little is known about the pathogen's evolutionary history or its presence in ancient human populations. Here, we present genomic evidence of S. pyogenes in the pre-Columbian Americas. We analysed a tooth from a naturally mummified individual dating to the Late Intermediate Period (1283-1383 cal AD), housed in the National Museum of Archeology (MUNARQ) in La Paz, Bolivia. Mitochondrial DNA analysis confirmed the host's Native American ancestry. Shotgun metagenomic sequencing and de-novo assembly enabled the near-complete reconstruction of an ancient S. pyogenes genome displaying close similarity to contemporary strains linked to pharyngitis. The genome contains core virulence genes, but prophages lack streptococcal pyrogenic exotoxins. Phylogenetic analyses place the strain at the base of modern S. pyogenes diversity, and Bayesian analyses indicate that most extant lineages diversified globally within the past ~5,500 years. Our results push back the confirmed presence of S. pyogenes in the Americas by several centuries and suggest that the pathogen circulated among Indigenous populations prior to the European contact.}, }
@article {pmid41974697, year = {2026}, author = {Espinosa, CA and Njunge, JM and Tickell, KD and Diallo, AH and Sayeem Bin Shahid, ASM and Gazi, MA and Kazi, Z and Yoshioka, E and Tigoi, C and Mburu, M and Ngari, M and Ngao, N and Omer, E and Gumbi, W and Gichuki, BM and Mitchel, A and Williams, J and Gogain, J and Janjic, N and Mandal, R and Jenkins, B and Browne, HP and Shao, Y and Rozday, T and Stares, MD and Dawson, NJR and Berson, E and Chang, A and Kim, Y and Mataraso, SJ and Shu, CH and Phongpreecha, T and Xue, L and Saleem, A and Singa, B and Ahmed, T and Voskuijl, WP and Wishart, DS and Houpt, ER and Liu, J and Ali, A and Mupere, E and Chisti, MJ and Bandsma, RHJ and Lawley, TD and Koulman, A and Lancioni, CL and Aghaeepour, N and Berkley, JA and Walson, JL and , }, title = {Multiomics characterization of acute child illness and mortality in Africa and South Asia.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974697}, issn = {2041-1723}, mesh = {Humans ; Multiomics ; Child, Preschool ; Infant ; Female ; Male ; Biomarkers/blood ; Asia, Southern ; Acute Disease/mortality ; Child ; Feces/microbiology ; Proteomics ; Metagenomics ; Africa South of the Sahara/epidemiology ; Metabolomics ; *Child Mortality ; }, abstract = {Childhood illnesses from infectious diseases in low- and middle-income countries contribute substantially to the global under-five mortality. Many hospitalized children experience incomplete recovery, readmission, and post-discharge mortality despite guideline-directed care. However, targeted interventions remain elusive due to limited understanding of underlying mechanisms. In this work, we employ multiomic profiling and multivariate modeling to investigate biological drivers of inpatient and post-discharge mortality in 3,101 acutely ill children across nine sites in sub-Saharan Africa and South Asia. In a nested case-cohort (N = 1008), we generate plasma proteomics, serum metabolomics and lipidomics, stool metagenomics, and fecal pathogen data at admission and discharge. Additionally, we profile 270 geographically matched community children for biological baselines. We identify a generalizable mortality signature marked by immune, inflammatory, and metabolic dysregulation with gut dysbiosis. We show that mortality-associated signals persist from admission through discharge, indicating unresolved disease and that malnourished children show greater baseline perturbations, explaining elevated risk. We also find some children with low clinical severity display high predicted mortality risk from targeted biomarkers. Finally, we distill predictive models to a clinically feasible biomarker panel and validate our findings in an independent cohort (N = 100). By linking inpatient and post-discharge mortality to specific biological mechanisms, our findings highlight why current care can fail and demonstrate how biomarker-guided risk stratification can identify vulnerable children currently missed by clinical assessments, enabling targeted interventions to reduce mortality in low- and middle-income countries.}, }
@article {pmid41974712, year = {2026}, author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y}, title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974712}, issn = {2041-1723}, support = {R21 AI180737/AI/NIAID NIH HHS/United States ; R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; Humans ; Male ; Mice ; Disease Models, Animal ; *Dysbiosis/diet therapy/immunology/microbiology ; *Faecalibacterium prausnitzii/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology/genetics ; *Lupus Erythematosus, Systemic/diet therapy/immunology/microbiology ; Metabolomics ; Metagenome ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration &amp; dosage ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; }, abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.}, }
@article {pmid41975031, year = {2026}, author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE}, title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41975031}, issn = {2399-3642}, support = {DairyBio//Dairy Australia/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Methane/metabolism ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Australia ; }, abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.}, }
@article {pmid41975041, year = {2026}, author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , }, title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.}, journal = {British journal of cancer}, volume = {135}, number = {1}, pages = {139-151}, pmid = {41975041}, issn = {1532-1827}, support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy/methods ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; Treatment Outcome ; }, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).<br><br>METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.<br><br>RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa&#xa0;-notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.<br><br>CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.<br><br>PROSPERO: CRD42023433704.}, }
@article {pmid41975095, year = {2026}, author = {Guan, K and Ocampo, RF and Matheus Carnevali, PB and Castelle, CJ and Gonzalez-Osorio, L and Castanzo, DT and Thomas, NC and Brothers, M and Dangerfield, TL and Hooper, MM and West, MS and Appleby, NM and Krudop, I and Lamothe, RC and Aliaga Goltsman, DS and Alexander, LM and Butterfield, CN and Johnson, KA and Brown, CT and Taylor, DW}, title = {Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency.}, journal = {Nature structural &amp; molecular biology}, volume = {33}, number = {5}, pages = {756-767}, pmid = {41975095}, issn = {1545-9985}, support = {R35 GM138348/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/chemistry/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/metabolism/genetics/chemistry ; Models, Molecular ; R-Loop Structures ; HEK293 Cells ; }, abstract = {Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing because of their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here we identify and characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Alistipes sp. Cas12f (Al3Cas12f), which supports robust genome editing in human cells. Through structural, biochemical and kinetic analyses, we compare Al3Cas12f to two recently described orthologs, Oscillibacter sp. Cas12f and Ruminiclostridium herbifermentans Cas12f. These orthologs present divergent architectures and regulatory features governing protospacer-adjacent motif recognition, guide RNA (gRNA) binding, dimerization and DNA cleavage. Notably, Al3Cas12f achieves efficient R-loop formation through a stable dimer interface and a naturally optimized gRNA. Leveraging these structural insights, we generate an engineered Al3Cas12f variant (RKK) that increases editing and improves activity across several tested genomic loci. By overcoming locus-dependent variability and an apparent potency threshold, this engineered compact editor seems to expand the feasibility of low-dose, AAV-compatible therapeutic genome editing. Our results elucidate mechanistic determinants of Cas12f activity and offer a framework for engineering compact genome editors that may bear therapeutic potential.}, }
@article {pmid41975182, year = {2026}, author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A}, title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41975182}, issn = {2045-2322}, support = {818431//Horizon 2020 Framework Programme/ ; }, mesh = {*Zea mays/microbiology/growth &amp; development ; *Soil Microbiology ; *Fertilizers ; *Microbiota ; *Microbial Consortia ; Rhizosphere ; Bacteria/classification/genetics ; Biodiversity ; Soil/chemistry ; }, abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.}, }
@article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, abstract = {BACKGROUND: The human microbiome plays an emerging role in cancer biology, yet its contribution to endometrial cancer (EC) remains poorly defined. This study investigates the microbial composition of the vaginal, rectal, and endometrial sites in women with and without EC, aiming to uncover microbial signatures associated with the disease.<br><br>RESULTS: We performed shotgun metagenomic sequencing on vaginal, rectal, and endometrial samples from 25 patients with EC and 27 control women undergoing hysterectomy for benign conditions. Vaginal and rectal swabs were collected before surgery, while endometrial swabs were obtained post-hysterectomy using a sterile brushing technique to prevent cross-contamination. Vaginal microbiota in patients with EC showed significantly higher microbial diversity and distinct community composition compared to controls. These differences remained significant after adjusting for age and body mass index. Several bacterial species, including Peptococcus niger, Anaerococcus murdochii, Mobiluncus, Porphyromonas, and Prevotella, were more abundant in the vaginal microbiota of patients with cancer. In contrast, Lactobacillus spp. were more abundant in vaginal and rectal samples of control subjects.<br><br>CONCLUSIONS: This work represents one of the few studies to comprehensively examine the relationship between the vaginal, rectal, and endometrial microbiomes in the context of EC, suggesting a potential role for microbial imbalance in disease development. The findings underscore the importance of site-specific microbial analyses in gynecologic oncology and support further investigation into the microbiome as a possible biomarker for early detection and a target for preventive strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05017-4.}, }
@article {pmid41975257, year = {2026}, author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z}, title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41975257}, issn = {1471-2105}, abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks. RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis. CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).}, }
@article {pmid41975274, year = {2026}, author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN}, title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655793}, pmid = {41975274}, issn = {1949-0984}, support = {RC2 DK118619/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Metabolome ; Female ; Male ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Middle Aged ; *Liver Cirrhosis, Biliary/microbiology/metabolism ; *Cholangitis, Sclerosing/microbiology/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adult ; Metagenome ; Aged ; Metabolomics ; }, abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.}, }
@article {pmid41975427, year = {2026}, author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P}, title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41975427}, issn = {1746-6148}, support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; }, abstract = {Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.}, }
@article {pmid41975703, year = {2026}, author = {Rong, R and Long, Y and Li, Y and Lin, L and Yang, J and Hu, Z and Liu, D and Chen, P}, title = {Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {7}, pages = {}, pmid = {41975703}, issn = {2075-4418}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; P12220011-230148//Undergraduate teachingquality and teaching reform licensing project SYSU/ ; }, abstract = {Metagenomic and targeted next-generation sequencing (NGS) technologies are rapidly transforming diagnosis and management for infectious diseases. This review comprehensively examines the current applications of metagenomic NGS (mNGS) and targeted NGS (tNGS) in clinical microbiology, highlighting their roles in pathogen detection, antimicrobial resistance profiling, virulence characterization, and outbreak investigation-particularly in complex cases such as pneumonia, critical illness with pulmonary infections, and pediatric acute respiratory illnesses. We discuss the diagnostic performance, advantages, and limitations of these approaches, including challenges related to sensitivity, specificity, standardization, bioinformatic complexity, and cost-effectiveness. Furthermore, we explore emerging opportunities for integrating NGS-based surveillance with public health strategies, such as wastewater epidemiology, to monitor healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) at the population level. Finally, we outline key steps needed to translate these powerful genomic tools from research settings into routine clinical and public health practice.}, }
@article {pmid41975975, year = {2026}, author = {Szala, &#x141; and Staninska-Pięta, J and Piotrowska-Cyplik, A}, title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {7}, pages = {}, pmid = {41975975}, issn = {2076-2615}, support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; }, abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.}, }
@article {pmid41976452, year = {2026}, author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y}, title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976452}, issn = {2304-8158}, support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.}, }
@article {pmid41976454, year = {2026}, author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J}, title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976454}, issn = {2304-8158}, abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.}, }
@article {pmid41976504, year = {2026}, author = {Buranavanitvong, N and Thanthithum, C and Kanyakam, K and Azzout-Marniche, D and Jouan-Rimbaud Bouveresse, D and Chotechuang, N and Prakitchaiwattana, C}, title = {Diet-Associated Gut Bacterial Microbiota and Metabolome Signatures Linked to Fermented Food Intake in Healthy Postmenopausal Women.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976504}, issn = {2304-8158}, support = {FOOD_FF_68_290_2300_073//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; GCUGR1125671022D//the 90th Anniversary of Chulalongkorn University Scholarship under the Ratchadapisek Somphot Endowment Fund/ ; NA//the Second Century Fund (C2F), Chulalongkorn University/ ; }, abstract = {Long-term adherence to plant-based diets can modify gut bacterial microbiota composition and metabolite profiles, which may be particularly relevant for postmenopausal women who frequently adopt such diets and experience age-related changes in nutrient absorption and metabolism. Fermented foods, commonly consumed in vegetarian diets, enhance dietary diversity and nutritional quality. This study compared gut bacterial microbiota and fecal metabolomes between vegetarians (VGs) and omnivores (OMs) and evaluated the contribution of fermented food intake. Thirty-two healthy postmenopausal Thai women (>55 years; 16 VGs, 16 OMs) were enrolled. Gut bacterial microbiota and fecal metabolites were analyzed using 16S rRNA metagenomic and untargeted [1]H-NMR metabolomics. The five most frequently consumed fermented foods were microbiologically characterized. Fermented food consumption was found to be significantly different between groups. OM participants reported infrequent consumption (<10% per week), whereas VG participants consumed fermented foods daily, often in multiple forms (>60% of weekly meals). VG participants exhibited enrichment of Prevotella, Faecalibacterium, and Blautia, while OM participants showed higher abundances of Bacteroides and Escherichia-Shigella. LEfSe identified Weissella as a bacterial taxon associated with the VG group. Functional prediction and metabolomic analyses indicated enhanced carbohydrate fermentation and increased short-chain fatty acid (SCFA) production in VGs, whereas OM profiles reflected greater protein catabolism. Fermented foods consumed by VGs shared microbial biomarkers with the VG gut bacterial microbiota and were rich in SCFAs and essential amino acids, supporting their potential role as microbial and metabolic contributors within the gut ecosystem and nutritional adequacy in postmenopausal vegetarians.}, }
@article {pmid41977149, year = {2026}, author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J}, title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977149}, issn = {1422-0067}, mesh = {*Malus/chemistry/microbiology/metabolism ; *Fermentation ; *Gastrointestinal Microbiome ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Fruit ; Bacteria/classification/genetics ; }, abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.}, }
@article {pmid41977414, year = {2026}, author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J}, title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977414}, issn = {1422-0067}, support = {2024YFF0907700//National Key R&amp;D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; }, mesh = {*Wood/microbiology/metabolism ; *Penicillium/metabolism/genetics/isolation &amp; purification ; *Microbiota ; Lignin/metabolism ; Biodegradation, Environmental ; }, abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.}, }
@article {pmid41978025, year = {2026}, author = {De Nat, M and Boscolo, S and Gallo, SP and Nanni, L and Fusaro, D}, title = {Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {7}, pages = {}, pmid = {41978025}, issn = {1424-8220}, mesh = {Humans ; *Deep Learning ; *Genome, Viral/genetics ; Convolutional Neural Networks ; Neural Networks, Computer ; Metagenomics/methods ; *Sequence Analysis, DNA/methods ; DNA, Viral/genetics ; Ensemble Learning ; }, abstract = {Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from 'viral dark matter.' In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to 'unseen' viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github.}, }
@article {pmid41979145, year = {2026}, author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA}, title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.}, journal = {Research report (Health Effects Institute)}, volume = {2026}, number = {237}, pages = {1-58}, pmid = {41979145}, issn = {1041-5505}, mesh = {Humans ; Female ; Infant ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; *Air Pollution/adverse effects/analysis ; *Environmental Exposure/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; California ; Particulate Matter/analysis/adverse effects ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; }, abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.<br><br>METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter &#x2264;2.5 &#xb5;m and &#x2264;10 &#xb5;m in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.<br><br>RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.<br><br>CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.}, }
@article {pmid41979617, year = {2026}, author = {Li, G and Dan, N and Lu, T}, title = {Two Cases of Severe Chlamydia psittaci Pneumonia with Respiratory Failure and Literature Review.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250675}, pmid = {41979617}, issn = {1433-6510}, mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation &amp; purification ; *Psittacosis/diagnosis/microbiology/drug therapy/complications ; *Respiratory Insufficiency/microbiology/diagnosis/etiology ; Male ; *Chlamydial Pneumonia/diagnosis/microbiology/drug therapy/complications ; Middle Aged ; Female ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; *Pneumonia, Bacterial/microbiology/diagnosis/drug therapy ; Treatment Outcome ; Metagenomics/methods ; }, abstract = {BACKGROUND: Chlamydia psittaci pneumonia is a zoonotic disease with non-specific clinical manifestations, often leading to delayed diagnosis. Metagenomic next-generation sequencing (mNGS) can help us identify pathogens in a timely manner and quickly adjust treatment strategies.<br><br>METHODS: We reported two cases of severe Chlamydia psittaci pneumonia with respiratory failure and reviewed relevant literature.<br><br>RESULTS: Both patients were diagnosed with Chlamydia psittaci infection through mNGS after routine pathogen testing failed. After using Omadacycline based treatment, the patients' clinical and radiological characteristics improved significantly and were successfully cured.<br><br>CONCLUSIONS: For patients infected with Chlamydia psittaci pneumonia, timely identification of the pathogen is crucial. mNGS can quickly detect Chlamydia psittaci in critically ill patients, guide clinical timely targeted treatment, and improve patient symptoms.}, }
@article {pmid41979623, year = {2026}, author = {Xie, BX and Chen, Y and Tan, YR and Jiang, T and Huang, MH and Zhu, YM and Chen, S}, title = {Challenges in the Diagnosis of Hematogenous Disseminated Pulmonary Tuberculosis with Multiple Organ Involvement.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250640}, pmid = {41979623}, issn = {1433-6510}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Pericardial Effusion/microbiology ; Tomography, X-Ray Computed ; Male ; *Tuberculosis, Miliary/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Ascitic Fluid/microbiology ; }, abstract = {BACKGROUND: Tuberculosis is a public health problem worldwide, and China is a high-burden country. Hematogenous disseminated pulmonary tuberculosis is one of the most serious forms of tuberculosis, and diagnosing hematogenous pulmonary tuberculosis is a challenge, even for the most experienced clinicians, who may also feel perplexed. We report a case of hematogenous disseminated tuberculosis involving multiple organs that was initially misdiagnosed as metastatic malignancy. The diagnosis was finally confirmed by metagenomic Next-Generation Sequencing (m-NGS) of peritoneal and pericardial effusions, which detected Mycobacterium tuberculosis complex.<br><br>METHODS: Appropriate laboratory tests, m-NGS, Chest and abdominal CT, Pericardiocentesis, and Peritoneal puncture.<br><br>RESULTS: Chest and abdominal CT showed diffuse nodules in both lungs, pericardial effusion, bilateral pleural effusion, and abdominal pelvic effusion. Tuberculosis bacillus antibody was negative, erythrocyte sedimentation rate increased to 42 mm/H, and the carcinoembryonic antigen (CEA) increased to 7.1 ng/mL, peritoneal effusion adenosine deaminase increased to 65.17 U/L, pericardial effusion adenosine deaminase increased to 142.39 U/L. m-NGS of pericardial effusion and peritoneal effusion detected 886,963 M. tuberculosis complex.<br><br>CONCLUSIONS: Miliary tuberculosis is a severe and rare form of tuberculosis. Delayed diagnosis may be the most important factor leading to death from miliary tuberculosis. We report a case where Mycobacterium tuberculosis was identified through mNGS of pericardial and peritoneal effusions, enabling rapid diagnosis of disseminated tuberculosis. This case provides a new approach for the rapid diagnosis of disseminated tuberculosis.}, }
@article {pmid41980062, year = {2026}, author = {Zhan, J and Yang, W and Guo, J and Yu, Y and Lai, S and Liu, X and Zhou, S}, title = {Iron plaques as terminal electron acceptors optimize clostridial fermentation and nitrogen fixation in rice rhizospheres.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41980062}, issn = {1751-7370}, support = {//Project of Fujian Provincial Department of Education/ ; //Project of Fujian Provincial Department of Science and Technology of China/ ; //National Natural Science Foundation of China/ ; //National Science Fund for Distinguished Young Scholars of China/ ; }, mesh = {*Oryza/microbiology ; *Nitrogen Fixation ; *Fermentation ; *Rhizosphere ; *Iron/metabolism ; *Clostridium/metabolism/genetics ; Oxidation-Reduction ; Plant Roots/microbiology ; Soil Microbiology ; Electron Transport ; Nitrogen/metabolism ; }, abstract = {Fermentative Clostridium species associated with rice roots can contribute substantially to biological nitrogen fixation (BNF) in anoxic paddy soils, yet whether their BNF is regulated by the redox chemistry of rhizosphere remains unclear. Here, we show that iron plaques on rice roots function as terminal electron acceptors that reprogram Clostridium fermentation and thereby enhance BNF. In nitrogen-fixation microcosms, Clostridium sensu stricto I was selectively enriched under plaque-associated Fe(III)-reducing conditions, coinciding with elevated nitrogen fixation. Metabolomic profiling coupled with metabolic flux analysis revealed that Fe(III) reduction redirects a portion of carbon and electron flow from low-energy-yield solventogenesis toward high-energy-yield acidogenesis. This shift increases cellular ATP generation and expands the reductant pool, thereby benefiting the energetic and reductant demands of nitrogenase. Integrated transcriptomic and metagenomic analyses further identified NosR, a flavin mononucleotide-binding protein that is upregulated during Fe(III) reduction and may facilitate electron delivery to plaque-associated Fe(III). Our findings establish a mechanism in which iron plaque reduction optimizes fermentation for BNF, providing fundamental insights into coupled Fe-N cycling in rice rhizospheres and suggesting potential strategies for sustainable nitrogen management in flooded agroecosystems.}, }
@article {pmid41980294, year = {2026}, author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Glucose metabolism's impact on Blastocystis presence in the human gut.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106647}, doi = {10.1016/j.clnu.2026.106647}, pmid = {41980294}, issn = {1532-1983}, mesh = {Humans ; *Blastocystis/isolation &amp; purification ; *Gastrointestinal Microbiome/physiology ; Female ; *Glucose/metabolism ; Feces/microbiology/parasitology ; Metformin/therapeutic use/pharmacology ; Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; Blastocystis Infections/metabolism ; Middle Aged ; Adult ; }, abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.<br><br>METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.<br><br>RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.<br><br>CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.}, }
@article {pmid41980639, year = {2026}, author = {Li, R and Li, S and Yan, Y and Xie, Y and Liu, L and Zhao, J and Zhang, J and Cai, Z and Huang, X}, title = {Reductive soil disinfestation and hydrothermal biochar regulate antibiotic resistance mechanisms by reshaping soil bacterial functional traits and interaction patterns.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134622}, doi = {10.1016/j.biortech.2026.134622}, pmid = {41980639}, issn = {1873-2976}, mesh = {*Soil Microbiology ; *Charcoal/pharmacology/chemistry ; *Bacteria/drug effects/genetics/metabolism ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The health risk posed by antibiotic resistance genes (ARGs) in agricultural soils has become a growing concern. However, a systematic understanding of how microbial life history strategies, functional traits, and community interactions jointly shape ARG dynamics remains lacking. This knowledge gap not only constrains our ability to elucidate the evolutionary mechanisms underlying microbial resistance but also hampers the precise prediction and effective management of soil ARG risks. Here, we established distinct soil habitats through diverse soil managements, including control (CK), reductive soil disinfestation (RSD), and RSD combined with hydrothermal biochar application (HCR), to investigate how microbial traits and interactions shape ARG resistance mechanisms using metagenomic analyses. Our results showed that RSD and HCR treatments significantly reduced the overall abundance and ecological risk of ARGs compared to CK. In CK soils, microbial communities characterized by intensive interactions, high metabolic activity, and rapid growth efficiency promoted the enrichment of ARGs conferring resistance via antibiotic target alteration, protection, or replacement. In contrast, RSD/HCR treatments favored slow-growing, functionally complex, and competition-dominated communities, which were enriched in ARGs associated with antibiotic efflux mechanisms. Moreover, ARGs exhibited pronounced co-occurrence patterns with antimicrobial biosynthetic gene clusters in highly competitive environments. Collectively, this study reveals the selective responses of ARG resistance mechanisms to distinct microbial ecological strategies and provides new insights for the precise management of environmental antibiotic resistance risks.}, }
@article {pmid41980640, year = {2026}, author = {Yang, H and Peng, N and Fan, Y and Huang, J and Zhang, J and Li, L and Ding, J and Tang, Z and Song, J and Liu, D and Hu, R and He, Z and Wang, C}, title = {Genome-Resolved insights into significance of DNRA Microbes in N2O production during manure composting.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134617}, doi = {10.1016/j.biortech.2026.134617}, pmid = {41980640}, issn = {1873-2976}, mesh = {*Nitrous Oxide/metabolism ; *Composting ; *Manure/microbiology ; Denitrification ; Nitrates/metabolism ; Ammonium Compounds/metabolism ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; }, abstract = {Nitrous oxide (N2O) production during manure composting has traditionally been attributed primarily to heterotrophic denitrification (HD), while the roles of alternative pathways remain poorly resolved. Using time-resolved multi-omics across 37 samples from various manure sources, our study investigated the transcriptional landscape of N2O-producing pathways during composting. Microorganisms associated with dissimilatory nitrate reduction to ammonium (DNRA), including Fermentimonas and JAHWKS01 lineages, accounted for 21.2-33.1% of N2O-producing gene expression-comparable to HD-revealing DNRA as a previously underappreciated source. DNRA-associated gene expression was regulated by viral factors, predominantly through lytic Caudoviricetes phages. Expanding our analysis to 174 public metagenomic datasets revealed that DNRA-derived N2O-producing gene abundance peaked under static and hyperthermophilic conditions, highlighting aeration and temperature as critical mitigation controls. Furthermore, our study identified a substantial proportion of microorganisms harboring both DNRA and HD pathways. These findings refine mechanistic understanding of composting N2O emissions and inform multi-pathway mitigation strategies.}, }
@article {pmid41980647, year = {2026}, author = {Song, M and Jiang, L and Lin, Z and Li, J and Luo, C and Qiu, R}, title = {Size-dependent effect of microplastics on sulfamethoxazole degraders in soil as revealed by integration of SIP and metagenomics.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134620}, doi = {10.1016/j.biortech.2026.134620}, pmid = {41980647}, issn = {1873-2976}, mesh = {*Sulfamethoxazole/metabolism ; *Soil Microbiology ; Biodegradation, Environmental/drug effects ; *Metagenomics/methods ; *Microplastics/chemistry ; *Bacteria/metabolism/genetics ; *Particle Size ; *Soil/chemistry ; }, abstract = {Microbes related to antibiotic degradation in situ in agricultural soil with MPs and their response to different sizes of MPs are ambiguity. This study investigated the microbes participating in antibiotic degradation in soils with 4.5 mm and 0.1 mm MPs by using DNA-SIP with metagenomics, Raman-activated cell sorting (RACS) with sulfamethoxazole (SMX) and polyethylene as the model compound and MPs. The 4.5 mm MPs enhanced SMX degradation by promoting diversity and abundance of degraders benefiting from improved soil properties, relation between degraders and SMX, and bacteria with positive co-occurrence relationship with degraders. The 0.1 mm MPs inhibited SMX degradation by decreasing diversity, abundance of degraders, and intensifying bacteria mutually exclusive with degraders due to harsher soil conditions. Furthermore, DNA-SIP-RACS successfully acquired cells of SIP-identified putative degraders, and directly linked SMX degradation potential with metC1, metF1and luxS1, proving possibility of applying this approach in antibiotic-degrading microbes in soil.}, }
@article {pmid41980652, year = {2026}, author = {Back, JP and Klain, V and Pintro, VO and Lopes, FC and Marques, AL and Kray, J and Beys-da-Silva, WO and Santi, L and Schrank, A and Mayer, FQ and Vainstein, MH}, title = {Viral Diversity of Coastal Restinga Soils From Southern Brazil.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70343}, pmid = {41980652}, issn = {1758-2229}, support = {441167/2023-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 382064/2025-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 383394/2024-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 314485/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305705/2025-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303971/2025-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313620/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303945/2025-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Brazil ; *Soil Microbiology ; *Viruses/classification/genetics/isolation &amp; purification ; *Biodiversity ; Metagenomics ; Phylogeny ; }, abstract = {Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.}, }
@article {pmid41980940, year = {2026}, author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z}, title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41980940}, issn = {2055-5008}, support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; }, mesh = {Animals ; *Ticks/microbiology ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Metagenome ; Sheep/microbiology ; Soil Microbiology ; Marmota/microbiology ; *Livestock/microbiology ; *Animals, Wild/microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Caves/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.}, }
@article {pmid41980943, year = {2026}, author = {Kim, J and Kim, N and Cha, JH and Ma, J and Lee, I}, title = {Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41980943}, issn = {2041-1723}, support = {2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; RS-2025-18362970//National Research Foundation of Korea (NRF)/ ; 2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Metagenome/genetics ; *Benchmarking ; Neural Networks, Computer ; Sequence Analysis, DNA ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic datasets, primarily focusing on short-read sequencing data. Our analysis highlights critical factors influencing binning efficacy: (i) Sequencing depth and taxonomic complexity strongly impact binning performance, while CAMI-simulated benchmarking datasets exhibit substantially lower complexity than human gut and environmental metagenomes, (ii) Chimeric genome rates vary widely across tools, (iii) Multi-sample binning is most effective with about 20 samples, as using too few or too many samples can reduce its benefits, and (iv) Binning efficacy was lower for single-end sequencing samples due to reduced contig quality and assembly fragmentation. Neural network-based tools consistently outperformed others in genome recovery from both real samples and simulated samples with realistic taxonomic complexity, though at higher computational cost. By integrating and refining genome bins from the top three binning tools, we recovered >30% more high-quality genomes than previous methods. This study provides practical guidance for improving metagenomic binning to facilitate the reconstruction of prokaryotic genomes.}, }
@article {pmid41980953, year = {2026}, author = {Luo, E and Pham, ND and Rogers, TJ and Sheam, MM and Benner, BE and Vallino, JJ and Trubl, G and Huber, JA}, title = {Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41980953}, issn = {2041-1723}, mesh = {*Metagenomics/methods ; Carbon Isotopes ; Isotope Labeling/methods ; Carbon Cycle ; *Viruses/genetics ; }, abstract = {Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year[1], more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative [12/13]C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.}, }
@article {pmid41981035, year = {2026}, author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA}, title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41981035}, issn = {2045-2322}, support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; }, abstract = {UNLABELLED: Although antimicrobial resistance is a contemporary public health concern, antimicrobial resistance genes (ARGs) have existed long before human use of antimicrobials, and recent attention has focused on whether permafrost thaw could release ARGs as the resistome shifts. We present a metagenomic analysis of permafrost samples from four sites in Alaska and Sweden, thawed under laboratory conditions. We used ABRicate, an alignment-based tool, and DeepARG, a deep learning tool, to identify ARGs, assessed their abundances under experimental thaw, measured taxonomic shifts, and examined metagenome-assembled genomes (MAGs) carrying ARGs. ARG abundance varied with depth, with some permafrost containing more ARGs than the seasonally thawed active layer. ARG abundance increased with soil carbon and decreased with pH across sites, suggesting site-specific influences. The majority of 164 high-quality MAGs contained ARGs, including 80 out of 105 species identified. This included bacteria from nine phyla, demonstrating widespread distribution across microbial taxa. Laboratory thaw experiments revealed that ARG abundances did not change significantly in two of the sites, but declined with thaw in the remaining two sites. Together, these findings demonstrate that ARGs are consistently present in permafrost microbiomes across multiple sites, but relative abundances generally do not increase during thaw. While ARGs that persist may pose potential risks, our results suggest that permafrost thaw may not substantially elevate environmental or public health risks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-46295-2.}, }
@article {pmid41981202, year = {2026}, author = {Benedicenti, O and Strand, DA and Mohammad, SN and Gulla, S and Amundsen, MM and Sindre, H and Vrålstad, T}, title = {Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41981202}, issn = {2045-2322}, support = {328724//Norges Forskningsr&#xe5;d/ ; 101136346//European Commission/ ; 901674//Fiskeri - og havbruksn&#xe6;ringens forskningsfond/ ; }, mesh = {Animals ; *Salmo salar/microbiology/virology ; *Metagenomics/methods ; *Aquaculture/methods ; Shotgun Sequencing ; Metagenome ; *Fish Diseases/virology/microbiology ; Seawater/microbiology/virology ; Workflow ; }, abstract = {Specific tools for detecting waterborne pathogens are essential for limiting disease spread in aquaculture. We evaluated a field-deployable workflow combining filtration of eDNA/eRNA with targeted (RT-)qPCR and complementary shotgun metagenomics to monitor pathogens and microbial community dynamics in a single-farm study following one Atlantic salmon production cohort from hatchery to slaughter. The primary aim was to assess workflow feasibility and performance under real farm conditions, while secondarily examining whether metagenomic profiles could contextualise microbial shifts associated with pathogen presence. ISAV was consistently detected in hatchery water at ~ 4 × 10[3]-9 × 10[3] copies/L, whereas PRV1 was detected only inside sea pens from August onward (~ 4 × 10[2]-1.5 × 10[4] copies/L) and increased by more than two orders of magnitude after wellboat delousing. Shotgun metagenomics yielded a median of ~ 1.5 × 10[5] reads per sample (mean read length ~ 2.5 kb; N50 > 2 kb), enabling broad taxonomic screening. PRV1-positive seawater samples showed modest decreases in richness and shifts in viral taxa, though patterns were subtle and should be interpreted cautiously given low pathogen loads. The workflow was practical for trained farm personnel, and this integrated approach offers a scalable system for routine pathogen surveillance and supports earlier, evidence-based biosecurity actions, providing broader microbial information than qPCR alone.}, }
@article {pmid41981426, year = {2026}, author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L}, title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].}, journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery}, volume = {40}, number = {4}, pages = {548-556}, pmid = {41981426}, issn = {1002-1892}, mesh = {Humans ; Female ; Male ; *Prosthesis-Related Infections/microbiology ; *Gastrointestinal Microbiome ; *Osteoarthritis/microbiology/surgery ; Aged ; *Dysbiosis/microbiology ; Middle Aged ; Arthroplasty, Replacement, Hip/adverse effects ; *Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; Feces/microbiology ; Bacteria/isolation &amp; purification/classification ; }, abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.<br><br>METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7&#xb1;1) and (14&#xb1;1); for the AF group, preoperatively and on postoperative day (7&#xb1;1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).<br><br>RESULTS: Analysis of gut microbiota diversity showed that the preoperative &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7&#xb1;1), the &#x3b1;-diversity indices in the PJI group on postoperative day (7&#xb1;1) were lower, but the difference was not significant (P>0.05); by postoperative day (14&#xb1;1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the &#x3b1;-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.<br><br>CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.}, }
@article {pmid41981555, year = {2026}, author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C}, title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41981555}, issn = {1472-6831}, support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is a major cause of oropharyngeal and other cancers, occurs more frequently among people with HIV (PWH). Despite antiretroviral therapy, HPV-related cancer incidence remains elevated in this group. Oral dysbiosis in PWH may impair mucosal immunity, promoting HPV persistence and inflammation. Periodontal disease, frequently observed in PWH, further contributes to microbial imbalance and immune dysregulation, increasing susceptibility to oral HPV infection. This study investigates the relationship among oral microbiome composition, periodontal disease and oral HPV infection behavior in PWH, considering immunologic and social determinants of health.<br><br>METHODS: The characterizing oral microbiome and periodontal disease in oral HPV-positive individuals (COMP-HPV), an observational longitudinal study will enroll 500 PWH and follow them up for two years. Oral rinse for HPV testing and periodontal assessment will be collected every six months; saliva for inflammatory markers, oral rinse for microbiome and oral cytobrush for immunological profiling will be collected annually. Immune profiling will include high-dimensional flow cytometry and 10X RNA-sequencing to characterize innate and adaptive immune subsets, with emphasis on HLA-DR&#x2013;positive populations, enabling evaluation of oral immune modulation during HPV infection. The study has four specific aims such as to examine associations between oral microbiome composition (16S and metagenomics) and oral HPV infection, including prevalence, incidence, persistence, and clearance; to assess the impact of periodontal disease on oral HPV infection and investigate whether the oral microbiome mediates this relationship; to determine how oral microbiome composition influences immunological responses in HPV-positive PWH and to evaluate the role of social determinants on oral microbiome composition and HPV infection. Data from this longitudinal study will be used to understand the natural history of oral HPV infection, the interplay with periodontal disease, microbial alterations, and immunological changes, providing evidence to guide interventions for reducing HPV-associated disease in PWH.<br><br>TRIAL REGISTRATION NUMBER: Not applicable.<br><br>DISCUSSION: The COMP-HPV study aims to contribute to the body of research designed to investigate mechanisms underlying oral HPV infection among PWH to improve immune responses to reduce HPV infection and relevant carcinoma.}, }
@article {pmid41981681, year = {2026}, author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD}, title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41981681}, issn = {2524-6372}, support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; }, abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.<br><br>METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63&#xa0;years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.<br><br>RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.<br><br>CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.}, }
@article {pmid41981684, year = {2026}, author = {Clough, J and Mikac, KM}, title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41981684}, issn = {2524-4671}, abstract = {BACKGROUND: The microbiome is significant for conservation biology and should be considered in threatened species management programs. Commensal microbes contribute important functions for host health, while pathogenic microbes can negatively impact the host, leading to morbidity, mortality, and population declines. Shotgun metagenomics, involving the agnostic sequencing of all DNA within a sample, has utility for simultaneous microbial community profiling and pathogen detection. Herein, we used shotgun metagenomics to profile the faecal bacteriome and mycobiome of the southern greater glider (Petauroides volans), an endangered Australian marsupial, and identify putative pathogens that could represent threats to population health. RESULTS: We analysed faecal samples collected from wild southern greater gliders (n = 48) across southeastern New South Wales, Australia. Geographic location had significant effects on both bacterial and fungal community composition. The bacteriome was dominated by Firmicutes, Proteobacteria and Bacteroidetes, with 58 core bacterial species shared among all locations. The mycobiome was dominated by the Ascomycetes, with 261 core fungal species shared among all locations. Geographic location was associated with significant differences in bacterial and fungal microbiota abundance but not host sex or weight. We identified 18 bacterial pathogens and 41 fungal pathogens of veterinary interest, ranging from low prevalence to ubiquitous. Bacteroides fragilis was associated with shifts in the Firmicutes:Bacteroidetes ratio, and therefore, potential dysbiosis. CONCLUSIONS: Geographic location is a key determinant of faecal microbial community structure and abundance in southern greater gliders. Core communities of faecal bacteria and fungi are conserved within and among populations. Southern greater gliders carry genetic material from a variety of putative bacterial and fungal pathogens. These microbes may present threats to the health of greater gliders, their possum relatives, or other animals in Australian forest ecosystems. Scientists and natural resource managers should consider the holobiont, rather than just the individual, when planning for conservation management actions such as translocation.}, }
@article {pmid41981860, year = {2026}, author = {Liu, B and Yang, J and Wang, J and Zhang, J and Wang, L and Qu, B and Guo, L and Zhang, X and Yang, X and Jiang, Y}, title = {Application of Whole-Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {3}, pages = {e70478}, doi = {10.1111/1541-4337.70478}, pmid = {41981860}, issn = {1541-4337}, support = {//Danone Asia-Pacific Management Co. Ltd./ ; }, mesh = {Animals ; *Milk/microbiology ; *Whole Genome Sequencing ; *Metagenomics ; *Food Microbiology ; }, abstract = {As dairy enterprises increasingly focus on microbial contamination, traditional detection technologies are gradually showing limitations in terms of detection capability, accurate source tracking, and rapid response, especially when dealing with microbial communities in complex processing environments. Fortunately, whole-genome sequencing (WGS) and metagenomic sequencing provide innovative alternative solutions. These technologies significantly improve the detection of harmful microbes by offering strain-level resolution, detecting low-abundance organisms, and uncovering previously undetectable microbes. This review discusses the application of WGS and metagenomic sequencing in microbial monitoring, contamination source tracking, and quality control across the entire milk powder production chain. In particular, it highlights the progress made in microbial typing and source tracking, as well as in the detection of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). This review also compares microbial control standards for milk powder and its processing environment across different countries and international organizations, providing a regulatory perspective. Furthermore, the integration of emerging technologies is also discussed, particularly machine learning (ML) and deep learning (DL). Artificial intelligence (AI) enables more efficient, predictive, and accurate microbial monitoring, improving contamination control and contributing to safer and higher-quality milk powder production processes. This review provides critical insights that contribute to improving microbial safety management and control strategies in milk powder production.}, }
@article {pmid41982876, year = {2026}, author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X}, title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799474}, pmid = {41982876}, issn = {1664-302X}, }
@article {pmid41982885, year = {2026}, author = {Santiago-Rodriguez, TM and Toranzos, GA}, title = {Editorial: Advances in phage applications: deciphering phage biological and ecological mechanisms through metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822387}, doi = {10.3389/fmicb.2026.1822387}, pmid = {41982885}, issn = {1664-302X}, }
@article {pmid41982959, year = {2026}, author = {Zhang, K and Zheng, J and Wei, A and Qin, M and Zhu, G}, title = {Pulmonary infection caused by Tropheryma whipplei in a child before hematopoietic stem cell transplantation: a case report.}, journal = {Translational pediatrics}, volume = {15}, number = {3}, pages = {91}, pmid = {41982959}, issn = {2224-4344}, abstract = {BACKGROUND: Tropheryma whipplei (TW) triggers Whipple's disease (WD), a rare, chronic multisystemic infection with heterogeneous clinical presentations that can be easily overlooked, particularly Whipple's pneumonia. The advent of metagenomic next-generation sequencing (mNGS) technology applied to bronchoalveolar lavage fluid (BALF) analysis has enabled the identification of an increasing number of patients with acute pneumonia due to TW. Most reports describe symptomatic middle-aged males with cough, while asymptomatic pediatric cases remain exceptionally rare. Without adequate antibiotic therapy, WD is invariably fatal, especially in patients undergoing hematopoietic stem cell transplantation (HSCT). There is no established consensus on the optimal treatment regimen or duration, particularly for pediatric patients.<br><br>CASE DESCRIPTION: An 8-year-old boy with primary immunodeficiency due to a genetic mutation presented without respiratory symptoms. Yet, high-resolution computed tomography (HRCT) revealed nodular lesions. Initially misdiagnosed as a fungal infection, subsequent mNGS analysis of BALF identified TW as the sole pathogen, leading to a diagnosis of TW-associated pneumonia. Following a combined anti-infective therapy regimen, the patient successfully underwent the myeloablative conditioning (MAC) regimen. Neutrophil and platelet engraftment occurred promptly, with no severe transplant-related complications.<br><br>CONCLUSIONS: This retrospective analysis describes a clinical scenario involving a pediatric patient who exhibited no respiratory symptoms prior to transplantation but showed characteristic nodular lesions on imaging studies, ultimately confirming acute pneumonia caused by TW. Under a combination anti-infection regimen consisting of intravenous ceftriaxone, oral doxycycline, and oral hydroxychloroquine, the child tolerated the MAC regimen well. Neutrophil and platelet engraftment proceeded without delay, and follow-up imaging confirmed complete resolution of the pulmonary lesions.}, }
@article {pmid41983569, year = {2026}, author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM}, title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41983569}, issn = {1751-7370}, support = {//WWTF Vienna Research Grant/ ; //ERC Starting Grant EvoLucin and ERC Consolidator Grant SeaSym/ ; 10.55776/COE7//Austrian Science Fund/ ; PCEGP3_181272//Swiss National Science Foundation Eccellenza/ ; 51NF40_180575//Swiss National Science Foundation National Center of Competence in Research Microbiomes/ ; 51N40_225148//Swiss National Science Foundation National Center of Competence in Research Microbiomes/ ; }, mesh = {Animals ; *Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Bivalvia/microbiology ; DNA, Bacterial/genetics/chemistry ; *Biodiversity ; Plant Roots/microbiology ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a "three-way" facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Candidatus Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots, raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S ribosomal RNA (rRNA) gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.}, }
@article {pmid41983714, year = {2026}, author = {Viguier, C and Mansuy, JM and Martin-Blondel, G}, title = {Recent advances in flavivirus encephalitis.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {189-200}, pmid = {41983714}, issn = {1473-6527}, mesh = {Humans ; *Flavivirus Infections/diagnosis/therapy/prevention &amp; control ; *Flavivirus ; *Encephalitis, Viral/diagnosis/therapy/prevention &amp; control ; Biomarkers ; Prognosis ; }, abstract = {PURPOSE OF REVIEW: Flaviviruses are an increasing public health concern, responsible for a broad spectrum of human disease ranging from asymptomatic or mild febrile illness to severe neuroinvasive infections such as encephalitis. Flavivirus encephalitis is associated with substantial mortality and long-term neurological sequelae, yet no specific antiviral therapy is currently available. Diagnosis remains challenging because of transient viremia and serological cross-reactivity, and preventive strategies are unevenly implemented. This review summarizes recent advances in the diagnosis, prognostic assessment, treatment, and prevention of flavivirus-associated encephalitis.<br><br>RECENT FINDINGS: Recent studies have reshaped diagnostic strategies through improved viral detection, including multimatrix molecular testing and metagenomic approaches, alongside better characterization of host-response markers in cerebrospinal fluid. Recent work has substantially refined understanding of host susceptibility, highlighting preexisting antitype I interferon autoantibodies as a major driver of severe disease across neurotropic flaviviruses, and identifying several biomarkers with potential prognostic value. Neuroimaging work has refined MRI pattern recognition across flaviviral encephalitis, with limited but evolving prognostic implications. While management remains largely supportive, the therapeutic pipeline is increasingly diverse, with growing interest in host-directed strategies.<br><br>SUMMARY: Flavivirus encephalitis represents a major clinical challenge driven by host vulnerability, diagnostic complexity, and the absence of validated therapies. Integrating recent advances in diagnostics, risk stratification, and prevention is essential, while ongoing therapeutic development offers cautious optimism for future management.}, }
@article {pmid41983840, year = {2026}, author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K}, title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e299936}, doi = {10.1590/1519-6984.299936}, pmid = {41983840}, issn = {1678-4375}, mesh = {Animals ; Camelus/microbiology ; *Microbiota/genetics ; Cattle/microbiology ; Chickens/microbiology ; Sheep/microbiology ; Horses/microbiology ; *Livestock/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.}, }
@article {pmid41983925, year = {2026}, author = {El Zibaoui, R and Venkatesan, A}, title = {An update on infectious encephalitis: from epidemiology to management.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {208-217}, pmid = {41983925}, issn = {1473-6527}, mesh = {Humans ; *Infectious Encephalitis/epidemiology/diagnosis/therapy/virology ; Animals ; Antiviral Agents/therapeutic use ; Communicable Diseases, Emerging/epidemiology/diagnosis ; Global Health ; Arboviruses ; }, abstract = {PURPOSE OF REVIEW: Infectious encephalitis (IE) is a serious neurological condition that poses a major global health threat. This review summarizes emerging pathogens, particularly arboviruses, updated diagnostic strategies, and evolving treatment approaches, emphasizing ongoing gaps in diagnosis and management.<br><br>RECENT FINDINGS: Established arboviruses such as West Nile virus, Japanese encephalitis virus, Powassan virus, and Eastern Equine virus have regained attention due to their geographic expansion and the appearance of distinct genotypes. In parallel, increasing reports of encephalitis by newly emerging pathogens such as Oropouche virus and scrub typhus speak to the evolving nature of the epidemiology of IE. Advances in diagnostics, including multiplex PCR and metagenomic next-generation sequencing, have enhanced the breadth and accuracy of pathogen identification. As treatment options remain scarce, the role of immunomodulatory agents and novel antiviral molecules in the management of IE is actively being investigated.<br><br>SUMMARY: The emergence of novel and reemerging pathogens highlights the need for rapid, accurate diagnostics. Advanced molecular techniques and the identification of novel therapeutic targets have the potential to change the landscape of IE. However, strengthening surveillance and vaccination strategies, along with ongoing efforts in vaccine development, remain crucial for optimizing patient outcomes, increasing public health preparedness, and mitigating future outbreaks.}, }
@article {pmid41984378, year = {2026}, author = {Tao, X and Du, Z and Wang, X and Lv, L and Zhang, G and Liang, J and Zou, W}, title = {Volatile Fatty Acid Production from Baijiu Distillers' Grains Via Anaerobic Fermentation with Rumen Microbes: Performance and Mechanism.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {7}, pages = {5192-5211}, pmid = {41984378}, issn = {1559-0291}, support = {52400160//National Natural Science Foundation of China/ ; 52360020//National Natural Science Foundation of China/ ; E2024202030//Natural Science Foundation of Hebei Province/ ; RKJH[2025]26//Renhuai Municipal Science and Technology Program/ ; Qiankehe Jichu QN [2025] 292//Youth Science and Technology Talent Project of the Guizhou Provincial Basic Research Program/ ; }, }
@article {pmid41984912, year = {2026}, author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , }, title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e86058}, pmid = {41984912}, issn = {1929-0748}, mesh = {Humans ; Longitudinal Studies ; Female ; Birth Cohort ; Prospective Studies ; Infant, Newborn ; Infant ; *Gastrointestinal Microbiome/drug effects ; South Africa ; *Drug Resistance, Bacterial ; Risk Factors ; Male ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.<br><br>OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.<br><br>METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.<br><br>RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.<br><br>CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.}, }
@article {pmid41985067, year = {2026}, author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR}, title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.}, journal = {Archives of insect biochemistry and physiology}, volume = {121}, number = {4}, pages = {e70159}, doi = {10.1002/arch.70159}, pmid = {41985067}, issn = {1520-6327}, support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science &amp; Technology, New Delhi, India (INSPIRE-JRF)/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; Metagenomics ; *Microbiota ; *Metamorphosis, Biological ; *Culicidae/microbiology/growth &amp; development ; Bacteria/classification/genetics ; }, abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.}, }
@article {pmid41985316, year = {2026}, author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P}, title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.}, journal = {Biomaterials advances}, volume = {185}, number = {}, pages = {214878}, doi = {10.1016/j.bioadv.2026.214878}, pmid = {41985316}, issn = {2772-9508}, mesh = {Animals ; *Inulin/chemistry/pharmacology ; *Diet, High-Fat/adverse effects ; *Bentonite/chemistry/pharmacology ; Rats ; Male ; *Inflammation/metabolism/drug therapy/chemically induced ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Lipid Metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.}, }
@article {pmid41985330, year = {2026}, author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K}, title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {198}, number = {}, pages = {119370}, doi = {10.1016/j.biopha.2026.119370}, pmid = {41985330}, issn = {1950-6007}, mesh = {*Metformin/adverse effects ; Humans ; *Bile Acids and Salts/metabolism ; *Probiotics/therapeutic use/administration &amp; dosage ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; *Hypoglycemic Agents/adverse effects ; Metabolomics ; Feces/microbiology ; Diabetes Mellitus, Type 2/drug therapy ; Male ; Female ; }, abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.<br><br>METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).<br><br>RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.<br><br>CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.}, }
@article {pmid41985671, year = {2026}, author = {Wang, Y and Liu, X and Li, Z and Kang, A and Bai, Y and Wang, Y and Liu, Y and Zhang, C and Yang, J and Cai, Q and Feng, Y and Yi, H and Zhang, M and Zhang, F and Liu, H and Xu, C}, title = {Oligofructose alleviates hyperandrogenism in polycystic ovary syndrome through gut microbiota-derived bile acids.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.036}, pmid = {41985671}, issn = {2090-1224}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-age women, characterized by hyperandrogenism and metabolic dysfunction. Dietary interventions are recommended as one of the first-line therapies. Oligofructose (OFS), a prebiotic fiber, has demonstrated clinical benefits in PCOS; however, its underlying mechanism remains unclear.<br><br>OBJECTIVES: To determine whether OFS alleviates PCOS-like phenotypes through bile acid-dependent mechanisms and to identify downstream ovarian steroidogenic responses.<br><br>METHODS: Letrozole-induced PCOS-like mice received OFS supplementation. Microbiota dependence was assessed using antibiotic depletion and fecal microbiota transplantation. Bile acid involvement was evaluated using cholestyramine. Gut microbial composition and function were profiled by 16S rRNA and metagenomic sequencing, and bile acids were quantified by UHPLC-MS/MS. Ovarian transcriptomics, ex vivo ovarian explants, and primary granulosa cells were used to examine steroidogenic changes, with pharmacological inhibition applied to assess TGR5-related signaling.<br><br>RESULTS: OFS improved reproductive and metabolic abnormalities in PCOS-like mice. These benefits were abolished by microbiota depletion and bile acid sequestration, indicating microbiota- and bile acid-dependent effects. OFS was associated with increased circulating hyodeoxycholic acid (HDCA), which negatively correlated with serum testosterone. HDCA supplementation partially reproduced endocrine improvements under microbiota-depleted conditions. Ovarian transcriptomic and functional analyses demonstrated enhanced aromatization following OFS treatment. In ex vivo ovarian explants and primary granulosa cells, HDCA increased estradiol production, reduced testosterone, and upregulated CYP19A1 (encoding aromatase). Under androgen stimulation, pharmacological inhibition of TGR5 attenuated HDCA-associated increases in estradiol and aromatase activity, supporting involvement of TGR5-related signaling.<br><br>CONCLUSION: OFS alleviates PCOS-like phenotypes in a microbiota- and bile acid-dependent manner and enhances ovarian aromatization. These findings move beyond descriptive bile acid alterations in PCOS by providing functional evidence that dietary fiber-induced bile acid remodeling is associated with modulation of ovarian steroidogenic regulation.}, }
@article {pmid41986005, year = {2026}, author = {Ansari, A and Shete, O and Ghosh, TS}, title = {Artificial intelligence in microbial metagenomics.}, journal = {Progress in molecular biology and translational science}, volume = {221}, number = {}, pages = {255-276}, doi = {10.1016/bs.pmbts.2026.01.009}, pmid = {41986005}, issn = {1878-0814}, mesh = {*Metagenomics ; *Artificial Intelligence ; Machine Learning ; Humans ; *Microbiota/genetics ; }, abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.}, }
@article {pmid41986051, year = {2026}, author = {}, title = {Correction to 'Clinical Value of Metagenomic Next-Generation Sequencing in Early Diagnosis of Peritoneal Dialysis-Associated Peritonitis: A Randomised Controlled Observational Trial'.}, journal = {Nephrology (Carlton, Vic.)}, volume = {31}, number = {4}, pages = {e70203}, doi = {10.1111/nep.70203}, pmid = {41986051}, issn = {1440-1797}, }
@article {pmid41986587, year = {2026}, author = {Ishibashi, N and Akase, Y and Ito, A and Kishimoto, K and Watanabe, S and Yokoyama, H and Mekata, T}, title = {Genome characterization and environmental DNA-based detection of a novel adenovirus from red seabream (Pagrus major).}, journal = {Archives of virology}, volume = {171}, number = {5}, pages = {}, pmid = {41986587}, issn = {1432-8798}, support = {25K09243//JSPS KAKENHI/ ; }, abstract = {A novel piscine adenovirus, Pagrus major adenovirus 1 (PmAdV-1), was identified in red seabream (Pagrus major) by metagenomic sequencing. The 29,519 bp genome encodes 22 predicted open reading frames and exhibits a unique organization, with the fiber gene positioned upstream of the conserved adenovirus gene cluster. Phylogenetic analyses indicate that PmAdV-1 forms a sister lineage to red-eared slider adenovirus 1 within a clade of fish and reptilian adenoviruses, but its assignment to the genus Testadenovirus remains uncertain. A virus-specific qPCR assay was developed to monitor PmAdV-1 in environmental DNA from rearing seawater. Viral loads transiently increased in some juvenile tanks without marked mortality. These findings expand current knowledge of fish adenovirus diversity.}, }
@article {pmid41986605, year = {2026}, author = {Sumithra, TG and Gayathri, S and Mannur, VS and Neethu, N and Ratheesh Kumar, R and Nair, AV and Ratheesh, L and Zainul Abid, PM and Sundari, BKR and Dharani, G and Krupesha Sharma, SR}, title = {Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41986605}, issn = {2045-2322}, support = {Deep-sea Metagenomics for enhanced next-generation bioethanol production' under Deep Ocean Mission (DOM) [MoES/PAMC/DOM/176/2023 (E-14624)]//Ministry of Earth Sciences/ ; }, abstract = {UNLABELLED: Mesopelagic sediments represent a critical yet understudied component of marine ecosystems, where environmental gradients strongly influence microbial community structure and function. This study profiles prokaryotic and fungal communities in the sediments along a bathymetric transect (500–1000 m) on the upper continental slope of the Lakshadweep Sea to identify community assembly processes and environmental drivers. Mesopelagic sediments supported diverse prokaryotic and fungal assemblages, with prokaryotes exhibiting higher α-diversity indices than fungi, indicating differential ecological adaptation of prokaryotic and fungal groups. Bacteria dominated over Archaea, with Firmicutes, Chloroflexi, Bacteroidota, Proteobacteria, and Desulfobacterota as the major prokaryotic phyla. Ascomycota and Basidiomycota were the major fungi. Diversity varied significantly (p ≤ 0.05) with depth, and most microbes were habitat specialists, indicating strong vertical structuring. The FEAST analysis revealed a limited proportional contribution of microbial communities in deeper sediments from 500 m. Beta nearest taxon index analysis suggested a dominant role of deterministic processes in governing the microbial community assembly. Canonical correspondence analysis identified temperature and DO as key drivers of prokaryotes, and nitrogen and temperature for fungi. Depth was significantly correlated (p ≤ 0.05) with the relative abundance of certain microbial taxa, including a decline in bacterial abundance and an increase in archaeal abundance, as well as positive associations with Dadabacteria, Halobacterota, and Chytridiomycota. This first study from the Lakshadweep Sea provides new insights into tropical mesopelagic sediment microbial diversity and community assembly, highlighting bathymetric and environmental controls that shape the prokaryotic and fungal communities.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-48651-8.}, }
@article {pmid41986657, year = {2026}, author = {Luchen, CC and Piedade, GJ and Chibuye, M and Simuyandi, M and Chisenga, CC and Chilengi, R and Bosomprah, S and Schultsz, C and Mende, DR and Harris, VC}, title = {Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986657}, issn = {2731-8745}, support = {2023159//Amsterdam University Medical Center Amsterdam Public Health Research Institute/ ; LSHM23007//Track-AMR/ ; LSHM23007//Track-AMR/ ; 09150161810022//Netherlands Organisation for Health Research and Development (ZonMw) VENI/ ; 219775/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; LSHM21033//Co-funding by PPP Allowance awarded by Health~Holland, Top Sector Life Sciences &amp; Health GLORIA/ ; AI173360/NH/NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.}, }
@article {pmid41986663, year = {2026}, author = {Luiken, REC and Prinsen, H and Dasari, SN and Zweerus, H and Timmerman, AJ and Speksnijder, DC and Dohmen, W and Wagenaar, JA and Heederik, DJJ and Zomer, AL}, title = {Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986663}, issn = {2731-8745}, abstract = {The use of antimicrobials in livestock farming drives selection and dissemination of antimicrobial resistance (AMR), prompting implementation of veterinary stewardship programs to reduce antimicrobial usage (AMU). We evaluated changes in AMR on 45 Dutch pig farms before and after tailored, coaching-based interventions using phenotypic testing of Escherichia coli and metagenomic profiling of pooled faeces. Post-weaning pig farms, including nursery and fattening units, entered the intervention in a stepped-wedge design, with intervention periods ranging from 10 to 27 months. Across farms, AMU and abundances of several antimicrobial resistance gene classes declined over time, alongside reductions in overall resistome levels. Proportions of phenotypic AMR in E. coli were more variable, although decreased AMU was associated with lower resistance for specific antimicrobial classes, such as tetracyclines and beta-lactams. While longer follow-up is required to fully assess long-term impacts, these findings indicate that veterinary antimicrobial stewardship programs can yield measurable short-term reductions in AMR at farm level.}, }
@article {pmid41986664, year = {2026}, author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J}, title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41986664}, issn = {2399-3642}, mesh = {*Soil Microbiology ; *Microbiota/genetics ; Arctic Regions ; *Metagenomics ; *Metagenome ; Russia ; *Bacteria/genetics ; *Genes, Microbial ; }, abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.}, }
@article {pmid41986859, year = {2026}, author = {Iñiguez-Luna, MI and Gómez-Godínez, LJ and Cadena-Zamudio, JD and Cadena-Zamudio, DA and Aguirre-Noyola, JL and Barrera-Guzmán, LA}, title = {Omics Sciences: Driving the Conservation and Characterization of Plant Genetic Resources.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3011}, number = {}, pages = {345-364}, pmid = {41986859}, issn = {1940-6029}, mesh = {Multiomics/methods ; *Genomics/methods ; Metabolomics/methods ; *Plants/genetics/metabolism ; Crops, Agricultural/genetics ; Genome, Plant ; Proteomics/methods ; *Conservation of Natural Resources/methods ; Computational Biology/methods ; Biodiversity ; Plant Breeding/methods ; }, abstract = {Omics sciences have revolutionized the conservation and characterization of plant genetic resources by enabling a comprehensive understanding of genetic diversity, molecular mechanisms, and adaptive traits. Advances in genomics, transcriptomics, proteomics, metabolomics, and metagenomics have facilitated the identification of genes and metabolic pathways associated with stress tolerance, nutritional value, and agronomic performance. These technologies have enhanced the efficiency of germplasm banks by improving genetic resource characterization, optimizing conservation strategies, and accelerating breeding programs for climate-resilient crops. Additionally, omics approaches contribute to biodiversity conservation by revealing evolutionary relationships, ecosystem dynamics, and the functional roles of microbial communities in plant health. The integration of multi-omics data with bioinformatics and artificial intelligence further enhances predictive capabilities, enabling targeted conservation and breeding efforts. This review highlights the pivotal role of omics sciences in securing plant genetic resources for sustainable agriculture and global food security.}, }
@article {pmid41987827, year = {2026}, author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR}, title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag036}, pmid = {41987827}, issn = {2730-6151}, abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.}, }
@article {pmid41987902, year = {2026}, author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S}, title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1729497}, pmid = {41987902}, issn = {2235-2988}, mesh = {Humans ; *Diarrhea/microbiology/prevention &amp; control/diagnosis ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Female ; *Probiotics/therapeutic use ; Pilot Projects ; Male ; Prognosis ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Prospective Studies ; DNA, Bacterial/genetics/chemistry ; Metagenome ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.<br><br>HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.<br><br>AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.<br><br>METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.<br><br>RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.<br><br>CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.}, }
@article {pmid41988145, year = {2026}, author = {Liu, L and Wang, L and Zhang, P and Gan, M and Liujiang, R and Cheng, G and Ge, M}, title = {Neonatal herpes simplex virus encephalitis: a single-center retrospective study of 14 cases.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1740937}, pmid = {41988145}, issn = {2296-2360}, abstract = {BACKGROUND: This single-center retrospective study aims to analyze the clinical characteristics, treatment strategies, and outcome at discharge of neonatal-onset herpes simplex virus encephalitis (NHSE).<br><br>METHODS: We conducted a single-center retrospective case review of infants diagnosed with NHSE at the Children's Hospital of Fudan University between February 1, 2016, and February 1, 2024. Clinical data, including demographics, clinical symptoms, laboratory findings, neuroimaging results, treatment regimens, and outcomes at discharge, were collected and analyzed.<br><br>RESULTS: A total of 14 infants with NHSE (7 males, 7 females) were identified at our center, with a median age at diagnosis of 26 days (range: 7-51 days). Initial symptoms predominantly included fever and seizures, with neurological involvement (e.g., seizures, lethargy, irritability or altered mental states) in 13 cases. Physical examinations, such as bulging anterior fontanel, were noted. Herpes simplex virus (HSV)-DNA was detected in 13 cases (6 HSV-1, 7 HSV-2) through cerebrospinal fluid (CSF) polymerase chain reaction (PCR) or metagenomic testing. Among these, 9 cases were identified via CSF-PCR, with 7 testing positive on the initial examination and 2 on repeated testing. Notably, 6 cases were diagnosed using metagenomic next-generation sequencing (mNGS), all of which yielded positive results on the first test. Ten out of the 12 children often exhibited temporal lobe spikes on video electroencephalograms (VEEGs). Early magnetic resonance imaging (MRI) revealed cytotoxic edema, progressing to multicystic encephalomalacia. All received acyclovir antiviral treatment. Seven discontinued treatments, one was referred for ocular lesions, and six improved and were discharged.<br><br>CONCLUSIONS: In this single-center cohort, NHSE often presents with nonspecific fever and seizures, with late onset and absent indicative rashes, complicating early diagnosis. For newborns suspected of having NHSE, early CSF HSV-DNA testing and prompt antiviral treatment are essential to improve outcomes. Metagenomic sequencing is especially valuable for accurate, rapid diagnosis when conventional methods fail.}, }
@article {pmid41989131, year = {2026}, author = {Schön, ME and Schvarcz, CR and Malkewitz, SV and Hinner, FC and Koslová, A and Mersdorf, U and Schimm, F and Rickert, S and Pozhydaieva, N and McBeain, K and Hackl, T and Schneider, AC and Barenhoff, K and Höfer, K and Edwards, KF and Steward, GF and Fischer, MG}, title = {Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41989131}, issn = {1751-7370}, support = {24-10280I//Czech Science Foundation/ ; 464500427//SPP 2330/ ; //Max Planck Society/ ; }, mesh = {*Giant Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; *Genetic Variation ; Hawaii ; Phylogeny ; *Cercozoa/virology ; DNA Methylation ; DNA, Viral/genetics ; }, abstract = {Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawai'i. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present in purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. We found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the same ChlorV strain. Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.}, }
@article {pmid41989380, year = {2026}, author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M}, title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659400}, pmid = {41989380}, issn = {1949-0984}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/metabolism ; Child ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Multiomics ; Diet ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; }, abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.}, }
@article {pmid41989870, year = {2026}, author = {Zhu, YC and Deng, Y and Zeng, JQ}, title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {73}, number = {2}, pages = {201-210}, doi = {10.1556/030.2026.02894}, pmid = {41989870}, issn = {1588-2640}, mesh = {Humans ; *Helicobacter Infections/microbiology/metabolism/complications ; Female ; *Helicobacter pylori/physiology ; *Intestine, Small/microbiology ; *Gastrointestinal Microbiome ; Male ; Multiomics ; Feces/microbiology ; *Metabolome ; Middle Aged ; Adult ; *Bacteria/classification/growth &amp; development/genetics/isolation &amp; purification/metabolism ; Aged ; }, abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.}, }
@article {pmid41990029, year = {2026}, author = {Sun, Y and Zhang, M and Wang, X and Huang, X and Yu, Y and Pan, H and Li, H and Shi, L and Yang, W and Zhang, C and Ding, B and Liu, X and Li, J and Qian, C and Cheng, B and Zhang, C and Ran, J and Li, M}, title = {Gut Microbiota of Gray Snub-Nosed Monkeys: Adaptation to Seasonal Variations Through Energy Compensation and Thermogenesis.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70092}, pmid = {41990029}, issn = {1749-4877}, support = {32330015//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; QLKH [2023] 11//Guizhou Forestry Administration Scientific Research Project/ ; QLKH [2025] 11//Guizhou Forestry Administration Scientific Research Project/ ; //Investigation of Nationally Protected Wildlife Species in Tongren Region/ ; GZKPC-2025-01//Guizhou Province/ ; QCZH [2023]82//Protection and Restoration of Forests and Grasslands in 2024 from the Central Finance/ ; [2023]188//Guizhou Science and Technology Support Plan Project/ ; QKHFQ [2023]009//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; YWZ[2024]005//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; QKHPT[2021]5625//Guizhou Outstanding Young Scientist Program/ ; QJJ[2024]337//Natural Science Research Projects of the Education Department of Guizhou Province/ ; [2022]031//Guizhou Provincial Department of Education/ ; 2024BS011//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; 2024BS006//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; }, abstract = {As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.}, }
@article {pmid41990134, year = {2026}, author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J}, title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {5}, pages = {}, pmid = {41990134}, issn = {1574-6941}, support = {32471603//National Natural Science Foundation of China/ ; XZ202601ZY0248//Key Research and Development Program of Xizang Autonomous Region/ ; 2024-TG16//Central Financial Funds for Forestry and Grassland Reform and Development in 2024/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Rats ; *Hypoxia/microbiology ; Male ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolic Reprogramming ; Altitude ; Metagenomics ; }, abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.}, }
@article {pmid41990403, year = {2026}, author = {Zhao, J and Li, T and Huang, H and Servellita, V and Sotomayor-Gonzalez, A and Yakovleva, O and Wang, X and Ragupathy, V and Biswas, S and Barilko, P and Sun, E and Huynh, S and Hunsicker, M and DeQuach, J and Morales, JD and Highbarger, H and Dewar, RL and Porth, C and Denny, TN and McGivern, DR and Chiu, CY and Hewlett, I}, title = {Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105941}, pmid = {41990403}, issn = {1873-5967}, support = {75N91019D00024/CA/NCI NIH HHS/United States ; FD999999/ImFDA/Intramural FDA HHS/United States ; U01 FD005978/FD/FDA HHS/United States ; }, mesh = {Humans ; *HIV-1/genetics/isolation &amp; purification/classification ; *HIV Infections/virology/diagnosis ; *Genetic Variation ; *Genome, Viral ; Viral Load ; RNA, Viral/genetics ; Cameroon ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Reference Standards ; }, abstract = {BACKGROUND: The high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.<br><br>OBJECTIVE: To develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains.<br><br>STUDY DESIGN: HIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.<br><br>RESULTS: Near full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n&#x202f;=&#x202f;18, 2.53 log10 copies/mL), medium (n&#x202f;=&#x202f;18, 3.61 log10 copies/mL), and high viral loads (n&#x202f;=&#x202f;15, 4.66 log10 copies/mL), yielding 51 panel members in total.<br><br>CONCLUSION: This diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.}, }
@article {pmid41990622, year = {2026}, author = {Liu, L and Wang, C and Qi, WK and Zhang, SJ and Li, YY and Peng, Y}, title = {Mechanisms of aerobic simultaneous nitrogen removal under low COD/N conditions: Diffusion-reaction coupling and particle size effects via self-recirculating microgranular system.}, journal = {Water research}, volume = {300}, number = {}, pages = {125937}, doi = {10.1016/j.watres.2026.125937}, pmid = {41990622}, issn = {1879-2448}, mesh = {*Nitrogen ; Particle Size ; Bioreactors ; Biological Oxygen Demand Analysis ; *Waste Disposal, Fluid/methods ; Nitrification ; Sewage ; Aerobiosis ; Denitrification ; Diffusion ; Wastewater ; }, abstract = {Nitrogen removal from ammonium-rich, carbon-limited wastewater remains constrained in continuous-flow microgranular sludge systems. In this study, a three-stage up-flow self-recirculating microgranular sludge reactor was developed to investigate nitrogen removal mechanisms under low chemical oxygen demand to nitrogen ratios (COD/N < 2.5) and high influent total nitrogen (TN > 400 mg/L). During long-term operation, the system achieved stable removal efficiencies of ammonium (98%), TN (94%), and COD (95%). Under ammonium stress, particle size decreased to a mean diameter of 249.2 μm, forming stable, non-flocculent microaggregates. Microgranules < 0.2 mm exhibited pronounced simultaneous partial nitrification-denitrification (SPND) and simultaneous nitrification-denitrification (SND) activities under aerobic conditions. Simultaneous nitrogen removal (SNR) activity peaked at 0.52 g TN/(g VSS·d) at a DO of 2 mg/L. In contrast, microgranules > 0.2 mm primarily followed SND-dominated pathways. Their SNR activity increased with DO and reached a maximum of 0.46 g TN/(g VSS·d). Microbial community and metagenomic analyses revealed a redox-stratified functional structural organization. Rubrivivax (11.5%) dominated the surface layer, likely linking organic matter degradation with nitrogen oxide reduction. Hyphomicrobium (11.9%) was enriched in intermediate layers and was associated with SND. In the core, the co-enrichment of Hyphomicrobium (7.2%) and Methylotenera (6.1%) supported the coupling of SND and SPND processes. These findings provide a basis for improving nitrogen removal from ammonium-rich, carbon-limited wastewater.}, }
@article {pmid41990624, year = {2026}, author = {Wang, G and Yang, F and Xu, S and Lin, D and Yang, R and Yan, P and Chen, Y and Fang, F and Guo, J}, title = {Microbial niches and metabolism drive spatial heterogeneity of hydroxyapatite precipitation in aerobic granular sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125923}, doi = {10.1016/j.watres.2026.125923}, pmid = {41990624}, issn = {1879-2448}, mesh = {*Sewage/microbiology/chemistry ; *Durapatite/chemistry ; Aerobiosis ; Bioreactors ; Phosphorus ; Chemical Precipitation ; Phosphates ; Waste Disposal, Fluid ; }, abstract = {Biologically induced phosphate precipitation (BIPP) in aerobic granular sludge (AGS) provides a promising approach to address phosphorus removal instability and granule structural fragility in practical applications. However, the roles of microbial communities, ecological niches, and metabolic activities in driving phosphate precipitation and shaping its spatial distribution within AGS remain underexplored. This study systematically investigates AGS physicochemical properties, reactor performance, phosphorus speciation, precipitation composition and distribution, microbial community structure, and metabolic activity using sodium propionate (RP) and sodium acetate (RA) as sole carbon sources. The findings reveal for the first time the mechanisms by which microbial communities, ecological niches, and metabolic functions regulate phosphate precipitation and determine its spatial heterogeneity. BIPP contributes 22.6% and 60.1% of total phosphorus removal in RP and RA, respectively, thereby enhancing phosphorus removal efficiency and granule structural stability. Multi-scale analyses-including Standards, Measurements and Testing, Raman spectroscopy, X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, and micro-computed tomography-reveal that hydroxyapatite (HAP) predominantly accumulates in the outer region of RP granules but in the inner region of RA granules. Periodic water quality variations, fluorescence in situ hybridization, granule-stratified sequencing, and metagenomic analyses indicate that the spatial heterogeneity of HAP is driven by the ecological niche separation and metabolic activities of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). In RP granules, PAO‑driven anaerobic phosphate release creates a high‑phosphate microenvironment, which promotes HAP formation in the granule outer region. In RA, GAO‑mediated endogenous denitrification increases local pH, thereby inducing HAP precipitation in the granule interior. Overall, this study elucidates the mechanisms underlying the spatial heterogeneity of phosphate precipitation in AGS from the perspectives of microbial community structure, ecological niches, and metabolic pathways. These findings provide guidance for optimizing AGS systems to achieve efficient phosphorus removal and stable operation.}, }
@article {pmid41990657, year = {2026}, author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D}, title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142056}, doi = {10.1016/j.jhazmat.2026.142056}, pmid = {41990657}, issn = {1873-3336}, mesh = {*Drug Resistance, Microbial/genetics ; Ecosystem ; Macau ; Sewage/virology ; Soil Microbiology ; Geologic Sediments/virology ; *Viruses/genetics ; *Virome ; }, abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.}, }
@article {pmid41991090, year = {2026}, author = {Lee, JS and Jeon, YJ and Kim, TH and Khan, W and Yun, YM}, title = {Multiscale destabilization of anaerobic digestion by chloramphenicol: Divergence between methanogen detectability and methane recovery.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134635}, doi = {10.1016/j.biortech.2026.134635}, pmid = {41991090}, issn = {1873-2976}, mesh = {*Methane/biosynthesis/metabolism ; *Chloramphenicol/pharmacology ; Anaerobiosis/drug effects ; Biomass ; Kinetics ; }, abstract = {Antibiotic residues in livestock waste streams can affect anaerobic digestion (AD), yet their functional impact on microbial viability and metabolic pathways remains unclear. This study evaluated concentration-dependent effects of chloramphenicol (CAP) by integrating process kinetics, cellular integrity, dissolved-phase responses, and functional gene profiles. Methane yield was maintained at ≤ 50 mg/L CAP but declined sharply at higher concentrations, reaching near-complete inhibition at 1,000 mg/L. Estimated inhibition thresholds were derived as IC30 = 285 mg/L, IC60 = 535 mg/L, and IC90 = 852 mg/L from the fitted concentration-response relationship. Severe inhibition coincided with residual organic acid accumulation, pH decline, and enrichment of propionate and butyrate fractions with undetectable acetate. Flow cytometry revealed a marked CAP-dependent decline in intact biomass, with live-cell (P2) counts decreasing from 4.8 × 10[6] cells/mL in the control to 1.0 × 10[5] cells/mL at 1,000 mg/L, accompanied by increased forward- (FSC-A) and side-scatter (SSC-A) area indicative of structural stress. Fluorescence excitation-emission matrix (FEEM) analysis showed concentration-dependent enrichment of soluble microbial products (SMPs) fluorescence, and inoculum-only incubation confirmed biomass-associated solubilization under CAP exposure. Although methanogens remained numerically detectable (76.0% vs. 81.1%), key genes related to cofactor synthesis and electron transfer (comD, frhB, fwdA/fwdC, mcr) declined substantially at 1,000 mg/L. These convergent signals were consistent with multiscale destabilization. Given that microbial activity was not directly measured, the observed discrepancy between methanogen detectability and methane recovery should be interpreted as indicative of a potential functional imbalance rather than definitive evidence of functional decoupling.}, }
@article {pmid41991504, year = {2026}, author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S}, title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {4}, pages = {e70343}, pmid = {41991504}, issn = {1399-3038}, support = {//snfmi-remi/ ; //fai2r/ ; }, mesh = {Humans ; Female ; Haploinsufficiency ; Male ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Phenotype ; Child ; Liver/pathology ; Adolescent ; Feces/microbiology ; *Inflammatory Bowel Diseases/genetics/microbiology ; Liver Diseases/genetics ; Child, Preschool ; Ruminococcus ; *Intestines ; *Autoimmune Diseases/genetics/microbiology ; Eubacteriales ; }, abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.<br><br>METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.<br><br>RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.<br><br>CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.}, }
@article {pmid41991788, year = {2026}, author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T}, title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41991788}, issn = {1573-0972}, abstract = {Increasing water scarcity poses significant threats to crop production and agricultural sustainability. Water deficit and the environmental impacts of synthetic nitrogen fertilization necessitate the development of sustainable cropping systems that enhance resource use efficiency while mitigating climate and economic risks. This study investigates the effects of Mesorhizobium ciceri inoculation (CMG6 strain (SI-DP 40653)), varying water–nitrogen regimes, and a potato-chickpea intercropping system (IC) on plant performance, metabolic responses, rhizospheric microbial diversity. Field trials, located in northeastern Tunisia, showed that IC combined with efficient M. ciceri inoculation significantly outperformed sole cropping (SC) across all physiological parameters. Under standard conditions, this synergy bolstered chickpea biomass and photosynthetic capacity. Notably, under reduced nitrogen input, inoculated intercropping (IC) boosted chickpea shoot biomass by more than twofold compared with sole cropping (SC). Intercropping also improved drought resilience, reducing stress-induced metabolic decline by approximately 40% relative to monocropping systems. Secondary metabolite production was stimulated, with higher accumulation of polyphenols and tannins observed particularly under reduced nitrogen conditions in inoculated systems. Additionally, intercropping improved potato productivity under low-nitrogen conditions while maintaining stable yields under drought stress. Metagenomic analysis showed that water stress accounted for approximately 22% of microbial community variation. However, intercropping and inoculation reshaped rhizosphere communities by enhancing the abundance and diversity of beneficial bacterial groups, particularly Bacilli, and buffering drought-induced shifts. These results emphasized the synergistic benefits of IC and Rhizobium inoculation in improving crop productivity, stress resilience, and soil health while reducing reliance on synthetic inputs.}, }
@article {pmid41991911, year = {2026}, author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q}, title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41991911}, issn = {2041-1723}, support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, mesh = {*Cheese/microbiology ; *Microbiota/genetics ; China ; Animals ; Fermentation ; Metagenome ; Food Microbiology ; Polymorphism, Single Nucleotide ; Lactobacillus helveticus/genetics ; Phylogeny ; Metagenomics ; Biodiversity ; beta-Galactosidase/metabolism ; }, abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.}, }
@article {pmid41992382, year = {2026}, author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F}, title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41992382}, issn = {2524-4671}, abstract = {The exponential growth of the human population and associated intensifications in animal farming, pet ownership, and habitat anthropisation have dramatically increased human-animal interactions. Global livestock production now exceeds 24 billion animals annually, and pet ownership has risen to over 70% of households in many developed nations, creating unprecedented interfaces for viral exchange. This heightened contact has multiplied opportunities for zoonotic and reverse-zoonotic transmission, as tragically exemplified by the SARS-CoV-2 pandemic. The fecal virome—defined as the totality of viral nucleic acids in the gastrointestinal tract—represents a crucial, yet largely unexplored, pathway for such exchanges. While the bacterial microbiome’s role is increasingly recognized, the virome’s composition, dynamics, and transmissibility between co-habiting humans and animals remain poorly characterized. This review compiles current evidence on the fecal virome of key domestic animals (equines, livestock, pets) and their human contacts under the “One Health” framework. We critically evaluate methodological approaches—from targeted PCR to viral metagenomics—and highlight the discovery of novel viruses and identification of zoonotic agents through metagenomic approaches. Critically, we identify significant knowledge gaps, including the absence of definitive evidence for contemporary cross-species transmission versus shared ancestry or convergent evolution. We propose a strategic research agenda focused on longitudinal studies of human-animal cohorts, standardized metagenomic methodologies, and functional analyses of the virome. Elucidating the fecal virome at this interface is paramount for developing proactive surveillance strategies to predict and prevent the next emerging viral disease.}, }
@article {pmid41992389, year = {2026}, author = {Gu, S and Jiang, C and Zhang, P and Luo, S and Gong, Y and Feng, W and Xiong, J and Zhang, J and Chen, K and Ning, K and Miao, W}, title = {Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41992389}, issn = {2524-6372}, support = {2022FY100400//the Science &amp; Technology Fundamental Resources Investigation Program/ ; 2022xjkk0204//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; SNJNP2022008//the Background Resources Survey in Shennongjia National Park/ ; SNJGKL2022008//the Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; }, abstract = {BACKGROUND: Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.<br><br>RESULTS: Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.<br><br>CONCLUSIONS: Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.}, }
@article {pmid41993122, year = {2026}, author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M}, title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {297-309}, pmid = {41993122}, issn = {2405-6383}, abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.}, }
@article {pmid41993390, year = {2026}, author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J}, title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993390}, issn = {2692-8205}, abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.}, }
@article {pmid41993414, year = {2026}, author = {Liu, S and Mehta, P}, title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993414}, issn = {2692-8205}, abstract = {A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.}, }
@article {pmid41993507, year = {2026}, author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T}, title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993507}, issn = {2692-8205}, abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline Evaluator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.}, }
@article {pmid41993555, year = {2026}, author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC}, title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1[R206H]-driven heterotopic ossification.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993555}, issn = {2692-8205}, abstract = {Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.}, }
@article {pmid41993727, year = {2026}, author = {Sun, Y and Qiu, JW and Chen, C and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {127}, pmid = {41993727}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.}, }
@article {pmid41993799, year = {2026}, author = {Yue, XL and Wu, YH and Zheng, DQ and Sun, C and Xu, L and Cui, L and Xu, XW}, title = {[13]C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag073}, pmid = {41993799}, issn = {2730-6151}, abstract = {Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with [13]C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. [13]C-induced shifts in cytochrome c (749, 1129, 1312, 1589 cm[-1]) and phenylalanine (1002 cm[-1]) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, Guyparkeria sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based in situ functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling in situ mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.}, }
@article {pmid41993915, year = {2026}, author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ}, title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {53}, number = {}, pages = {101218}, pmid = {41993915}, issn = {2666-3546}, abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.<br><br>METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n&#xa0;=&#xa0;18), healthy controls (n&#xa0;=&#xa0;21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n&#xa0;=&#xa0;8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.<br><br>RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.<br><br>CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.}, }
@article {pmid41993958, year = {2026}, author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y}, title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {4}, pages = {e71681}, pmid = {41993958}, issn = {2048-7177}, abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.}, }
@article {pmid41994130, year = {2026}, author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL}, title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41994130}, issn = {2693-5015}, support = {R01 AI170111/AI/NIAID NIH HHS/United States ; }, abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae, 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.}, }
@article {pmid41994193, year = {2026}, author = {Jiang, T and Yan, F and Liu, B and Li, Q and Wang, K and Ru, X and Hao, Y and Guan, Y and Wang, Y}, title = {Intraventricular hemorrhage, suspected EBV reactivation, and TBA-positive epilepsy after deep cervical lymphovenous anastomosis in Alzheimer's disease: a case report.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1791011}, pmid = {41994193}, issn = {1663-4365}, abstract = {Lymphovenous anastomosis (LVA) is emerging as a potential surgical intervention to ameliorate cervical lymphatic outflow and enhance glymphatic clearance in Alzheimer's disease (AD). However, the spectrum of neurological sequelae associated with this procedure remains poorly characterized. We report the case of a 67-years-old male with amyloid PET-confirmed AD who underwent bilateral deep cervical LVA. Twenty-three days postoperatively, he presented with high-grade fever and altered consciousness. Head CT revealed acute hemorrhage in the posterior horn of the left lateral ventricle (∼2 mL). Cerebrospinal fluid (CSF) analysis demonstrated lymphocytic pleocytosis and significantly elevated protein levels; the fluid was uniformly bloody, confirming intraventricular hemorrhage. Plasma metagenomic next-generation sequencing (mNGS) identified Epstein-Barr virus (EBV), with serology supporting reactivation. Following antiviral and empirical antibiotic therapy, the patient's condition stabilized, and the hemorrhage resolved. Four months postoperatively, he developed new-onset generalized seizures. Despite negative results from a conventional autoimmune encephalitis antibody panel in both serum and CSF, a tissue-based assay (TBA) proved positive in both samples. Seizures were successfully controlled with levetiracetam. This case suggests a potential association between invasive lymphatic procedures and a hemorrhage-infection-immune cascade in highly vulnerable AD patients with preexisting metabolic and neurodegenerative risk factors.}, }
@article {pmid41994268, year = {2026}, author = {Zhang, F and Chen, J and Yuan, Y and Chen, J and Jiang, W and Xiang, W and Wang, N and Wu, Z and Fan, S and Zhang, K and Ma, Y and Liu, T and Zhang, J and Yu, Q and Zhang, J}, title = {The enhancing therapeutic effect of neonatal jaundice by bifidobacterium through regulating inflammation and gut microbiota in combination with phototherapy-a randomized controlled trial.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761245}, pmid = {41994268}, issn = {1664-302X}, abstract = {BACKGROUND: Hyperbilirubinemia is among the most common conditions in neonates, and phototherapy is currently the most widely used treatment. However, it can induce side effects such as skin rashes, diarrhea, and gut microbiota dysbiosis, particularly affecting Bifidobacterium levels. This study aimed to investigate whether the supplementation of Bifidobacterium can alleviate dysbiosis and improve clinical outcomes in jaundiced neonates.<br><br>METHODS: A total of 79 jaundiced neonates were enrolled and divided into four groups: Phototherapy Control, M-16V, Bb-12, and the combined M-16V+Bb-12 group. Probiotics were administered until 30 days post-discharge, and neurodevelopment was assessed at 1.5-2 years using the Griffith Development Scales. Fecal samples collected before, during, and after treatment were analyzed using metagenomic sequencing and non-targeted metabolomics.<br><br>RESULTS: Probiotic supplementation significantly increased daily defecation frequency, accelerated the reduction rate of transcutaneous bilirubin, and shortened hospital stays. Griffith scores indicated that Bb-12 supplementation improved scores in personal-social and performance domains. Metagenomic analysis revealed significant differences in beta diversity between the control and probiotic groups; specifically, M-16V and combined supplementation increased the abundance of Bifidobacterium breve. Pathway enrichment analysis showed up-regulation of pyrimidine-containing compound metabolic processes, intramolecular transferase activity, and DNA conformation change. Metabolomics further demonstrated that combined supplementation elevated levels of 5-methyltetrahydrofolate (linked to DNA synthesis), benzoic acid and indoleacetic acid (linked to growth and development), and the anti-inflammatory metabolite indole-3-lactic acid.<br><br>DISCUSSION: For neonates receiving phototherapy, the addition of M-16 V + Bb-12 probiotics can improve the diversity of microflora, reduce the fixed value of harmful bacteria in the intestine, and enhance the excretion of bilirubin from the intestine, to improve the inflammatory damage and microbiota disorder caused by phototherapy, and achieve the effect of clinically improving jaundice, reducing bilirubin, shortening the length of hospitalization, and promoting neurodevelopment. It provides a safer and more effective treatment for neonatal jaundice.}, }
@article {pmid41994275, year = {2026}, author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X}, title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753643}, pmid = {41994275}, issn = {1664-302X}, abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.<br><br>METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.<br><br>RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.<br><br>CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.}, }
@article {pmid41994276, year = {2026}, author = {Xian, J and Li, Y and Feng, Z and Jin, Y and Cai, T and Cao, M and Cao, Y}, title = {High-fat diet-driven gut microbial sphingolipid metabolic reprogramming is associated with stress susceptibility in CUMS rats.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1802003}, pmid = {41994276}, issn = {1664-302X}, abstract = {The escalating comorbidity between depression and metabolic syndromes induced by a high-fat diet (HFD) poses a substantial social and economic burden on society. However, the precise molecular mechanisms by which a HFD qualitatively alters the basal pathophysiology of chronic unpredictable mild stress (CUMS) remain unclear. In this study, the differential roles of microbial and metabolic pathways in the onset and exacerbation of depression were investigated using CUMS rat models fed a normal diet (ND-CUMS) or HFD (HFD-CUMS). Our findings indicated that HFD intervention showed a trend toward aggravating depressive behaviors and resulted in significantly more severe neuronal injury in the hippocampus relative to the ND-CUMS group. Notably, integrated multi-omics (metagenome and metabolome) analysis revealed a crucial pathway divergence: basal CUMS depression was strongly associated with the dysregulation of glycerophospholipid metabolism, linked to microbiota such as Bacteroides thetaiotaomicron and Terrisporobacter glycolicus, while HFD triggered a predominant disruption of the sphingolipid metabolism pathway. Exploratory mediation analysis suggested that a sphingolipid-related signature that may statistically connect HFD-associated microbial shifts with neural injury and behavioral readouts. Therefore, our findings reveal a distinct mechanistic shift underpinning metabolic-comorbid depression. HFD does not merely exacerbate stress-induced depression but fundamentally transitions the underlying pathology from glycerophospholipid to sphingolipid signaling, highlighting the potential of targeting specific lipid metabolic reprogramming as a promising therapeutic strategy for combating metabolic-comorbid depression.}, }
@article {pmid41994278, year = {2026}, author = {Dang, M and Tang, Y and Chen, J and Xie, W and Zhong, Y and Yu, B and Zhang, E and Wang, Z}, title = {Rhizospheric soil microbial community structure and metabolic characteristics of wild Cymbidium mastersii at different altitudes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1720137}, pmid = {41994278}, issn = {1664-302X}, abstract = {INTRODUCTION: Cymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates (<15%), habitat degradation, and illegal harvesting. It is listed as a Category II Nationally Protected Plant Species in China.<br><br>METHODS: We examined the rhizosphere microbial communities and metabolomes of C. mastersii across elevation gradients. We investigated the rhizospheric soil microbial community composition and metabolic characteristics of C. mastersii across different elevations.<br><br>RESULTS: The dominant bacterial phylum was Pseudomonadota, with relative abundances of 38.22% (CmL, low elevation), 36.91% (CmM, mid-elevation), and 62.54% (CmH, high elevation). While the dominant bacterial genera varied significantly with elevation, taxonomic richness exhibited a consistent decline with increasing altitude (p&#x202f;<&#x202f;0.05, linear regression), indicating altitudinal filtering of microbial diversity. LC-MS/MS metabolomic profiling identified 1,516 metabolites, predominantly enriched in lipid and lipid-like molecules, carbohydrates and derivatives, and aromatic compounds. Functional contribution analysis revealed Bradyrhizobium as the most influential taxon (10% variance explained), displaying a nonlinear elevational response. Correlation analysis of differential metabolites confirmed significant species-metabolite correlations (P < 0.05, R > 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.<br><br>DISCUSSION: This study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.}, }
@article {pmid41994292, year = {2026}, author = {Sun, M and Lei, Z and Li, B and Gao, SH and Fan, L}, title = {Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1785655}, pmid = {41994292}, issn = {1664-302X}, abstract = {Hypoxic zones in estuaries threaten the ecological balance and the productivity in coastal areas. However, it is poorly understood how viruses regulate metabolic processes of their microbial hosts to adapt to the hypoxic environment, and consequently impact the biogeochemical cycles in hypoxic zones. In this study, the diversity and functional potentials of the bacterial, archaeal and viral communities of a hypoxic zone at the Pearl River Estuary was characterized along with local environmental factors, with a particular focus on viral auxiliary metabolic genes (AMGs). The viral community derived from the virion fraction and the cellular fraction of the seawater were distinctly different, with the cellular fraction generating fewer unique viruses, but more types of AMGs. Overall, more AMGs were identified in samples with higher dissolved oxygen levels. Globally conserved AMGs were infrequently observed in the current samples, suggesting a certain level of adaptation of AMGs to the local environment. There were strong correlations in abundances among cyanobacteria, cyanophages, and photosynthesis AMGs, suggesting potential viral participation in estuarine primary production. Many AMGs involved in nutrient limitation endurance were found, potentially assisting their host with phosphorus, iron and B family vitamin shortages. Although putative hosts were predicted for the viruses, the functionality of their AMGs appears to be a better predictor of their distribution than the hosts they infect. Our study provides a functional insight into the viral community in poorly researched estuarine hypoxic zones, and sheds light on the potential interactions of viruses with their microbial hosts for co-adaptation to this unique environment.}, }
@article {pmid41994309, year = {2026}, author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R}, title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.}, journal = {Gastro hep advances}, volume = {5}, number = {5}, pages = {100907}, pmid = {41994309}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.<br><br>METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.<br><br>RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.<br><br>CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.}, }
@article {pmid41994369, year = {2026}, author = {Bao, Q and Zhang, X and Guo, J}, title = {Enterovirus D68 and mycobacterial coinfection: case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261432918}, pmid = {41994369}, issn = {2049-9361}, abstract = {The threat of viral epidemics to long-standing diseases, such as mycobacterial infection, is constantly evolving. Enterovirus D68 (EV-D68) is an emerging cause of respiratory infection and has raised great interest since its first outbreak in 2014. Very few studies have been done to describe the clinical aspects of the coinfection of EV-D68 and mycobacteria, so this study was conducted to help round out the understanding of this coinfection pattern. We observed three adult cases of EV-D68 and mycobacteria, who were admitted to the first affiliated hospital of Zhejiang University in August/September 2024. Only one case had a definite past history of immunodeficient disease and received long-term corticosteroid treatment, and the other two were previously healthy. The diagnoses of EV-D68 and mycobacterial infection were all simultaneously confirmed through the metagenomic Next-Generation Sequencing in bronchoalveolar lavage fluid specimens. All three patients were presented with severe respiratory symptoms, such as fever, cough, dyspnea and tachypnea, without any manifestations of central nervous system involvement. The radiological findings in chest CT scans varied from patchy opacity to massive consolidation. The individualized anti-mycobacterium treatment showed little therapeutic effect, while the improvement of symptoms and pulmonary lesions in chest CT was observed after starting or intensifying the administration of corticosteroid. All patients had a marked clinical improvement when discharged from hospital, and it took about 6-9 months for the lung lesions of mycobacterial infections to nearly resolve. These cases illustrate the potential for EV-D68 coinfection to exacerbate pulmonary inflammation in patients with mycobacterial disease, highlighting the need for vigilance regarding possible viral coinfections in settings with a high tuberculosis burden, such as China.}, }
@article {pmid41994453, year = {2026}, author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C}, title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1780981}, pmid = {41994453}, issn = {2296-858X}, abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n&#x202f;=&#x202f;28) and myopia patients who underwent intraocular lens (ICL) implantation (n&#x202f;=&#x202f;31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.<br><br>RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p&#x202f;=&#x202f;0.066; Simpson index, p&#x202f;=&#x202f;0.065) and distinct community structures (PERMANOVA, p&#x202f;=&#x202f;0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.<br><br>CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.}, }
@article {pmid41994458, year = {2026}, author = {Jiang, L and Ye, T and Cai, H and He, F}, title = {Case Report: A rare case of Pneumocystis jirovecii infection with left hydropneumothorax following immunotherapy for stage IVB clear cell renal cell carcinoma.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1784855}, pmid = {41994458}, issn = {2296-858X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that predominantly affects immunocompromised individuals, most commonly HIV-infected patients with significantly reduced CD4+lymphocyte counts, and is associated with high clinical mortality. Currently, there are few reports of pneumothorax secondary to PJP, and most cases occur in HIV-infected populations. However, PJP complicated by hydropneumothorax in cancer patients receiving immunotherapy is exceedingly rare, with limited reports in the literature. To our knowledge, this article reports a rare clinical case of Pneumocystis jirovecii infection complicated by left-sided hydropneumothorax in a patient with stage IVB clear cell renal cell carcinoma after immunotherapy, aiming to provide valuable insights for the early diagnosis and management of PJP and its complications in cancer patients undergoing immunotherapy.<br><br>CASE: A 57-year-old male patient had previously undergone surgical treatment for left renal clear cell carcinoma, and developed recurrent metastases to the descending colon, liver, and upper pole of the left kidney after surgery, with a clinical stage of T4NxM1 stage IVB. After receiving targeted combination immunotherapy with sequential PD-1 inhibitors (toripalimab) plus anti-angiogenic agents (sunitinib, axitinib)-a regimen that enhances anti-tumor immunity but may disrupt pulmonary immune homeostasis-the patient gradually developed progressive dyspnea, chest tightness, hypoxemia, and anuria. Multiple auxiliary examinations were performed clinically, including chest X-ray, bronchoalveolar lavage, and metagenomic sequencing of pathogenic microorganisms. Based on the above examination results, the final diagnosis was Pneumocystis jirovecii pneumonia complicated by left-sided hydropneumothorax.<br><br>CONCLUSION: Although PJP complicated by hydropneumothorax after immunotherapy is rare, it should be considered as a possible etiology when cancer patients develop progressive dyspnea with difficulty maintaining oxygen saturation after receiving immune checkpoint inhibitor-based therapy, particularly in the context of immune checkpoint inhibitor use. While biomarkers for predicting immunotherapy efficacy and irAEs are well-studied, the identification of specific biomarkers for predicting opportunistic infections like PJP in this context remains an area of active research.}, }
@article {pmid41994961, year = {2026}, author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J}, title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.}, journal = {Biotechnology journal}, volume = {21}, number = {4}, pages = {e70228}, pmid = {41994961}, issn = {1860-7314}, support = {82203056//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Thalidomide/therapeutic use/pharmacology ; *Small Cell Lung Carcinoma/drug therapy/microbiology/metabolism ; *Lung Neoplasms/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Multiomics ; *Nausea/chemically induced/drug therapy/microbiology ; *Vomiting/chemically induced/drug therapy/microbiology ; Male ; Female ; Middle Aged ; Aged ; Metabolome/drug effects ; Metabolomics ; Antineoplastic Agents/adverse effects/therapeutic use ; }, abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.}, }
@article {pmid41995327, year = {2026}, author = {Chen, Y and Tang, X and Lu, S and Guo, L and Wang, L and Min, L and Niu, T and Zhou, Y}, title = {The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0338425}, pmid = {41995327}, issn = {2165-0497}, support = {2022YFC2406804//National Key Research and Development Program of China/ ; 82370192, U24A20680//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 82402588//National Natural Science Foundation of China/ ; 2024NSFSC1746//Natural Science Foundation of Sichuan Province/ ; 2025M772028//China Postdoctoral Science Foundation/ ; GZB20230475//the Postdoctoral Fellowship Program of China Postdoctoral Science Foundation/ ; 2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; }, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/blood/mortality ; Prognosis ; Retrospective Studies ; Female ; Biomarkers/blood ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Middle Aged ; Galactose/analogs &amp; derivatives ; beta-Glucans/blood ; Mannans/blood ; Aged ; *Aspergillus/genetics/isolation &amp; purification ; ROC Curve ; Coinfection/microbiology/diagnosis ; Proteoglycans ; }, abstract = {UNLABELLED: Differentiating invasive pulmonary aspergillosis (IPA) from colonization in patients with Aspergillus-positive blood metagenomic next-generation sequencing (mNGS) remains a clinical challenge. This study aims to evaluate the diagnostic and prognostic value of blood mNGS-derived fungal load (reads per million [RPM]) and two key serological biomarkers (galactomannan [GM] and 1,3-β-D-glucan [BDG]) in distinguishing these two entities. This retrospective study enrolled 95 patients with Aspergillus detected by blood mNGS, stratified into infection (n = 60) and colonization (n = 35) groups using modified EORTC/MSGERC criteria. We analyzed clinical characteristics, co-infection spectra, and serological biomarkers (GM and BDG). Diagnostic performance was evaluated via receiver operating characteristic (ROC) analysis, and prognostic factors for 28-day mortality were identified using least absolute shrinkage and selection operator-Cox regression. Distinct co-infection patterns were observed between groups: the infection group was dominated by polymicrobial co-infections, including clinically significant pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Mucor spp., and Human cytomegalovirus; in contrast, the colonization group primarily featured single viral co-infections. While mNGS effectively detected Aspergillus, RPM alone showed limited ability to discriminate infection from colonization, with area under the curves (AUCs) ranging from 0.406 to 0.657 across patient groups. The optimal RPM cutoff varied substantially by immune status, being highest in immunocompetent patients (RPM cutoff: 1.77). Diagnostic performance significantly improved when RPM was integrated with GM (AUC up to 0.900 at a cutoff of 0.36 optical density index) or BDG (AUC up to 0.881 pg/mL), particularly in immunocompetent individuals. RPM also correlated with albumin, hemoglobin, platelet counts, and lymphocyte counts (all P < 0.05). Multivariate analysis identified reversed halo sign (hazard ratio [HR] = 2.143), decreased ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2/FiO2; HR = 1.361), and elevated lactate dehydrogenase (HR = 1.055) as independent predictors of 28-day mortality. Blood mNGS demonstrates high sensitivity for detecting Aspergillus but requires integration with serological biomarkers to differentiate IPA from colonization. The RPM can offer prognostic utility. A multimodal strategy is crucial for early diagnosis and improving outcomes in high-risk patients.<br><br>IMPORTANCE: First large-scale validation of blood mNGS for invasive pulmonary aspergillosis diagnosis-this study represents the first sizable cohort systematically evaluating blood metagenomic next-generation sequencing (mNGS) for distinguishing invasive pulmonary aspergillosis from colonization, addressing a critical gap in non-invasive diagnostic approaches for critically ill patients. Comprehensive Aspergillus co-infection profiling-we identified distinct co-infection patterns, with the infection group showing significantly higher rates of polymicrobial infections, providing crucial insights into co-infection dynamics in Aspergillosis. Optimized diagnostic integration strategy-our findings demonstrate that while mNGS-derived reads per million alone show limited diagnostic value, their integration with serological biomarkers significantly improves performance, establishing a clinically relevant multimodal diagnostic framework. Robust prognostic stratification model-through least absolute shrinkage and selection operator-Cox regression, we established a validated prognostic model identifying reversed halo sign, decreased PaO2/FiO2, and elevated lactate dehydrogenase as independent predictors of 28-day mortality, providing clinically actionable tools for risk stratification.}, }
@article {pmid41995478, year = {2026}, author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS}, title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.70677}, pmid = {41995478}, issn = {1365-2036}, abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.<br><br>AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.<br><br>METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.<br><br>RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.<br><br>CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.}, }
@article {pmid41995796, year = {2026}, author = {Vial, M and Costil, K and Agogué, J and Eustache, S and Heighton, S and Gissat, L and Gueuné, H and Caplat, C}, title = {Spatial and temporal variability of biofouling communities during early development in three French harbors of the English Channel.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {5}, pages = {}, pmid = {41995796}, issn = {1573-2959}, mesh = {*Biofouling/statistics &amp; numerical data ; France ; Biofilms/growth &amp; development ; *Environmental Monitoring ; Seawater/microbiology/chemistry ; Aquatic Organisms ; }, abstract = {Biofouling, the colonization of submerged surfaces by marine organisms, causes major economic losses in maritime activities. Although non-biocidal surface coatings are promoted as environmentally friendly antifouling solutions, the respective roles of surface properties and environmental conditions in shaping biofouling stages remain unclear. We hypothesized that coating surface properties primarily control early biofilm formation, whereas local environmental conditions govern subsequent macrofouling development. To test this hypothesis, we studied biofouling on two non-biocidal coatings - an anticorrosion epoxy and a fluoropolymer foul-release coating (FRC) - immersed under static conditions in three French harbors along the English Channel during the spring bloom. Early biofilm formation was assessed after 2 weeks in April, May, and June 2023 using chlorophyll a and the carbohydrate/protein ratio of extracellular polymeric substances (EPS). Macrofouling development over 3 months was evaluated through biomass, surface coverage rate, taxonomic composition, and microorganism abundances. Metagenomic analyses complemented the visual observations in Cherbourg during April and May 2023. The FRC showed a higher EPS carbohydrate/protein ratio, indicating greater resistance to initial microbial colonization, but exhibited significantly lower macrofouling intensity than the epoxy. This decoupling supports the hypothesis that surface properties and settlement processes operate at different spatial and temporal scales. Spatial variability in biofouling patterns may largely be associated with differences in nutrient availability and anthropogenic pressure. These findings demonstrate that early biofilm metrics alone cannot predict long-term fouling and highlight that antifouling performance depends on both material properties and environmental context. Integrating surface physicochemistry with site-specific ecological drivers can improve both coating design and antifouling evaluation strategies.}, }
@article {pmid41996042, year = {2026}, author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS}, title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41996042}, issn = {1618-1905}, abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.}, }
@article {pmid41996045, year = {2026}, author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P}, title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41996045}, issn = {1573-4978}, support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; }, abstract = {BACKGROUND: The symbiotic relationship between gut microbiota and their fish hosts has fuelled extensive research into microbial distribution besides their active role in host body metabolisms and paving the way for the sustainable aquaculture. This study aims to optimize and evaluate DNA extraction techniques for characterizing the gut microbiota of fish with diverse feeding habits: Hilsa (planktivorous), Catla (zooplankton feeder), Rohu (herbivorous), and Mrigal (illiophagus). METHODS AND RESULTS: Microbial genomic DNA was extracted using five traditional methods—PLICKS A, B, C, and CTAB (Methods D and E)—and three commercial kits (MN® Microbial, MN® Soil, and MN® Faecal), each with modifications. The efficacy of these methods was assessed based on DNA yield (traditional: 74–3070 ng/µL; commercial: 8.8–224 ng/µL), purity (traditional: A260/280: 1.38–1.92, A260/230: 1.03–2.21; commercial: A260/280: 1.30–3.25, A260/230: 0.5–2.0), and successful PCR amplification, a key step for downstream 16 S rRNA gene sequencing. Among traditional methods, PLICKS A (Catla), PLICKS C (Hilsa), CTAB (Mrigal and Catla), and PLICKS B (Catla, Rohu, Hilsa, Mrigal) delivered the highest DNA recovery (342–2080 ng/µL) and purity across different species. Similarly, among commercial kits, the MN® Microbial Modified Kit (Catla, Hilsa), MN® Soil Kit (Hilsa), MN® Soil Modified Kit (Catla, Rohu), MN® Faecal Kit (Catla), and MN® Modified Faecal Kit excelled, achieving optimal DNA recovery (108–224 ng/µL) and purity across various feeding habits. Overall, among traditional methods, PLICKS B proved to be the most effective, delivering high DNA yields (342–2080 ng/µL) with excellent purity (A260/280: 1.77–1.92; A260/230: 1.67–2.21) and enabling successful PCR amplification across fish species with diverse feeding habits. Similarly, among commercial kits, the MN Modified Faecal Kit achieved the highest DNA recovery (108–224 ng/µL) and purity (A260/280: 1.74–1.90; A260/230: 1.78–2.01), consistently supporting reliable amplification. CONCLUSIONS: These findings highlight effective DNA extraction methods tailored to fish with different feeding habits. Careful selection and optimization of extraction protocols are therefore essential for the accurate characterization of fish gut microbiota.}, }
@article {pmid41996243, year = {2026}, author = {Lin, D and Ma, QX and Ye, YQ and Wanek, W and Gregory, AS and Jones, DL and Graham, DW and Zhu, D and Penuelas, J and Zhu, YG}, title = {Nutrient balance regulates soil microbial health under long-term fertilization.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117274}, pmid = {41996243}, issn = {2211-1247}, abstract = {Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.}, }
@article {pmid41996362, year = {2026}, author = {Buni, D and Kovács, &#xc1;B and Wehmann, E and Grózner, D and Bányai, K and Nagy, EZ and Bradbury, J and Bottinelli, M and Stefani, E and Catania, S and Lysnyansky, I and Kovács, L and Gyuranecz, M and Kreizinger, Z}, title = {Identification and detection of genetic markers associated with antimicrobial susceptibility and evaluation of efflux pump mechanisms in Mycoplasma iowae.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347345}, pmid = {41996362}, issn = {1932-6203}, mesh = {Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Genetic Markers ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; *Membrane Transport Proteins/genetics/metabolism ; }, abstract = {Mycoplasma iowae is an economically significant pathogen that causes reduced hatchability, late embryo mortality and leg deformities, chondrodystrophy and skeletal lesions in poults. While prevention is essential in the control of infection, the appropriate administration of antibiotics may reduce economic losses during outbreaks. As a first step in the exploration of antimicrobial resistance mechanisms in M. iowae, target modification and efflux pump activity were examined in the present study. Point mutations were analyzed in previously described antibiotic binding sites in the whole genome sequences of 99 M. iowae strains. Mismatch amplification mutation assays (MAMAs) were designed and validated for the differentiation of mutations corresponding to elevated minimum inhibitory concentration (MIC) values for fluoroquinolones. Broth microdilution assays were performed to evaluate the effect of efflux pump inhibitors. In the presence of orthovanadate (OV), MIC values were significantly lower than in the absence of OV for spiramycin, tilmicosin, tylosin and oxytetracycline, which may indicate the presence of an active efflux system in M. iowae. Putative promoter regions of efflux-related genes were predicted and characterized. Genetic mutations, previously described in other bacteria, were described to be associated with elevated fluoroquinolone, macrolide and lincomycin MICs in M. iowae, although certain resistant phenotypes remained unexplained, promoting future examinations for deeper insights. The developed MAMAs may support rapid identification of M. iowae strains with elevated MIC values for fluoroquinolones. The better understanding of the efflux pump mechanisms enables the development of alternative methods for the support of therapy against this pathogen.}, }
@article {pmid41996550, year = {2026}, author = {Bechtner, J and Hosek, J and Schwab, C}, title = {Fecal Material of Captive Wild Animals as Source of CAZymes With Application Potential.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {27}, number = {8}, pages = {e70315}, pmid = {41996550}, issn = {1439-7633}, support = {grant NNF22OC0079746//Novo Nordisk Fonden/ ; grant AU FF-F-2020-7//Aarhus Universitets Forskningsfond/ ; }, mesh = {Animals ; *Feces/microbiology ; *Animals, Wild/microbiology ; Polysaccharides/metabolism ; Metagenome ; *Glycoside Hydrolases/metabolism ; }, abstract = {Gastrointestinal systems of mammals and birds host taxonomically complex and functionally diverse microbial communities. Microbial activities contribute to community functioning and interaction with the host but can also be exploited as a source of novel enzymes or other industrially relevant microbial traits. With the overall goal to identify new resources for carbohydrate-active enzymes (CAZymes), we bioprospected fecal microbial communities of the little-explored source of captive wild animals. Using dbcan3, we identified a CAZyome dominated by glycosyl hydrolases (GHs) specialized in degrading oligo- and polysaccharides with much lower diversity and abundance of glycosyl transferases, carboxyl esterases, polysaccharide lyases, and redox enzymes with auxiliary activity. CAZyome profiles differed between animals depending on gut physiology and diet. Crude cell extracts conferred hydrolytic activity against compositionally and structurally diverse polysaccharides and nitrophenyl-sugar analogs. We identified five candidate GH68 and GH70 enzymes with the potential to produce oligo- and polysaccharides from sucrose, highlighting that fecal metagenomes are a source of rare CAZymes with industrial relevance. Taken together, we exemplify the functional potential captive wild animal fecal microbiota and suggest such a gene pool as a largely untapped resource for the discovery of novel biotechnological applications.}, }
@article {pmid41996772, year = {2026}, author = {Haydar, MS and Alzate Zuluaga, MY and Astolfi, S and Del Buono, D and Cesco, S and Pii, Y}, title = {Nanoparticle-rhizosphere crosstalk: Insights into transformation, microbial interaction, plant uptake and translocation.}, journal = {Chemosphere}, volume = {403}, number = {}, pages = {144936}, doi = {10.1016/j.chemosphere.2026.144936}, pmid = {41996772}, issn = {1879-1298}, mesh = {*Rhizosphere ; *Nanoparticles/metabolism/chemistry ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Plant Roots/metabolism/microbiology ; *Plants/metabolism ; Biological Transport ; Soil/chemistry ; }, abstract = {For soil-applied engineered nanomaterials, the rhizosphere is the critical frontline zone where they encounter crop roots, microbes, and soil, determining their agronomic potential and environmental risks. Within this dynamic interface, nanoparticles (NPs), depending on their surface chemistry, particle size, properties, and composition, undergo physicochemical and biological transformations that govern their stability, dissolution, mobility, availability, and ecotoxicological outcomes. This review synthesizes current mechanistic evidence linking root exudation patterns, microbial activity, and soil physico-chemical conditions to NPs aggregation, dissolution, redox conversions, and eco-/bio-corona formation. Microbial extracellular polymeric substances, low-molecular-weight metabolites, siderophores, and biofilms further reshape particle speciation, modulating ion release, immobilization, nutrient availability, and potential toxicity to soil biota and crops. Once inside roots, nanoparticles follow multiple uptake routes, including apoplastic diffusion, endocytosis, plasmodesmata-mediated transport, and vascular translocation, while undergoing in-planta transformations into ionic or ligand-bound forms with distinct physiological and agronomical consequences. These processes are strongly context-dependent, shaped by plant species, development stage, NPs concentration, and soil-climate conditions, and mediated by a tripartite molecular dialogue among NPs, microbes, and plant signalling pathways that regulate root system architecture, rhizosphere microbial recruitment, and nutrient acquisition efficiency. Advances in high-resolution and multi-omics tools-such as synchrotron-based spectroscopy, single-particle ICP-MS, NanoSIMS, stable-isotopic tracers, and metagenomics are offering new insights into these interactions under realistic agricultural scenarios. We propose an integrated agroecological framework linking rhizospheric NPs transformations to plant uptake and responses, emphasizing the need for standardized exposure metrics, realistic concentrations, and long-term field trials for safe and sustainable nanotechnology use in agriculture.}, }
@article {pmid41996801, year = {2026}, author = {Chen, Y and Sun, Y and Yang, Y and Hu, S and Cui, K and Zhu, C and Fu, XZ and Li, CX and Jiang, P and Huang, Q}, title = {Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142080}, doi = {10.1016/j.jhazmat.2026.142080}, pmid = {41996801}, issn = {1873-3336}, mesh = {*Metals, Heavy/analysis/toxicity ; *Geologic Sediments/chemistry/analysis ; Rivers/chemistry ; *Water Pollutants, Chemical/analysis/chemistry ; Lakes/chemistry ; Seasons ; Environmental Monitoring ; }, abstract = {River-lake systems are critical zones for heavy metal biogeochemical cycling, yet the mechanisms linking heavy metal pollution to heavy metal resistance genes (MRGs) across hydrological gradients remain elusive. This study selected the Chaohu Lake Basin as a representative river-lake system to investigate the distribution characteristics of MRGs and their driving mechanisms on heavy metal speciation. Based on metagenomic sequencing and ICP-MS analysis of 78 sediment samples collected in wet and dry seasons, we found that the resistome was dominated by multi-metal, Cu, and As resistance genes, with the arsenic resistance gene pstA identified as a consistent network hub. MRGs diversity and network complexity exhibited significant seasonal depletion and spatial heterogeneity along the river-lake gradient. Heavy metals were predominantly fractionated into the stable residual phase; however, the river-lake gradient significantly influenced the spatial distribution of bioavailable fractions. Crucially, Structural Equation Modeling (SEM) revealed a seasonal shift in the regulatory mechanisms controlling heavy metal speciation. In the wet season, the river-lake system operated under a "biologically mediated" mode, where MRGs directly facilitated the mobilization of the reducible fraction. In the dry season, it shifted to a "physicochemically driven" mode, governed primarily by basic physicochemical factors. These findings highlighted that seasonal dynamics and the river-lake gradient jointly coordinated heavy metal fate through a complex interplay of biotic and abiotic factors, providing molecular-level insights for pollution management in continuous aquatic systems.}, }
@article {pmid41996860, year = {2026}, author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A}, title = {Relationship between pesticide exposure, gut microbiota, and hypertension.}, journal = {Environment international}, volume = {211}, number = {}, pages = {110250}, doi = {10.1016/j.envint.2026.110250}, pmid = {41996860}, issn = {1873-6750}, mesh = {Humans ; *Hypertension/epidemiology ; *Pesticides/blood/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Environmental Exposure/statistics &amp; numerical data ; China/epidemiology ; Adult ; Male ; Female ; }, abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.<br><br>METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.<br><br>RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC&#xa0;=&#xa0;0.897) for hypertension.<br><br>CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.}, }
@article {pmid41997101, year = {2026}, author = {Liu, W and Yang, Y and Bian, J and Li, X and Lu, Z}, title = {Niche adaptation of marine heterotrophic nitrification-aerobic denitrification bacterium in mariculture wastewater treatment: Synergistic mechanism of nitrogen removal and sulfamethoxazole biotransformation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125914}, doi = {10.1016/j.watres.2026.125914}, pmid = {41997101}, issn = {1879-2448}, mesh = {Denitrification ; Nitrification ; *Sulfamethoxazole/metabolism ; *Wastewater ; Nitrogen/metabolism ; Heterotrophic Processes ; Biotransformation ; }, abstract = {Efficient removal of nitrogen from mariculture wastewater (MW) by marine heterotrophic nitrification-aerobic denitrification (MHNAD) bacteria is an innovative approach to overcoming salt inhibition. However, their performance and survival strategies under long-term antibiotics exposure in real wastewater conditions remain elusive, limiting practical implementation. Here, a bench-scale biofloc-biological aerated filter (BF-BAF) system treating real MW was operated for 100 days. Under long-term exposure to sulfamethoxazole (SMX) (1.3 ± 0.4 mg/L), the stabilized nitrogen removal system achieved removal efficiencies of 97.2 ± 2.5 % and 91.6 ± 4.1 % for NH4[+]-N and SMX, respectively. MHNAD bacteria, dominated by Marinobacter and Celeribacter, were enriched (2.3-67.7 %) and identified as habitat-specific genera, while the growth of Nitrosomonas (0.02-0.04 %)-the sole ammonia-oxidizing bacteria (AOB) detected-was severely inhibited. Metagenomic analysis revealed upregulation of nitrogen assimilation (glnA and nasA) and denitrification genes (nirK and norC), driving niche differentiation. A novel MHNAD strain, Marinobacter sp. LAN01, was isolated from the settleable bioflocs. Multi-omics analysis indicated that LAN01 adapts to SMX stress by reallocating intracellular resources via NH4[+]-N assimilation (glnA-driven) and facilitates SMX degradation via N-acetylation, S-N bond cleavage, and hydrolysis. Nucleotide metabolism was downregulated to suppress DNA synthesis, thereby reducing the accumulation and transfer of sulfonamide resistance genes (sul1 and sul2). Overall, this works revealed the mechanism of synergistic nitrogen removal and antibiotic degradation, and highlighted the long-term application potential of BFT, paving the way for sustainable MW treatment.}, }
@article {pmid41997104, year = {2026}, author = {Zhang, X and Weng, S and Zhen, Z and Tang, Z and Huang, X}, title = {Phage predation mitigates the spread of antibiotic resistance in anaerobic digestion under shortened solid retention times.}, journal = {Water research}, volume = {300}, number = {}, pages = {125921}, doi = {10.1016/j.watres.2026.125921}, pmid = {41997104}, issn = {1879-2448}, mesh = {*Drug Resistance, Microbial/genetics ; Anaerobiosis/physiology ; *Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/physiology ; Water Purification/methods ; Sewage/microbiology/virology ; }, abstract = {Optimizing anaerobic digestion (AD) via shortening solid retention time (SRT) enhances methane recovery, yet the mechanistic impact of SRT reduction on antimicrobial resistance (AMR) dissemination remains underexplored. Herein, we employed metagenomics to investigate how reduced SRTs (from 60 to 5 days) regulated the dynamics of antibiotic resistance genes (ARGs) mediated by pathogenic hosts, plasmids, and phages in mesophilic and thermophilic AD systems. Shortened SRTs elevated ARG abundance by 5.9-388% under mesophilic conditions, driven by the SRT-elicited niche expansion of antibiotic-resistant bacteria (ARB) and the persistent dominance of ESKAPE pathogen Enterobacter hormaechei, the latter intrinsically harbored and transmitted high-risk ARGs (aadA, sul1, and qacEdelta1) via multi-resistant plasmids. Notably, plasmid-mediated and cross-phylum transmission substantially enhanced ARG mobility. Contrastingly, thermophilic conditions eliminated ARGs by 17.0-57.1% under shortened SRTs, driven by thermophilic ARB niche differentiation. Crucially, both homology search and phage-host prediction indicated the lack of ARGs matching between phages and hosts under reduced SRTs, denoting a negligible contribution of transduction to horizontal ARG transfer. The dominance of lytic phages (85.3%), intensified lytic phage-host interactions, and heightened abundance of lytic phages lysing ARB collectively imposed potent phage top-down control over ARG hosts, with the lytic phage predation on ARB being validated by laboratory assays. We also identified 9 high-risk digestate ARG biomarkers (ANT(6)-Ia, aadA, ermA, mel, qacEdelta1, sul1, tet44, tetM, tetQ) by integrating criteria of prevalence, gene mobility, clinical relevance, and host pathogenicity to inform monitoring. Overall, this study underlined the significance of phage predation in mitigating ARG propagation under shortened SRTs, informing the development of novel AMR control strategies in AD practices.}, }
@article {pmid41997155, year = {2026}, author = {Yang, W and Lee, YJ and Silva, RMB and DeLiberto, A and Yancey, CE and McCallum, D and Buss, JA and Moncion, R and Ong, JL and Mabuchi, M and Hough, DM and Weigele, PR and Ettwiller, LM}, title = {The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.}, journal = {Molecular cell}, volume = {86}, number = {9}, pages = {1598-1613.e11}, doi = {10.1016/j.molcel.2026.03.027}, pmid = {41997155}, issn = {1097-4164}, mesh = {*5-Methylcytosine/metabolism ; *DNA Methylation ; Cytosine/metabolism ; Substrate Specificity ; Deamination ; High-Throughput Nucleotide Sequencing ; *Viral Proteins/genetics/metabolism ; Sequence Analysis, DNA/methods ; DNA, Single-Stranded/genetics/metabolism ; }, abstract = {Mining phages for new enzymatic activities continues to be important for the development of new tools for biotechnology. In this study, we used MetaGPA-a method linking genotype to phenotype in metagenomic data-to identify deoxycytidine deaminases, a protein family highly associated with cytosine modifications in metaviromes. Unexpectedly, a subset of these deaminases exhibited a preference for 5-methylcytosine (5mC) over cytosine (C) in both mononucleotide and single-stranded DNA substrates. In a methylome-sequencing workflow, deamination of 5mC by these enzymes enabled direct conversion of methylated cytosine while completely eliminating any background deamination of unmodified cytosine. This direct conversion allows for precise identification of methylated sites at single-base resolution with unmatched sensitivity enabling broad applications for the simultaneous sequencing of genome and methylome.}, }
@article {pmid41997245, year = {2026}, author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z}, title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134641}, doi = {10.1016/j.biortech.2026.134641}, pmid = {41997245}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; *Phenols/metabolism/isolation &amp; purification ; *Fresh Water/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/isolation &amp; purification ; *Bacteria/metabolism/genetics ; Oxygen ; }, abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.}, }
@article {pmid41998153, year = {2026}, author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM}, title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41998153}, issn = {1546-1696}, support = {W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; R01 AI173318/AI/NIAID NIH HHS/United States ; R01 AI173318/AI/NIAID NIH HHS/United States ; }, abstract = {Whole-cell bioelectronic sensors are particularly well-suited for environmental and health monitoring as they can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies lack modularity, are limited to a few microbial chassis and depend on specialized instruments for signal detection. We present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play system for whole-cell bioelectronic sensor development. Here a 'sender' bacterium produces electron mediators in response to analytes and a 'receiver' bacterium utilizes the electron mediators to generate electrical signals via extracellular electron transfer. Modularly swapping the sender bacterium and its associated genetic sensing elements achieved bioelectronic sensing of metals, small molecules and peptides in distinct environments, such as urban waterways, milk, saliva and microbial communities. We designed a centimeter-sized bioelectronic device for portable signal readout using a household digital multimeter. The e[-]COSENS system simplifies the whole-cell bioelectronic sensor design and expands the potential of bioelectronic sensor applications.}, }
@article {pmid41998361, year = {2026}, author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, &#xdc; and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP}, title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41998361}, issn = {1432-184X}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and microorganisms play a crucial role in its metabolism. While N2O cycling among soil microorganisms is well studied, there is a major knowledge gap regarding the distribution and diversity of these microorganisms within tree ecosystems. In this study, we aimed to comprehensively assess the potential for nitrogen (N) cycling and the diversity of N2O-reducing microorganisms in shoots (leaves and terminal branches) and wood cores of four tree species — European beech (Fagus sylvatica), European hornbeam (Carpinus betulus), birch (Betula pendula and Betula pubescens) and Norway spruce (Picea abies). We assessed N2O exchange through shoot incubation experiments and measured internal N2O concentrations in stem wood. Inorganic N species were studied as indicators of microbial transformation, and a targeted metagenomic approach was used to determine the relative abundance of N-cycling genes and nosZ clade I and II diversity. Our study revealed that hornbeam shoots showed potential N2O emissions (0.002–0.007 ng N2O g[-1] FW h[-1]), while beech shoots indicated N2O consumption (-0.001 to -0.017 ng N2O g[-1] FW h[-1]). Birch had internal stem wood N2O concentration of + 150.39 ppb, and beech − 9.74 ppb when compared to the ambient concentration. Targeted metagenomic analysis revealed the presence of key nitrification and denitrification genes in both tissue types. In particular, nosZ genes were detected in shoots (0 to 26.48 per 100,000 reads) and in wood cores (0 to 31.95 per 100,000 reads), with clade I dominating over clade II and Rhizobiales prevalent within clade I. Overall, our findings show that internal tree tissues harbour distinct N‑cycling microbial assemblages dominated by nosZ clade I, suggesting that trees may function as localized N2O sinks or sources depending on tissue type and microbial composition.}, }
@article {pmid41998362, year = {2026}, author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R}, title = {Early microbial colonization study of daily-use plastics exposed to river water.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41998362}, issn = {1573-0972}, abstract = {In rivers, microorganisms colonize plastic surfaces, initiating processes that can lead to their microbial decomposition. Our study investigates the bacterial community composition and diversity on the surfaces of plastics used daily, such as polyethylene terephthalate (PET) and low-density polyethylene (LDPE), which were exposed to river water from the Aller and Fusche rivers. Glass was used for comparison purposes. 16s rRNA sequencing revealed that the type of surface and the native microbial community in the river water, including the water quality, significantly influenced biofilm community assembly. River water samples, especially from the Fusche site, supported the highest microbial richness, while plastic exhibited moderate diversity, and glass beads hosted the lowest richness and diversity. Proteobacteria and Bacteroidetes dominated across all samples, with notable enrichment of functionally relevant families such as Rhodobacteraceae and Comamonadaceae. Ecologically relevant genera such as Flavobacterium, Hydrogenophaga, Rhodoferax, Sediminibacterium, and Rhodobacter dominated across samples. Alpha diversity reflected the richness of taxa within each sample, while beta diversity revealed distinct clustering based on both plastic type and site, indicating the influence of ecological pressure and niche partitioning. These findings highlight the capacity of plastic surfaces to harbour diverse and specialised bacterial assemblages, with implications for biogeochemical cycling, pollutant interactions, and potential microbial degradation pathways. This work contributes to deciphering the ecological roles of biofilms in freshwater plastisphere micro-environments and underscores the importance of material-specific microbial dynamics in assessing environmental risks.}, }
@article {pmid41998666, year = {2026}, author = {Yang, F and Du, Y and Ji, J and Zhang, P}, title = {Eosinophilic granulomatous inflammation and multi-organ involvement probable caused by Paragonimus heterotremus infection in a pediatric patient: a rare case report.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41998666}, issn = {1471-2431}, abstract = {BACKGROUND: Paragonimus heterotremus is a parasitic flatworm endemic to Southeast Asia that causes pulmonary and extrapulmonary infections. While more common in adults, pediatric cases are rare and often present atypically, posing diagnostic challenges. Eosinophilic granulomatous inflammation due to parasitic infection is especially difficult to identify in children.<br><br>CASE PRESENTATION: A 9-year-old female child initially exhibited subcutaneous swelling and notable peripheral blood eosinophilia, resulting in two hospital stays without a conclusive diagnosis. Upon admission to our center, laboratory results showed increased white blood cell count, hemoglobin, platelets, and persistent eosinophilia, along with a significantly increased total IgE levels. Imaging revealed granulomatous inflammation in the skin and lungs with mild pleural effusion. Despite negative parasitic serology, a newly developed umbilical mass during hospitalization was surgically excised. Anatomopathological examination and metagenomic next-generation sequencing (mNGS) supported a probable diagnosis of P. heterotremus infection.<br><br>CONCLUSIONS: This case highlights the diagnostic challenges of pediatric eosinophilic granulomatous inflammation due to rare parasitic infections, particularly in non-endemic areas. It highlights the need for heightened clinical awareness, thorough evaluation, and advanced diagnostic tools for timely and accurate identification of uncommon parasitic diseases in children.}, }
@article {pmid41998767, year = {2026}, author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD}, title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.}, journal = {Tropical medicine and health}, volume = {54}, number = {1}, pages = {}, pmid = {41998767}, issn = {1348-8945}, support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.}, }
@article {pmid41998770, year = {2026}, author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH}, title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {41998770}, issn = {1756-994X}, support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition. METHODS: We performed a longitudinal nested case–control study involving 128 well-characterized mother–offspring dyads from defined cases (offspring with atopic dermatitis (AD); n = 64) and controls (offspring without AD; n = 64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6 months of age for gut microbiome and metabolome analyses. RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation. CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome–immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring. TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).}, }
@article {pmid41998806, year = {2026}, author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z}, title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.}, journal = {Journal of medical primatology}, volume = {55}, number = {3}, pages = {e70074}, doi = {10.1111/jmp.70074}, pmid = {41998806}, issn = {1600-0684}, support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Diarrhea/veterinary/microbiology/immunology/drug therapy ; *Macaca mulatta/immunology/microbiology ; Longitudinal Studies ; *Monkey Diseases/immunology/microbiology ; *Gastrointestinal Microbiome ; Multiomics ; Anti-Bacterial Agents/therapeutic use ; Feces/microbiology ; Chronic Disease/veterinary ; Male ; }, abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.}, }
@article {pmid41999333, year = {2026}, author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG}, title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {17}, pages = {12853-12867}, doi = {10.1021/acs.est.6c02641}, pmid = {41999333}, issn = {1520-5851}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteriophages ; *Herbicide Resistance ; Herbicides ; }, abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.}, }
@article {pmid42000179, year = {2026}, author = {Iakovides, IC and Vasileiadis, S and Christou, A and Karaolia, P and Mina, T and Rocha, J and Duan, Y and Beretsou, VG and Gallois, N and Changey, F and Michael, C and Coelho, LP and Manaia, CM and Merlin, C and Fatta-Kassinos, D}, title = {Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125889}, doi = {10.1016/j.watres.2026.125889}, pmid = {42000179}, issn = {1879-2448}, mesh = {*Microbiota ; *Agricultural Irrigation ; Soil/chemistry ; *Wastewater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Bacteria/genetics ; Water Purification ; }, abstract = {Reclaimed water (RW) offers a sustainable solution for agricultural irrigation and freshwater conservation, but its microbial and chemical composition, shaped by treatment and storage processes, requires careful consideration for environmental and public health impacts. This study compared two RW types (conventional activated sludge with sand filtration and chlorination - CAS + SFC-RW - and membrane bioreactor - MBR-RW) with a tube well (TW) water control. The goal was to assess how storage influences the microbial composition, key antibiotic resistance and mobilome genes, and RW the impact on irrigated lysimeter soils during lettuce cultivation. Total bacteria were profiled using 16S rRNA gene sequencing and ddPCR, while antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were quantified by ddPCR and analysed by metagenomics. Initial RW samples had 1-1.5 orders of magnitude more 16S rRNA copies compared with the control, with significantly different bacterial and ARG/MGE profiles. Actinomycetota dominated CAS + SFC-RW, Bacteroidota the MBR-RW, and Pseudomonadota the TW water. Class 1 integrons and Tn916/Tn1545 were more abundant in CAS + SFC-RW compared with the MBR-RW. Storage reduced these differences toward convergence with the TW water profile, with putative pathogenic taxa, however, being more recalcitrant to change. RW irrigation altered soil bacterial composition, with MBR-RW having a greater impact as declared by the enhanced presence of Bacteroidota in the receiving soils. The RW influence was inversely related with vertical distance of the irrigation point, while the lettuce crop presence showed minimal/no impact. These results highlight the need for careful management of RW treatment and storage to ensure safe, resilient agricultural practices.}, }
@article {pmid42000463, year = {2026}, author = {Devika, NT and Jayaraman, K and Nadimuthu, S and Nathamuni, SP and Sreya, PS and Jangam, AK and Katneni, VK}, title = {Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101834}, doi = {10.1016/j.cbd.2026.101834}, pmid = {42000463}, issn = {1878-0407}, mesh = {Animals ; *Penaeidae/virology/microbiology ; *White spot syndrome virus 1/physiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.}, }
@article {pmid42000510, year = {2026}, author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S}, title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142094}, doi = {10.1016/j.jhazmat.2026.142094}, pmid = {42000510}, issn = {1873-3336}, mesh = {*Composting/methods ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Manure/microbiology ; *Humic Substances/analysis ; Animals ; Microbiota ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.}, }
@article {pmid42000517, year = {2026}, author = {Han, W and Liu, Y and Liang, X and Liu, J and Jiang, Q and Zhang, C and Zhang, Y}, title = {A Trojan Horse in the soil: Tetracycline hijacks plant organellar ribosomes to stunt growth and unbalance the rhizosphere microecology.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {141792}, doi = {10.1016/j.jhazmat.2026.141792}, pmid = {42000517}, issn = {1873-3336}, mesh = {*Tetracycline/toxicity ; *Rhizosphere ; *Ribosomes/drug effects/metabolism ; *Anti-Bacterial Agents/toxicity ; Soil Microbiology ; RNA, Ribosomal/metabolism/drug effects ; *Glycine max/drug effects/growth &amp; development/metabolism ; *Soil Pollutants/toxicity ; Photosynthesis/drug effects ; Soil/chemistry ; Chloroplasts/drug effects ; }, abstract = {Tetracycline, a widely used antibiotic, accumulates in agricultural soils and poses significant risks to crop development and soil health. This study elucidates novel mechanisms of TC phytotoxicity by demonstrating its specific binding to the structurally conserved A-site of ribosomal small subunit RNA (SSU rRNA) in plant mitochondria and chloroplasts-organelles of prokaryotic origin. Through integrated physiological, transcriptomic, and structural analyses, we show that TC disrupts ribosomal function, induces oxidative stress, and impairs photosynthesis and antioxidant defense in soybean, and unbalances the SSU/LSU (ribosomal large subunit RNA) rRNA ratio. We further developed a comprehensive Ecological Risk Index (ERI) framework that integrates soil physicochemical properties, enzyme activities, microbial metabolism, and community structure to evaluate soil microecological shifts under TC stress. Metagenomic analysis uncovered functional adaptations in microbial nitrogen/phosphorus cycling and emphasized the role of multidrug resistance genes-rather than tetracycline-specific resistance-via mobile genetic elements, including those from ssDNA viruses. Our findings provide unprecedented insights into the evolutionary conservation of ribosomal targets of antibiotics and establish a holistic framework for assessing the ecological impact of antibiotic residues in agroecosystems.}, }
@article {pmid42000556, year = {2026}, author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K}, title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.}, journal = {Marine environmental research}, volume = {218}, number = {}, pages = {108055}, doi = {10.1016/j.marenvres.2026.108055}, pmid = {42000556}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Environmental Monitoring/methods ; Norway ; Iceland ; Animals ; *Microbiota ; }, abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.}, }
@article {pmid42000565, year = {2026}, author = {Wan, X and Zhan, J and Chen, Z and Wu, B}, title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.}, journal = {Research in veterinary science}, volume = {206}, number = {}, pages = {106196}, doi = {10.1016/j.rvsc.2026.106196}, pmid = {42000565}, issn = {1532-2661}, mesh = {Animals ; *Chickens ; *Housing, Animal ; *Drug Resistance, Bacterial/genetics ; *Ventilation ; Public Health ; *Drug Resistance, Microbial/genetics ; *Air Microbiology ; Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.}, }
@article {pmid42000726, year = {2026}, author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T}, title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42000726}, issn = {2041-1723}, mesh = {Humans ; *Bacteriophages/genetics/physiology ; Feces/microbiology/chemistry ; *Fatty Liver/microbiology/metabolism/virology ; *Gastrointestinal Microbiome/genetics/physiology ; Ruminococcus/virology/metabolism/genetics ; Metagenomics ; Faecalibacterium prausnitzii/metabolism/genetics/virology ; Bile Acids and Salts/metabolism ; Dysbiosis/microbiology ; *Bacteria/metabolism/genetics ; Metabolomics ; Female ; Male ; Case-Control Studies ; Eubacteriales ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.}, }
@article {pmid42001033, year = {2026}, author = {Galgano, S}, title = {Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {42001033}, issn = {1471-2105}, mesh = {*Software ; Linear Models ; *Metagenomics/methods ; Genomics/methods ; }, abstract = {BACKGROUND: The analysis of ortholog genes derived from metagenomic experiments provides an invaluable opportunity to assess the functional role of microbial communities towards, for example, antimicrobial resistance or biochemical pathways under different experimental conditions. Nevertheless, the integration of the statistical analysis of these complex data sets and the enrichment of the derived significantly differential abundant orthologs is not currently facilitated by existing software. Genomica is an R package that, with minimal input from the user, allows to perform a double-step analysis of functional orthologs from the KEGG Orthology. The pipeline is carried out via combining false discovery rate corrected linear mixed models to functional enrichment analysis through integrating established R pipelines (i.e., lme4 and MicrobiomeProfiler).<br><br>RESULTS: Only two data frames are needed as input to run Genomica, which contain data and metadata, respectively. The fast pipeline integrated within the function Genomica allows to analyze 4000 orthologs in circa 3 min. The outputs are collected in a single directory, containing publication-ready results from the linear mixed model and from the enrichment analysis. The Benjamini &amp; Hochberg correction is applied to the results from the linear mixed model, therefore only P adjusted significant comparisons are further included in the enrichment analysis.<br><br>CONCLUSIONS: Genomica is a simple-to-use R package to analyze complex datasets, integrating a well-founded statistical analysis, accounting for the calculation of the type I error under repeated testing, with the enrichment analysis of the significantly differential abundant orthologs across experimental conditions, all with minimal input from the user.}, }
@article {pmid42001152, year = {2026}, author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J}, title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {42001152}, issn = {2524-6372}, support = {2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologies/ ; }, abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.}, }
@article {pmid42001834, year = {2026}, author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A}, title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158119}, doi = {10.1016/j.phymed.2026.158119}, pmid = {42001834}, issn = {1618-095X}, mesh = {Animals ; *Catechin/analogs &amp; derivatives/pharmacology ; *Diarrhea/drug therapy/microbiology/veterinary ; Swine ; *Energy Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; Lymphocytes/drug effects/metabolism ; Escherichia coli ; Escherichia coli Infections ; }, abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.<br><br>OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.<br><br>METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and type&#x2161;innate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.<br><br>RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-&#x3b1;, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.<br><br>CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.}, }
@article {pmid42002156, year = {2026}, author = {Jeon, J and Nguyen, HT and Yeo, G and Lee, C and Cho, SK and Oh, S}, title = {Integrating metagenomics and explainable artificial intelligence for modeling of food waste treatment using full-scale anaerobic digestion.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134649}, doi = {10.1016/j.biortech.2026.134649}, pmid = {42002156}, issn = {1873-2976}, mesh = {*Artificial Intelligence ; Anaerobiosis ; Food Loss and Waste ; Methane/biosynthesis ; *Metagenomics/methods ; Random Forest ; Data Analytics ; }, abstract = {Anaerobic digestion (AD), a biochemical process that can convert food waste (FW) into methane, offers great promise as a sustainable form of energy production. While several attempts have been made to optimize AD systems using various mathematical models, more precise modeling approaches that fully consider the complexity of the AD process are required, leading to the adoption of artificial intelligence (AI) as a suitable alternative to numerical modeling. In line with this, the present study tested 11 AI-based models on their prediction of the methane yield for a full-scale AD process using FW as a feedstock. The models incorporated operational parameters, environmental conditions, and microbial information to improve their predictive performance. Although a one-dimensional convolutional neural network (1D-CNN) was the most precise, random forest regression (RFR) was selected as the optimal model for further analysis due to its superior interpretability and stability. Explainable AI (XAI) was then used to determine the most important input features contributing to the predictions of the optimal AI model, thus allowing for detailed model interpretation. Methanothrix was identified as a key predictor of methane yield, and metagenomic analysis provided independent genome-level evidence broadly consistent with the XAI results. Overall, this study proposes a novel approach to the interpretation and optimization of AD performance, rather than focusing only on enhancing the predictive performance of a discrete model.}, }
@article {pmid42002296, year = {2026}, author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C}, title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70304}, doi = {10.1111/1462-2920.70304}, pmid = {42002296}, issn = {1462-2920}, support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth &amp; development/chemistry ; *Gastrointestinal Microbiome ; Metabolome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.}, }
@article {pmid42002357, year = {2026}, author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z}, title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.}, journal = {Carbohydrate polymers}, volume = {382}, number = {}, pages = {125292}, doi = {10.1016/j.carbpol.2026.125292}, pmid = {42002357}, issn = {1879-1344}, mesh = {Animals ; *Curcuma/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Fructans/pharmacology/chemistry/therapeutic use/isolation &amp; purification ; Mice ; Dextran Sulfate ; Male ; *Colitis/chemically induced/drug therapy/metabolism ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Metabolic Networks and Pathways/drug effects ; Colon/drug effects/pathology ; Dysbiosis/drug therapy ; Disease Models, Animal ; }, abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.}, }
@article {pmid42002784, year = {2026}, author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C}, title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42002784}, issn = {2049-2618}, support = {2023YFD1301005//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Aflatoxin B1/toxicity ; *Curcumin/pharmacology/administration &amp; dosage ; *Rumen/microbiology/drug effects ; *Liver/drug effects/metabolism ; Sheep ; *Autophagy/drug effects ; *Pyroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Aflatoxin Poisoning ; }, abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.<br><br>RESULTS: In the experimental setup, 800&#xa0;mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500&#xa0;&#x3bc;g/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-&#x3ba;B-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.<br><br>CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.}, }
@article {pmid42002835, year = {2026}, author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E}, title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659397}, pmid = {42002835}, issn = {1949-0984}, mesh = {Humans ; *Adenine/analogs &amp; derivatives/adverse effects/therapeutic use ; *Piperidines/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Male ; Female ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects/metabolism ; Treatment Outcome ; *Pyrimidines/adverse effects/therapeutic use ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Diarrhea/chemically induced ; Aged ; *Pyrazoles/adverse effects/therapeutic use ; Metagenomics ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.}, }
@article {pmid42003340, year = {2026}, author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H}, title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70143}, pmid = {42003340}, issn = {1755-0998}, support = {2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; //The University of Melbourne's Research Computing Services/ ; }, mesh = {*Genome, Plastid ; *Metagenomics/methods ; *Computational Biology/methods ; Software ; *Eukaryota/genetics/classification ; }, abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.}, }
@article {pmid42003642, year = {2026}, author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE}, title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0008526}, pmid = {42003642}, issn = {2576-098X}, abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.}, }
@article {pmid42003644, year = {2026}, author = {Iizuka, R and Moriya, T and Oshima, T and Uemura, S and Yohda, M}, title = {Amplicon sequence collection of putative polyethylene terephthalate hydrolases from two different composts in Japan.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0017326}, pmid = {42003644}, issn = {2576-098X}, support = {22K05310//Japan Society for the Promotion of Science/ ; 25K08915//Japan Society for the Promotion of Science/ ; G-2021-3-047//Institute for Fermentation, Osaka/ ; JPMJCR2231//Japan Science and Technology Agency/ ; //Mitsui Chemicals, inc./ ; }, abstract = {We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.}, }
@article {pmid42003651, year = {2026}, author = {Kocakahya, &#x130; and Şahin, G and Büyükkahraman, E and Arıkan, M}, title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0140525}, pmid = {42003651}, issn = {2576-098X}, support = {1919B012420662//Scientific and Technological Research Council of Turkey/ ; 41481//Scientific Research Coordination Unit of Istanbul University/ ; }, abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.}, }
@article {pmid42004019, year = {2026}, author = {Yuan, G and Zhu, X and Zhang, L and Wang, X and Wang, Y and Guo, D and Zhang, T and Wang, G and Wang, N}, title = {Shading affects the nitrogen cycling process and plant nitrogen uptake by altering the rhizosphere microbial community.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1780344}, pmid = {42004019}, issn = {1664-462X}, abstract = {Plants adapt to environmental changes by affecting the rhizosphere environment and microbial pathways. Shading affects nitrogen absorption and accumulation in plants by directly or indirectly altering the light intensity. However, the effects this has on the rhizosphere micro-environment and especially the microbial community are not fully understood. Utilizing non-targeted metabolomics and metagenomics, we investigated the changes in the microbial community structure in the cigar tobacco rhizosphere and the nitrogen cycling process and its relationship with nitrogen absorption by the plants under artificial shading conditions. Shading significantly increased the rhizosphere soil organic carbon, hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and nitrogen contents in tobacco plants. Metabolomics revealed that shading significantly affected the arginine biosynthesis pathway in the rhizosphere soil, with the expression levels of L-oxornithine, citrulline and L-arginine significantly increasing. Metagenomics analysis indicated that shading significantly altered the rhizosphere microbial community structure and the nitrogen cycling process. The abundances of organic nitrogen-decomposition (gdh A, ansB) and nitrification genes (amoA_B, amoB_B, amoC_B, hao) significantly increased. Flavobacterium and Stenotrophomonas may play important roles in the nitrogen cycle in the rhizosphere. Correlation analysis indicated that Flavobacterium and Stenotrophomonas were significantly positively correlated with L-glutamic acid, L-ornithine and L-arginine (p < 0.05). These results reveal the biological mechanism by which shading affects nitrogen absorption in crops via changes in the rhizosphere microbial community and the nitrogen cycling process, providing a scientific foundation for guiding nutrient management strategies in shaded cultivation.}, }
@article {pmid42004152, year = {2026}, author = {You, G and Wang, S and Hua, Y and Su, J and Yang, Y and Shi, B and Cen, S}, title = {A four-year misdiagnosis of spinal Burkholderia pseudomallei infection: A case report and literature review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02558}, pmid = {42004152}, issn = {2214-2509}, abstract = {Melioidosis, traditionally an endemic disease, is increasingly reported in non-endemic regions. Its causative pathogen, Burkholderia pseudomallei, exhibits distinct characteristics from common pathogens but is prone to misdiagnosis due to clinical overlap with other infections. Despite advances in diagnostics, metagenomic next-generation sequencing (mNGS) has not been featured in case reports. We present a case of melioidosis, misdiagnosed for four years, where mNGS proved pivotal for definitive diagnosis. Based on our findings and literature review, we advocate for mNGS in melioidosis diagnosis. Furthermore, we identify subtle distinctions between melioidosis and tuberculosis amidst their similarities and propose integrating these features into a differential diagnostic framework.}, }
@article {pmid42004164, year = {2026}, author = {Chong, KL and Liew, KJ and Salleh, FM and Chong, CS}, title = {Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {163}, pmid = {42004164}, issn = {2190-572X}, abstract = {UNLABELLED: Mangrove ecosystems contain abundant lignocellulosic biomass and mangrove microorganisms that are capable of degrading plant polymers. In this study, a shotgun metagenomic approach was employed to explore the bacterial communities from Tanjung Piai National Park, Malaysia and their genes involved in lignocellulosic biomass degradation. A total of 148 of carbohydrate active enzymes (CAZy) genes spanning GH, CE, and AA families were identified with lignocellulolytic abilities. These enzymes included 20 cellulases, 46 hemicellulases, and 82 lignin-modifying enzymes. Approximately 89.19% of these genes were found from underexplored bacterial lineages. A set of lignocellulolytic genes derived from diverse bacterial taxa highlighted the synergistic action of mangrove bacteria in lignocellulose degradation. To validate the functionality of these genetic resources, one of the genes (BGL3_GH1) encoding a β-glucosidase was selected for expression and characterisation. The recombinant enzyme showed optimal activity at 60 ℃ and pH 7, retained up to 75% activity at 10% (w/v) NaCl. The enzyme exhibited a 1.6 to 2.1-fold in enzyme activity with glucose concentration up to 2 M. In a two-step saccharification assay using sugarcane bagasse, supplementation with recombinant BGL3_GH1 enhanced the saccharification yield (0.0674 g g[- 1] biomass) compared with treatments using commercial cellulase or recombinant BGL3_GH1 alone. These findings reveal the functional diversity of lignocellulose-degrading genes in mangrove bacteria and identify recombinant BGL3_GH1 as a potential enzyme candidate for biomass conversion application.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04788-x.}, }
@article {pmid42004407, year = {2026}, author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H}, title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73367}, pmid = {42004407}, issn = {2045-7758}, abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.}, }
@article {pmid42004633, year = {2026}, author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D}, title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e174893}, pmid = {42004633}, issn = {1314-2828}, abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.<br><br>NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).}, }
@article {pmid42004896, year = {2026}, author = {Pourghasem, M and Tabatabaii, SA and Modarresi, SZ and Jafari Nodoushan, A and Fadavi, N and Soflaee, M and Hosseini Vajari, A and Khazaii, F and Shahhosseini, B and Fakhimi Derakhshan, K and Sadat Mansouri, S}, title = {Fungal Infections in Pediatric Patients With Hematologic Malignancies and Stem Cell Transplantation: Impact on the Upper and Lower Respiratory Systems.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2026}, number = {}, pages = {8766717}, pmid = {42004896}, issn = {1712-9532}, abstract = {Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in children with hematological malignancies as well as those undergoing hematopoietic stem cell transplantation (HSCT). Extreme immunological dysregulation secondary to severe neutropenia, T-cell lymphopenia, graft-versus-host disease (GVHD), intensive chemotherapy regimens, and conditioning therapy for HSCT, as well as primary immunodeficiencies (PIDs), render these patients highly susceptible to both opportunistic and pathogenic fungal infections. Despite advances in antifungal drugs and diagnostic tools, it is very difficult in these children to provide timely diagnosis and optimal management of IFIs because of the nonspecific clinical manifestations, the invasiveness of present diagnostic modalities in pediatric patients, and biomarker kinetics differences in various pediatric age groups, along with a lack of incorporation of immunological-pharmacological maturity-associated variability in the existing scoring systems borrowed from adults. This narrative review provides a comprehensive and contemporary assessment of the epidemiology, host-related risk factors, clinical presentations, diagnostic criteria, and management practices for IFIs in children with hematological malignancies and following HSCT. It also highlights the role of EORTC/MSGERC criteria in defining IFIs as probable, proven, and possible infections and explores the sensitivity and specificity of noninvasive methods such as the galactomannan index, polymerase chain reaction (PCR), ß-D-glucan assay, high-resolution CT scans (HRCTs), and the latest approaches including next-generation sequencing (NGS) and metagenomics. This review points out significant gaps in pediatric research studies and supports efforts to optimize healthcare use with risk-prediction models rather than just relying on current algorithms.}, }
@article {pmid42005541, year = {2026}, author = {Naitchede, LHS and Ihearahu, OC and Saha, K and Igwe, DO and Yan, J and Osano, AA and Ray, S and Ude, G}, title = {Microbial community characterization in semi-hydroponic systems of Starbor kale (Brassica oleracea L.) grown under normal gravity and simulated microgravity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100592}, pmid = {42005541}, issn = {2666-5174}, abstract = {Kale is a member of the Brassicaceae family and contains a range of beneficial compounds. Given the global context of climate change, various vegetable production systems using advanced technologies, such as hydroponics, are being explored to alleviate food insecurity. Herein, we characterized the comprehensive microbial community associated with Starbor kale cultivation systems under normal gravity and simulated microgravity in coco coir, representing an innovative approach compared to previous studies. The kale seedlings were planted in growth vessels set into custom 2D clinostats and placed in a CONVIRON growth chamber for 43 days. The microbial DNA from coco-coir and root samples of grown kale was extracted and subjected to shotgun metagenomic sequencing. Comparisons between components revealed a higher abundance of bacteria in the soilless, while the kale roots were dominated by Eukaryota and archaea. The phyla Pseudomonadota and Actinomycetota were highly prevalent across all samples, with relatively high abundance in the coco coir samples from horizontal clinostats (HCR) under simulated gravity and from rotating vertical clinostats (VCR). The HCR group was associated with the highest number of biomarkers (28). Both CAZymes, glycoside hydrolases and carbohydrate esterases, exhibited higher relative abundances in the coco coir samples under normal gravity, whereas carbohydrate-binding modules were more abundant in HCR and VCR. The root samples showed much higher abundances of polysaccharide lyases (ranging from 0.00088 to 0.00097) and carbohydrate esterases (ranging from 0.030 to 0.033). The top four prevalent antibiotic resistance genes were adeF, vanY, vanT, and qacG. The findings of this investigation are crucial for the cultivation of kale and leafy green agriculture in hydroponic systems.}, }
@article {pmid42005844, year = {2026}, author = {Ibañez-Lligoña, M and Colomer-Castell, S and Campos, C and González-Camuesco, &#xc1; and Llauradó, A and Garcia-Larroy, J and Sánchez-Tejerina, D and Rando-Segura, A and Andrés, C and Esperalba, J and Nadal, P and Ferrer, R and Cortese, MF and Tabernero, D and Gregori, J and Riveiro-Barciela, M and Ruiz-Cobo, JC and Ruiz, A and Del Barco, E and Buti, M and Goya, M and Antón, A and Cano, A and Juntas-Morales, R and Quer, J}, title = {Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786985}, pmid = {42005844}, issn = {1664-302X}, abstract = {INTRODUCTION: Shotgun metagenomic sequencing (mNGS), an untargeted approach that sequences all nucleic acids in a sample, has emerged as a powerful tool for pathogen detection and genome characterization. However, its implementation in clinical diagnostics remains limited due to technical challenges such as contamination and reduces sensitivity, especially in low-biomass samples.<br><br>METHODS: We applied mNGS to 144 clinical samples representing chronic infections, acute infections, and respiratory co-infections. To address contamination, we established a framework integrating negative controls, lab-specific contaminant watchlists, and computational filtering. Viral detection performance and genome recovery were assessed across sample types and viral loads.<br><br>RESULTS: Viral load was shown to be the primary determinant of sensitivity, with reliable recovery achieved only at higher titers. Our framework substantially improved contamination management, reducing false-positive signals and enhancing viral genome recovery. mNGS enabled the detection of clinically relevant co-infections and refined viral classification beyond targeted diagnostics, while also revealing the substantial risk of spurious detections in the absence of contamination-aware workflows.<br><br>DISCUSSION: These findings define practical sensitivity thresholds for clinical mNGS and underscore the need for contamination-aware workflows, particularly for low-biomass samples, while providing an open-source contaminants watchlist that enhances reliability and utility of clinical metagenomics.}, }
@article {pmid42005864, year = {2025}, author = {Steindler, L and Durán Canché, MA and Ilan, M and Bar-Shalom, R and Lopez, JV and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges &amp; Vacelet, 1995, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {466}, pmid = {42005864}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.}, }
@article {pmid42005923, year = {2026}, author = {Lafon, T and Weingart, M and Vaidie, J and Calfee, CS and Jacob, ST and Freund, Y and Shapiro, NI and Barraud, O and Monneret, G and van der Poll, T and Fromage, Y and François, B}, title = {Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.}, journal = {EClinicalMedicine}, volume = {94}, number = {}, pages = {103864}, pmid = {42005923}, issn = {2589-5370}, abstract = {In this narrative review, we aimed to provide a comprehensive overview of emerging diagnostic strategies and precision medicine approaches in sepsis, while explicitly acknowledging the heterogeneity of clinical contexts. In the Emergency Department (ED), timely recognition of infection and sepsis represents one of the most frequent and challenging tasks, which may delay management directly increasing morbidity and mortality. Even if very popular and widely used, traditional scores and routine biomarkers remain of limited interest to confirm diagnosis and predict deterioration. Nevertheless, emerging point-of-care tools hold promise such as "real-time microbiology", bedside immune profiling, and echocardiography for on-time hemodynamic phenotyping. More advanced strategies, such as omics technologies and transcriptomic signatures, offer deeper biological precision, while machine learning and artificial intelligence can integrate high-dimensional ED data to anticipate deterioration and capture the dynamic evolution of sepsis subphenotypes. Many of these tools are already feasible at the bedside and only await integration into routine ED workflows. Embedding them within dedicated sepsis pathways and multidisciplinary teams could optimize global patient care and accelerate the transition toward precision medicine in acute sepsis. Sustainable improvements in sepsis outcomes will most likely not come from isolated devices but from their integration into coordinated and sepsis-specific pathways.}, }
@article {pmid42006114, year = {2025}, author = {Dorobantu, S and Grigorescu, A and Fratea, A and Mirauta, B and Neghina, A and Bica, G and Neacsu, A and Dumitrescu, F and Streata, I and Netea, M and Riza, AL}, title = {Strength of Omics in Uncovering Sepsis Mechanisms-A Perspective.}, journal = {Current health sciences journal}, volume = {51}, number = {4}, pages = {425-436}, pmid = {42006114}, issn = {2067-0656}, abstract = {BACKGROUND: Sepsis is a significant life-threatening condition due to a dysregulated response to infection. Large datasets yield unprecedented views and transformative insights into processes through various computational frameworks. Our aim was to highlight significant contributions from genomics, transcriptomics, proteomics in the field of sepsis, as modeled from human data. We are showcasing key findings in each omics that have improved the understanding of sepsis pathophysiology, while presenting a perspective from the group's own contribution to the field.<br><br>DISCUSSION AND CONCLUSIONS: Each of the presented omics has advanced our mechanistic understanding on sepsis pathogenicity, biomarker identification for diagnosis, prognosis, and molecular stratification purposes. Multi-omics sepsis research shows strong input from genomics, transcriptomics, proteomics. These have revealed mechanistic links and produce robust endotypes but faces challenges on the path to clinical integration. Integrative sepsis studies combine large-scale omics, paired sampling, and computational multi-omics frameworks to link molecular layers to phenotype. Addressing gaps in standardization, and age/ethnicity representation could yield actionable biomarkers, stratified therapies and improved outcomes.}, }
@article {pmid42006125, year = {2026}, author = {Azuma, N and Wada, N and Aoki, R and Sampei, M and Mawatari, T and Saito, Y}, title = {Administration of bifidobacteria and dietary fiber improves cognitive function by increasing short-chain fatty acid-producing bacteria and reducing inflammation.}, journal = {Bioscience of microbiota, food and health}, volume = {45}, number = {2}, pages = {139-148}, pmid = {42006125}, issn = {2186-6953}, abstract = {Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505), commercially known as the "BifiX" strain in Japan, reaches the intestine alive, proliferates after a single intake, and is associated with several positive health effects. A randomized, double-blind, placebo-controlled, parallel-group clinical trial of this probiotic strain in combination with inulin (a prebiotic) reported an improvement of cognitive function in the elderly. In the present study, a follow-up analysis was performed to elucidate the underlying mechanism, using a multi-omics approach that integrated a high-throughput assay of blood inflammatory markers and metagenomic analysis of the fecal bacterial composition. After probiotic and prebiotic administration, short-chain fatty acid producers such as Faecalibacterium and Bifidobacterium were increased in the gut. Moreover, in the subgroup with greater improvement in cognitive function scores, the levels of inflammatory markers were decreased. Subgroup analysis revealed that the improvement of cognitive function was associated with a reduction of inflammation and an increase of Faecalibacterium. These results suggest that GCL2505 and inulin can improve cognitive function by alleviating inflammation via an increase of short-chain fatty acid-producing bacteria, which appears to elevate levels of short-chain fatty acids, particularly acetate and butyrate, in the gut. The present results contribute to a deeper comprehension of the gut-brain axis and propose new avenues for potential therapeutic intervention in cognitive disorders.}, }
@article {pmid42006869, year = {2026}, author = {Li, Y and Zhu, H and Zhan, Z and Li, G and Zhou, Q and Zheng, C and Huang, F}, title = {Clinical features and prognostic factors of Chlamydia psittaci pneumonia: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1804156}, pmid = {42006869}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia psittaci pneumonia (CPP) is frequently misdiagnosed and can progress to severe illness. A deeper understanding of its clinical and imaging features is crucial for early detection and effective treatment.<br><br>METHODS: This retrospective study analyzed 74 patients diagnosed with CPP via metagenomic (mNGS) and targeted next-generation sequencing (tNGS) between January 2022 and September 2025. Patients were categorized into severe (n&#x202f;=&#x202f;21) and non-severe (n&#x202f;=&#x202f;53) groups based on established criteria for severe community-acquired pneumonia. Data on demographics, clinical manifestations, laboratory findings, and imaging characteristics were collected and compared.<br><br>RESULTS: The cohort had a median age of 60&#x202f;years, with a male predominance (62.2%). A history of poultry/bird exposure was reported by 87.8% of participants. Common symptoms included fever (94.6%), cough (63.5%), and fatigue (29.7%), with no significant differences between groups. Hospitalization was significantly longer in the severe group (12.95&#x202f;&#xb1;&#x202f;6.08&#x202f;days) than in the non-severe group (8.13&#x202f;&#xb1;&#x202f;3.30&#x202f;days) (p&#x202f;<&#x202f;0.001). Chest CT revealed consolidation and ground-glass opacities in all patients. Pleural effusion was significantly more common in the severe group (76.2% vs. 45.3%, p&#x202f;=&#x202f;0.016), as was bilateral lung involvement (52.4% vs. 22.6%, p&#x202f;=&#x202f;0.013). Multivariate analysis identified elevated D-dimer (OR&#x202f;=&#x202f;2.737, p&#x202f;=&#x202f;0.007) and reduced lymphocyte percentage (L%) (OR&#x202f;=&#x202f;0.813, p&#x202f;=&#x202f;0.026) as independent predictors of severe disease. ROC curve analysis showed an AUC of 0.765 for D-dimer and 0.739 for L% reduction. Following tetracycline or quinolone therapy, 94.6% of patients recovered, with an overall mortality rate of 5.4%.<br><br>CONCLUSION: Severe CPP is associated with prolonged hospitalization, bilateral pulmonary infiltrates, and pleural effusion. D-dimer and lymphocyte percentage are valuable prognostic indicators for disease severity. Early targeted antibiotic therapy is effective, but timely respiratory support is critical for severe cases.}, }
@article {pmid42006894, year = {2026}, author = {Cui, T and Huang, M}, title = {Case Report: A case of refractory tuberculous peritonitis mimicking and complicating suspected encapsulating peritoneal sclerosis in a long-term peritoneal dialysis patient.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1777805}, pmid = {42006894}, issn = {2296-858X}, abstract = {BACKGROUND: Tuberculous peritonitis (TBP) is a rare but severe complication in peritoneal dialysis (PD) patients, often presenting with non-specific symptoms. Its diagnosis is particularly challenging in patients with pre-existing or co-existing peritoneal pathology, such as changes suggestive of encapsulating peritoneal sclerosis (EPS).<br><br>CASE PRESENTATION: A 59-year-old male on PD for 14&#x202f;years with no prior history of peritonitis presented with recurrent abdominal pain, fever, and cloudy effluent, following a recent episode of Staphylococcus caprae peritonitis. Initial contrast-enhanced computed tomography (CT) revealed diffuse peritoneal thickening, omental "caking," and localized ascites, raising strong suspicion for EPS. However, the patient's condition relapsed despite broad-spectrum antibiotic therapy. Metagenomic next-generation sequencing (mNGS) of peritoneal fluid definitively identified Mycobacterium tuberculosis complex. The diagnosis was thus revised to TBP manifesting with secondary peritoneal inflammatory changes mimicking EPS. Management involved laparoscopic PD catheter removal, transition to hemodialysis, and initiation of a renal-adjusted anti-tuberculous regimen (levofloxacin and linezolid), leading to gradual clinical and biochemical improvement.<br><br>CONCLUSION: This case highlights that TBP can clinically and radiologically mimic EPS in long-term PD patients, leading to diagnostic delay. High clinical suspicion and the utilization of advanced molecular diagnostics like mNGS are crucial for accurate diagnosis. Catheter removal combined with appropriate anti-tuberculous therapy forms the cornerstone of management in such complex scenarios.}, }
@article {pmid42007374, year = {2026}, author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS}, title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.}, journal = {Microbiome research reports}, volume = {5}, number = {1}, pages = {2}, pmid = {42007374}, issn = {2771-5965}, abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.}, }
@article {pmid42007699, year = {2026}, author = {Carroll, AC and Hinz, A and Hicks, AMA and Khov, E and Van Bakel, T and Doukhanine, E and Fralick, M and Nott, C and Kassen, R and Thampi, N and Hug, LA and MacFadden, D and Wong, A}, title = {Targeted metatranscriptomic detection of viruses from floors for simultaneous evaluation of respiratory disease burden and viral variant identification.}, journal = {mSphere}, volume = {11}, number = {5}, pages = {e0008626}, pmid = {42007699}, issn = {2379-5042}, mesh = {Humans ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Metagenomics/methods ; *COVID-19/epidemiology/virology ; Influenza A virus/genetics/isolation &amp; purification ; Canada/epidemiology ; *Viruses/genetics/isolation &amp; purification/classification ; Respiratory Syncytial Virus Infections/epidemiology ; }, abstract = {UNLABELLED: Built environment surveillance is a proven approach for tracking disease burden of some viruses within hospitals and long-term care facilities. However, studies in clinical settings are lacking for simultaneously surveying targets in a built environment using targeted metatranscriptomics. We swabbed six discrete floor locations within an acute care center's emergency department (ED) in Ottawa, Canada, and sequenced cDNA using a 132 viral taxa panel, identifying viral burden across sampling locations and time. The determined SARS-CoV-2 variant profile across time was matched to provincial variant prevalence. The correlation between metatranscriptomic read abundances and reported cases of influenza A, SARS-CoV-2, and RSV was assessed. We quantified these via qPCR and assessed the correlation of Cq versus metatranscriptomic reads for these viruses. We sequenced a median of 1,302,882 reads per sample from 38 floor swabs collected during peak respiratory viral season (November 2022-February 2023). Diversity of viral communities varied significantly across locations in the ED. SARS-CoV-2 variant abundance shifts matched the changing infection landscape concurrently reported in Ontario. Relationships between targeted metatranscriptomic read ratios and clinical burden were not statistically significant, although we found modest correspondence between qPCR signal and read depth for RSV and SARS-CoV-2. This approach characterized the viral communities and the within-species diversity within an ED. Correlating sequencing-derived data with disease burden for three key respiratory viruses was inconsistent, with the exception of significant correlation between metatranscriptomic reads and Cq data for SARS-CoV-2. We were able to recover the distribution of clinically reported SARS-CoV-2 variants from the floor swab data.<br><br>IMPORTANCE: Environmental surveillance is useful for estimating the disease burden for certain viruses. qPCR is commonly used for surveillance of wastewater and built environments, including during the COVID-19 pandemic, but single, multiplexed reaction targets are limited. Targeted metagenomic or metatranscriptomic approaches can accurately quantify microbial populations of interest in an environment, reduce off-target sequencing, and evaluate a broader number of targets than qPCR assays. Here, we assessed the capacity of a targeted viral metatranscriptomic panel to correlate viral abundance in the hospital built environment with key pathogens of interest, including influenza A, RSV, and SARS-CoV-2. Our results suggest that targeted metatranscriptomics may identify viral communities in healthcare facilities, including strain-level detection capability. However, this approach must be validated for its effectiveness in viral surveillance that accurately reflects disease burden. This work contributes to a growing toolkit for pathogen surveillance, a critical endeavor to safeguard against outbreaks of known and emerging pathogens.}, }
@article {pmid42007817, year = {2026}, author = {Chen, M and Kang, Y and Cheng, M and Li, X and Keng, J and Zhao, P and Sui, H and Dong, J and Sun, L and Liu, B and Hu, Y and Jiang, J and Yang, F}, title = {Co-circulation of multiple arboviruses in acute febrile patients in Yunnan, China, identified by metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {64}, number = {5}, pages = {e0167025}, pmid = {42007817}, issn = {1098-660X}, support = {2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; China/epidemiology ; Phylogeny ; Metagenomics ; Chikungunya virus/genetics/isolation &amp; purification ; Female ; *Coinfection/epidemiology/virology ; Male ; Dengue Virus/genetics/isolation &amp; purification ; *Arboviruses/genetics/classification/isolation &amp; purification ; Adult ; Disease Outbreaks ; Zika Virus/genetics/isolation &amp; purification ; *Arbovirus Infections/epidemiology/virology ; *Fever/virology/epidemiology ; Chikungunya Fever/epidemiology ; Middle Aged ; Zika Virus Infection/epidemiology ; Adolescent ; Dengue/epidemiology ; Young Adult ; }, abstract = {UNLABELLED: Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by Aedes mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, China, bordering Southeast Asia, is a hotspot for viral importation due to intensive cross-border mobility. However, systematic surveillance for these arboviruses among acute febrile patients remains insufficient. We performed metagenomic sequencing on serum specimens from 990 acute febrile patients at the China-Myanmar border between 2017 and 2023. The pathogens were confirmed by PCR and viral isolation. Phylogenetic and spatiotemporal analyses were used to infer viral origins and transmission dynamics. In this study, a CHIKV outbreak was confirmed in 2019, with strains closely related to those from Myanmar and Thailand. Four DENV serotypes 1-4 were identified, with the predominant serotype varying annually. ZIKV was detected and closely related to strains from Myanmar. Co-infections were identified, including one case each of CHIKV with DENV-1, CHIKV with DENV-3, CHIKV with ZIKV, and DENV-1 with DENV-2. Bayesian spatiotemporal analysis of CHIKV reconstructed global transmission routes, indicating that the 2019 outbreak in China likely originated in India and spread sequentially through Bangladesh, Thailand, and Myanmar. In addition, we also detected enterovirus, hepatitis virus, Saffold virus, and rhinovirus. This study reveals a comprehensive spectrum of pathogens, including the co-circulation of DENV, CHIKV, and ZIKV, and underscores the potential risk of arbovirus importation into China, highlighting the need for strengthened border surveillance.<br><br>IMPORTANCE: Arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV), are expanding their range and threatening global public health. Yunnan, situated along the China-Southeast Asia border, is highly susceptible to viral introduction. By applying viral metagenomic sequencing to acute febrile patients, this study uncovered a comprehensive spectrum of pathogens and the co-circulation of DENV, CHIKV, and ZIKV. Phylogenetic analyses revealed that arboviruses were closely related to strains from Myanmar and Thailand, indicating possible frequent cross-border viral introductions. Meanwhile, we reconstructed the global transmission pathways of CHIKV through Bayesian spatiotemporal analysis, providing valuable insights for regional prevention and control of arboviruses. These findings demonstrate that Yunnan serves as a critical interface for viral importation and underscore the urgent need to strengthen border surveillance and early warning systems to mitigate the spread of arboviruses.}, }
@article {pmid42008001, year = {2026}, author = {Hu, C and Yu, J and Chu, T and Wang, Q and Chen, L and Yu, Y and Wang, Y}, title = {Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42008001}, issn = {1432-072X}, abstract = {Virophages are small double-stranded DNA viruses that parasitize giant viruses, modulating virus–host interactions and influencing microbial community dynamics. Despite their ecological significance, virophages and giant viruses remain poorly studied in extreme environments. Here, we present the first metagenomic survey of virophage and giant virus diversity in Lake Namtso, a high-altitude saline lake on the Tibetan Plateau. Metagenomic assembly and phylogenomic analyses uncovered 93 virophage major capsid protein sequences spanning seven established families, alongside numerous unclassified lineages. Two nearly complete virophage genomes were reconstructed: Namtso Virophage 1 (NMV1), which encodes both replication- and integration-associated genes and likely represents a novel family, and Namtso Virophage 2 (NMV2), affiliated with Omnilimnoviroviridae but distinguished by duplicated protease genes and dual DNA methyltransferases. Parallel analyses identified over 18,000 giant virus marker genes, with DNA PolB affiliated to Imitervirales, Pimascovirales, Asfuvirales, Algavirales, and Chitovirales, as well as divergent lineages representing potential novel Nucleocytoplasmic large DNA viruses (NCLDVs). Homologous protein analysis and tetranucleotide clustering suggest extensive host–virus–virophage interactions. These findings significantly expand the known diversity and genomic repertoire of virophages and giant viruses, highlight their ecological roles in sustaining microbial resilience, and provide new insights into viral evolution and adaptation in extreme high-altitude ecosystems.}, }
@article {pmid42008944, year = {2026}, author = {Liu, J and Li, Y and Wang, H and Wang, L and Wu, G and Zhao, B}, title = {Biphasic dynamics of N-nitrosodimethylamine precursors in effluent-receiving rivers: Insights from multi-omics into microbial nitrogen metabolism regulation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125933}, doi = {10.1016/j.watres.2026.125933}, pmid = {42008944}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Dimethylnitrosamine ; Multiomics ; *Nitrogen/metabolism ; Wastewater ; Water Pollutants, Chemical ; }, abstract = {Wastewater effluent introduces substantial dissolved organic nitrogen into rivers, thereby increasing the risk of carcinogenic N-nitrosodimethylamine (NDMA) formation from its precursors. However, the microbial metabolic mechanisms governing dynamics of these precursors along receiving rivers remain unclear. Here, through a 21-day time-series incubation of sediments from upstream, outfall, and downstream areas of a representative wastewater treatment plant, combined with multi-omics analyses i.e., 16S rRNA gene sequencing, metagenomics, and metabolomics, the transformation of precursors and microbially mediated nitrogen metabolism were elucidated. A biphasic pattern of NDMA precursors measured as formation potential (FP) was observed during incubation, characterized by a rapid formation from days 0 to 3 followed by a remarkable degradation until day 7 and subsequent stabilization. Nitrate peaked paralleling NDMA FP, with nitrite accumulation following the onset of precursors degradation. Multi-omics analysis revealed that this turnover was driven by strong functional coupling between key nitrogen-cycling taxa and specific metabolites, particularly short-chain peptides. Community structure in the early phase was dominated by r‑strategists e.g., Bacillota, which promoted organic nitrogen degradation and nitrification, resulting in the accumulation of NDMA precursors. As anoxia developed, the community shifted toward K‑strategists such as Pseudomonadota and Chloroflexota, which likely degraded precursors through co-metabolism and consumption of ammonia source. Metabolomics revealed the conversion of precursors into short-chain peptides and amino acid analogues. Notably, effluent exposure established a functionally specialized legacy effect in downstream sediments, stabilizing into a microbial metabolic hotspot with a peak NDMA FP of 1285 ng/L, 158% and 80.7% higher than those in the upstream and outfall area, respectively. This study establishes a mechanistic framework for evaluating the transformation and risk of NDMA precursors in river systems, with direct implications for monitoring strategies and designing of the wastewater outfall location.}, }
@article {pmid42010118, year = {2026}, author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV}, title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.}, journal = {Nature medicine}, volume = {32}, number = {6}, pages = {2096-2106}, pmid = {42010118}, issn = {1546-170X}, support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i P&#xeb;rbashk&#xeb;t i BE-s&#xeb; p&#xeb;r K&#xeb;rkimet mbi S&#xeb;mundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/genetics ; Female ; Male ; *Genetic Predisposition to Disease ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Feces/microbiology ; *Glucosylceramidase/genetics ; Risk Factors ; Case-Control Studies ; *Microbiota/genetics ; Metagenomics ; Disease Progression ; }, abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.}, }
@article {pmid42010313, year = {2026}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M}, title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42010313}, issn = {2052-4463}, support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; }, mesh = {China ; *Wetlands ; Archaea/genetics/classification ; *Geologic Sediments/microbiology ; *Metagenome ; Phylogeny ; Bacteria/genetics/classification ; Metagenomics ; }, abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.}, }
@article {pmid42010457, year = {2026}, author = {Guo, J and Liang, C and Cairang, L and Si, L and Yan, J and Liu, D}, title = {Metagenomics reveals gut microbial differences and ecological adaptation in plateau zokor (Eospalax baileyi) populations.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42010457}, issn = {1471-2180}, support = {LHZX-2023-02//Sanjiangyuan National Park Joint Grant from the Chinese Academy of Sciences and the People's Government of Qinghai Province/ ; }, abstract = {UNLABELLED: Nine geographically distinct populations of plateau zokors (Eospalax baileyi) from Qinghai Province were selected for metagenomic analysis to investigate the composition of gut microbial communities among different populations. The results showed that the core gut microbiota of plateau zokors from different geographic populations was dominated by Firmicutes, Bacteroidetes, and Proteobacteria, with significant differences in community composition among populations. Alpha diversity analysis revealed marked variation in gut microbial diversity and richness across the different geographic populations. Functional prediction further demonstrated significant differences in multiple metabolic pathways, including carbohydrate metabolism, amino acid metabolism, replication and repair, and membrane transport. Notably, carbohydrate-active enzymes associated with the degradation of cellulose, hemicellulose, and lignin exhibited significant differences among populations. In addition, correlation analyses between environmental factors and the gut microbiota indicated that environmental variables such as altitude, annual precipitation, and isothermality had significant effects on gut microbial community structure. Regression analysis between genetic and geographic distances showed that genetic distance among plateau zokor populations increased with increasing geographic distance. Overall, these results suggest that geographic isolation and environmental heterogeneity may jointly drive the differentiation of gut microbial communities in plateau zokors. This study provides microbiological evidence and theoretical support for understanding the ecological adaptation of plateau zokors and offers a scientific basis for the integrated management of grassland rodent pests.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05069-6.}, }
@article {pmid42010622, year = {2026}, author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M}, title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42010622}, issn = {1756-994X}, support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; }, abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood. METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages. RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution. CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.}, }
@article {pmid42010710, year = {2026}, author = {Long, L and An, Y and Zhu, LT and Xu, XL and Lin, JJ and Xu, WJ and Chen, JY and Liu, FY and Liu, XY and Huang, Q}, title = {Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010710}, issn = {2049-2618}, support = {(42177362)//National Natural Science Foundation of China/ ; (2025J02030, 2025J01256)//Fujian Provincial Natural Science Foundation of China/ ; (NO. NBSDC-DB-21)//National Basic Science Data Center "Environment Health DataBase"/ ; }, mesh = {Child ; Humans ; Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; China ; *Dust/analysis ; Family Characteristics ; *Fungi/genetics/isolation &amp; purification/classification/pathogenicity ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.<br><br>RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39&#x2009;&#xd7;&#x2009;10[5] and 2.83&#x2009;&#xd7;&#x2009;10[6] DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF&#xa0;profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.<br><br>CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.}, }
@article {pmid42010711, year = {2026}, author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z}, title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010711}, issn = {2049-2618}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; }, mesh = {*Rhizosphere ; *Plant Roots/microbiology ; Streptomyces/genetics/metabolism/isolation &amp; purification ; *Metabolome ; Soil Microbiology ; Fusarium/isolation &amp; purification ; *Microbiota ; *Plants, Medicinal/microbiology ; *Angelica sinensis/microbiology/metabolism ; *Plant Diseases/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.<br><br>RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.<br><br>CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.}, }
@article {pmid42010713, year = {2026}, author = {Tang, J and Wang, L and Yang, Z and Song, Y and Wu, S and Liang, Q and Li, Z and Zhou, S and Xiong, H and Chen, D and Li, J and Li, F}, title = {Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010713}, issn = {2049-2618}, support = {32272874//National Natural Science Foundation of China/ ; 2021YFF1000601//National Key R&amp;D Program of China/ ; 2662025DKPY008//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Male ; Mice ; STAT5 Transcription Factor/metabolism ; *Gastrointestinal Microbiome/physiology ; Mice, Knockout ; *Spermatogenesis ; *gamma-Glutamyltransferase/genetics/deficiency/metabolism ; *Infertility, Male/microbiology/metabolism ; *Dysbiosis/microbiology ; STAT3 Transcription Factor/metabolism ; Fecal Microbiota Transplantation ; Testis/metabolism ; Signal Transduction ; *Glycine/analogs &amp; derivatives/metabolism ; Phenylacetates/metabolism ; Suppressor of Cytokine Signaling 3 Protein ; }, abstract = {BACKGROUND: Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.<br><br>RESULTS: This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1[-/-]) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1[-/-] mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1[-/-] mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1[-/-] mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1[-/-] mice (Ggt1[-/-]-FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&amp;Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites&#xa0;(TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates &#x3b2;2-adrenergic receptor (&#x3b2;2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.<br><br>CONCLUSION: Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via &#x3b2;2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced &#x3b2;2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B&#xa0;dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.}, }
@article {pmid42010746, year = {2026}, author = {Yun, CS and Kim, JK and Kwon, H and Her, M and Moon, JS}, title = {Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42010746}, issn = {2524-4671}, abstract = {BACKGROUND: Granuloma lesions in poultry are a frequent pathological finding, representing a chronic inflammatory response to persistent infectious agents, most commonly bacteria or fungi. Accurate differentiation of the underlying cause requires additional diagnostic tests, such as acid-fast staining, fungal culture, or bacterial isolation and genetic identification. However, the pathogens often remain undetermined when conventional detection methods fail. The present case aimed to investigated granulomatous disease in multiple organs of layer chickens by applying metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing. CASE PRESENTATION: A total of 35 deaths occurred in a flock of layer chickens, accompanied by a decrease in daily feed intake from 144 g to 104 g. Six carcasses from 38-weeks-old layer chickens were submitted for disease diagnosis. During necropsy, granuloma/neoplastic lesions were observed in the liver, ovary, proventriculus, pancreas and kidney. Histopathological examination revealed compartmentalized infiltration of lymphocytes and multinucleated giant cells in liver, ovary, proventriculus, pancreas and renal parenchyma. While Escherichia coli was isolated from the oviduct, no viral agents (IBV, CIAV, MDV, ALV, REV, or HEV) were detected by RT-PCR. Notably, some of the initial metagenomic shotgun results were recognized as different taxa due to the misclassification of certain reads. Following a re-analysis of these shotgun reads against the nucleotide database, both metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing identified E. coli as the dominant species in liver samples. CONCLUSION: The present case indicates that E. coli may contribute to granuloma lesions in layer chickens. While 16S rRNA amplicon sequencing provided more reliable bacterial identification for diagnostic purposes, metagenomic shotgun sequencing offers complementary insight by detecting broader microbial communities. Therefore, integrating both approaches alongside conventional diagnosis may improve the accuracy of diagnosis for granulomatous diseases in poultry.}, }
@article {pmid42010766, year = {2026}, author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K}, title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2661415}, pmid = {42010766}, issn = {1949-0984}, mesh = {Humans ; *Obesity/metabolism/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; }, abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.}, }
@article {pmid42010993, year = {2026}, author = {Wu, Y and Guo, X and Wang, X and Guo, F}, title = {Fatal Non-Hepatic Hyperammonemia Post-Glofitamab: Ureaplasma and Genetic Susceptibility: A Case Report.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70443}, pmid = {42010993}, issn = {2050-4527}, mesh = {Humans ; Male ; Middle Aged ; *Hyperammonemia/etiology/chemically induced/diagnosis/genetics ; Fatal Outcome ; Genetic Predisposition to Disease ; *Ureaplasma Infections ; *Lymphoma, Large B-Cell, Diffuse/drug therapy ; *Antineoplastic Agents, Immunological/adverse effects ; }, abstract = {BACKGROUND: Although primarily reported in solid organ transplant recipients and patients undergoing chimeric antigen receptor T-cell immunotherapy (CAR-T), non-hepatic hyperammonemia (NHHA) is a rare but lethal complication in the broader context of post- chemo-immunotherapy hematologic malignancies. It often presents with unexplained encephalopathy that mimics primary central nervous system (CNS) progression, leading to diagnostic delays. With the expanding use of bispecific antibodies (e.g., glofitamab), the etiology of NHHA, particularly the complex interplay between opportunistic infections and potential metabolic susceptibility, remains poorly understood.<br><br>CASE PRESENTATION: We report a fatal case of NHHA in a 58-year-old male with diffuse large B-cell lymphoma (DLBCL) following glofitamab-based chemo-immunotherapy. The patient developed sudden onset altered mental status with extreme hyperammonemia (peak blood ammonia 638.9&#x2009;&#xb5;mol/L) despite preserved liver function. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Ureaplasma urealyticum. Furthermore, post-mortem whole-exome sequencing (WES) identified a heterozygous variant of SLC25A13 (NM_014251.3:c.2&#x2009;T&#x2009;>&#x2009;C). As biochemical confirmation of citrin deficiency was not available, the clinical significance of this variant remains uncertain, though it may represent a contributory metabolic susceptibility factor. Despite aggressive ammonia-lowering strategies, including continuous renal replacement therapy (CRRT) and targeted antibiotics, the patient succumbed to fulminant cerebral edema.<br><br>CONCLUSION: This case highlights the Ureaplasma urealyticum infection as a critical precipitant of fatal NHHA following glofitamab therapy, occurring in the background of possible genetic metabolic susceptibility (an unverified heterozygous SLC25A13 variant of uncertain functional significance). These findings underscore the critical need for early blood ammonia monitoring and rapid mNGS screening in immunocompromised patients with unexplained encephalopathy. We propose a structured diagnostic algorithm to expedite the recognition and management of this reversible yet life-threatening condition.}, }
@article {pmid42011017, year = {2026}, author = {Sadia, H and Amin, A and Ahmed, I}, title = {Metagenomic and Phenotypic Insights Into Biofilm-Forming Pathogens in Patients With Nosocomial Sepsis.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e8989667}, pmid = {42011017}, issn = {2314-6141}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Metagenomics ; *Sepsis/microbiology/genetics ; *Cross Infection/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; Phenotype ; *Bacteria/genetics/pathogenicity/classification ; }, abstract = {Biofilm-related infections significantly contribute to bacterial diseases, with estimates suggesting that at least 80% of such infections are associated with biofilms. These infections often involve opportunistic pathogens, which not only influence the type of infection but also impact the microenvironment by interacting with other polymicrobial pathogens, thereby altering microbial diversity within the infection site. The present study was designed to assess potential changes in bacterial communities across various infection types. The 50 samples were collected and pooled from different anatomical locations: II-H1 (calf), ul-H2 (thighs), ft-H3 (upper leg), ct-H4 (chest), and Ca-H5 (catheter). The 16S rDNA sequencing was performed on 10 representative samples using the Sanger method to identify bacterial taxa, whereas the metagenomic analysis was conducted on the Illumina MiSeq platform (Illumina, Inc., San Diego, California). Sanger sequencing identifying several bacterial strains including Bacterium MS-AsIII-61, Bacterium HB33-1, Mammaliicoccus sciuri SSB38, multiple Staphylococcus species (S. aureus DA101 and S8, Staphylococcus sp. C0021-01R and TSA25S, S. cohnii FC2265, and S. saprophyticus A), and Enterobacter hormaechei D15. The metagenomics analysis revealed variations and diversity in the different location across the organ by relative abundance of 5 bacterial phyla and 38 species. The Proteobacteria phylum was the most abundant phylum across all sites, with the highest prevalence observed in Ca-H5, followed by ul-H2, ct-H4, II-H1, and ft-H3 in the decreasing order. In contrast, the Bacteroidetes phylum exhibited the highest abundance in ft-H3. Catheter-associated infections (Ca-H5 site) show a homogeneous ARG profile, dominated by genes supporting biofilm formation and persistence. MSA samples reflect diversity in methicillin and multidrug resistance genes, consistent with surgical-site and opportunistic infections. Trypto samples may represent an environmental or experimental condition leading to alternative ARG expression, highlighting site- or condition-specific variations. The different virulence factor responsible for the boost in the establishment of biofilms in these pathogens includes, surface adhesion proteins, increasing resilience to environmental, efflux pumps, quorum-sensing regulators, stresses, and antibiotic treatments. The study demonstrates the dynamic nature and impact of biofilm-related infections at anatomical sites. It also focused on biofilm-associated infections at surgical sites, their progression into chronic conditions, and the corresponding treatment patterns. The integration of metagenomic analysis with phenotypic studies provided deeper insights into the roles of key genes and their mechanisms in biofilm formation.}, }
@article {pmid42011181, year = {2026}, author = {Li, Z and Zhang, Y and Xu, H and Wang, D and Yuan, L and Su, N and Lu, H and Li, W}, title = {Prosthetic Joint Infection Caused by Staphylococcus argenteus: mNGS-Guided Diagnosis and Whole-Genome Characterization of an ST2250 Strain.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {594406}, pmid = {42011181}, issn = {1178-6973}, abstract = {BACKGROUND: Staphylococcus argenteus, a member of the Staphylococcus aureus complex, has increasingly been recognized as a human pathogen but is frequently misidentified as S. aureus in routine clinical laboratories. Reports of prosthetic joint infection (PJI) caused by this species remain rare.<br><br>METHODS: We describe a case of delayed-onset PJI in a 71-year-old woman following total knee arthroplasty. Repeated conventional cultures were negative after empirical vancomycin therapy. Metagenomic next-generation sequencing (mNGS) of wound exudate detected S. argenteus, which guided extended culture and subsequent isolation of low-abundance colonies. Species identification was confirmed by whole-genome sequencing (WGS), multilocus sequence typing (MLST), and reinterpretation of MALDI-TOF MS results. Antimicrobial susceptibility testing (AST) was performed and compared with WGS-based resistance prediction. Phylogenetic analysis was conducted using 452 publicly available S. argenteus genomes.<br><br>AIM: This study aimed to describe the clinical diagnosis, microbiological identification, and genomic characterization of a Staphylococcus argenteus strain causing prosthetic joint infection.<br><br>RESULTS: The isolate was identified as sequence type ST2250 and lacked the staphyloxanthin operon, consistent with the non-pigmented phenotype. WGS and phenotypic AST showed 100% concordance across 11 clinically relevant antibiotics. Phylogenomic analysis revealed that the strain clustered closely with Southeast Asian lineages. Following targeted therapy with intravenous vancomycin and surgical wound management, the patient showed rapid clinical improvement with resolution of local inflammation and complete wound healing.<br><br>CONCLUSION: This is the first confirmed case of S. argenteus PJI in Suzhou, China. The case highlights the diagnostic value of mNGS in culture-negative PJI, the importance of molecular tools for correctly differentiating S. argenteus from S. aureus, and the potential of WGS to support resistance prediction for rare staphylococcal pathogens.}, }
@article {pmid42011762, year = {2026}, author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL}, title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.}, journal = {Zoological research}, volume = {47}, number = {2}, pages = {606-620}, doi = {10.24272/j.issn.2095-8137.2025.134}, pmid = {42011762}, issn = {2095-8137}, mesh = {Animals ; *Genetic Variation ; *Virome ; *Bacteriophages/genetics/classification ; *Mammals/virology ; *Animals, Zoo/virology ; Phylogeny ; *Viruses/genetics/classification ; }, abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.}, }
@article {pmid42011768, year = {2026}, author = {Oba, S and Okuno, K and Watanabe, S and Yamamoto, Y and Takaoka, A and Hanaoka, M and Yamauchi, S and Kagawa, H and Tokunaga, M and Ban, D and Kinugasa, Y}, title = {Intratumoral fungal burden of Candida tropicalis as a novel prognostic biomarker for recurrence and mortality in colorectal cancer.}, journal = {Cancer}, volume = {132}, number = {8}, pages = {e70408}, pmid = {42011768}, issn = {1097-0142}, support = {JP23K19499//Japan Society for the Promotion of Science/ ; JP24K18571//Japan Society for the Promotion of Science/ ; 2023DI008//Kobayashi Foundation for Cancer Research/ ; }, mesh = {Humans ; *Candida tropicalis/isolation &amp; purification/genetics ; *Colorectal Neoplasms/microbiology/mortality/pathology ; Prognosis ; *Neoplasm Recurrence, Local/microbiology/pathology ; Male ; Female ; Middle Aged ; Aged ; Biomarkers, Tumor ; }, abstract = {BACKGROUND: The crucial role of gut fungus dysbiosis in the carcinogenesis and progression of colorectal cancer (CRC) has recently garnered increasing attention. In this study, the potential role of Candida tropicalis, commensal gut fungi, in predicting CRC prognosis was investigated.<br><br>METHODS: A total of 304 frozen surgical cancer tissue specimens were obtained from patients with CRC and evaluated the intratumoral C. tropicalis burden using quantitative polymerase chain reaction assays. Mycobial composition and diversity analyses were performed by analyzing publicly available metagenomic datasets.<br><br>RESULTS: Metagenomic dataset analysis revealed significant differences in fungal composition and diversity of Candida species among adjacent normal and CRC tissues. The 5-year recurrence-free survival and disease-specific survival rates were significantly worse in patients with a high intratumoral C. tropicalis burden than in those with a low burden (78.0% vs. 86.6%; p&#xa0;=&#xa0;.03 and 88.9% vs. 98.0%; p&#xa0;<&#xa0;.01, respectively). Furthermore, multivariate Cox regression analysis revealed that increased intratumoral C. tropicalis burden was a significant independent predictor for recurrence-free survival (hazard ratio [HR]: 1.92; 95% CI, 1.08-3.44; p&#xa0;=&#xa0;.03) and disease-specific survival (HR: 4.29; 95% CI, 1.36-13.5; p&#xa0;=&#xa0;.03).<br><br>CONCLUSIONS: These results have demonstrated, possibly for the first time, the potential of intratumoral C. tropicalis burden as a novel prognostic biomarker for recurrence and mortality in patients with CRC.}, }
@article {pmid42012066, year = {2026}, author = {Guo, R and Gao, J and Zhang, C and Chang, Z and Sun, Y}, title = {Multi-Omics Analysis Reveals Coordinated Adaptations in Genes, Metabolism, and Gut Microbiota Underpinning Herbivory in Lordiphosa Flies.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70110}, pmid = {42012066}, issn = {1749-4877}, support = {202401BC070011//Yunnan Fundamental Research Projects/ ; 32060112//Natural Science Foundation of China/ ; }, abstract = {Herbivorous insects are among the most ecologically successful animal groups. However, the adaptive mechanisms that allow them to exploit plant hosts, which are often nutrient-poor (low in simple sugars, high in structural carbohydrates) and defended by toxic secondary metabolites, are not fully resolved. Here, we investigated the evolutionary basis of herbivory in Lordiphosa clarofinis, a drosophilid species feeding on living plant tissues, using multi-omics approaches. Behavioral experiments revealed a strong oviposition preference for Galinsoga parviflora (a host rich in secondary metabolites), accompanied by elevated expression of chemosensory genes linked to host discrimination. Comparative genomic analyses revealed lineage-specific expansions of gene families associated with detoxification (e.g., cytochrome P450s) and carbohydrate metabolism, alongside positive selection on genes involved in fatty acid utilization and glycogen synthesis. Transcriptomic data showed differential expression of energy metabolism pathways in response to low-sugar plant diets, with upregulation of genes linked to lipid oxidation and gluconeogenesis. Metagenomic profiling of gut microbiota identified key taxa (e.g., Bacteroidetes) capable of degrading plant polysaccharides and synthesizing essential vitamins, potentially complementing host nutritional intake. Our results demonstrate that herbivory in L. clarofinis is associated with coordinated genomic, transcriptional, and microbial changes, rather than being attributable to a single adaptive mechanism. This study highlights how multi-level biological features covary with plant-based feeding and provides a framework for investigating the complex evolutionary and ecological correlates of herbivory in insects.}, }
@article {pmid42012165, year = {2026}, author = {Werner, A and Chibani, CM and Schmitz, RA}, title = {Navigating prokaryotic viral genome analysis from metagenomic data.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0124925}, pmid = {42012165}, issn = {2379-5077}, support = {031B0851B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; SCHM1052/26-1, SCHM1052/26-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenomics/methods ; *Genome, Viral ; Archaea/virology ; *Archaeal Viruses/genetics ; Bacteria/virology ; Computational Biology/methods ; *DNA Viruses/genetics ; }, abstract = {Viruses play crucial roles in microbial ecosystems, yet viromic analysis remains challenging due to the field's complexity and rapid evolution. This minireview supports non-specialists through the evolving landscape of viromics, focusing on the analysis of bacterial and archaeal DNA viruses from metagenomic data. We address major challenges, including viral diversity, methodological biases, and the overwhelming array of available tools and pipelines. While describing a typical viromic workflow, we provide users with background information for each of the steps from data acquisition, preprocessing, and quality control to viral characterization and common downstream analyses. The included references and resources will provide users with the information needed to confidently start their own virome analysis.}, }
@article {pmid42012213, year = {2026}, author = {Couto-Rodriguez, M and Danko, DC and Wells, HL and Rey, S and Jirau Serrano, X and Fidler, G and Papciak, J and Combs, PF and Plourde, A and Augenbraun, M and Mason, CE and Otto, C and O'Hara, NB and Nagy-Szakal, D}, title = {Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0202625}, pmid = {42012213}, issn = {2165-0497}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Urinary Tract Infections/microbiology/diagnosis/urine ; *Bacteria/genetics/isolation &amp; purification/classification ; Sensitivity and Specificity ; Metagenomics/methods ; *Urine/microbiology ; }, abstract = {Urinary tract infections (UTIs) are diagnosed based on symptoms and confirmed by urine culture, despite its limitations in sensitivity. False-negative cultures can lead to inappropriate antimicrobial use or urosepsis in high-risk patients. Next-generation sequencing (NGS)-based metagenomics offers a comprehensive and precise alternative but is rarely applied clinically. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for pathogen detection in urine. Remnant clinical and spiked urine samples underwent extraction, metagenomic library preparation, and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning to identify pathogens and resistance markers. BIOTIA-DX was intentionally designed and trained to increase stringency and reduce false positive detection of urogenital commensals or opportunistic microbes present at colonization levels. Internal controls ensured standardized, high-stringency results. The assay was validated on 1,470 urine specimens evaluating over 14.5k analytes. The clinical validation achieved a 97.2% sensitivity and 99.6% specificity with a limit of detection (LoD) of <15,000 CFU/mL for most bacterial species and <5,000 CFU/mL for fungal species. Discordant results were reconciled by target-specific qPCR or 16S Sanger sequencing, and 87% of the NGS results were concordant with the comparator. A subset of 332 clinical specimens was tested and validated for antimicrobial resistance (AMR). sul and blaSHV genes were commonly associated with Escherichia coli and Klebsiella pneumoniae, while cfxA was found in Prevotella and Pseudomonas spp. detected by BIOTIA-ID. Overall, these data demonstrate that BIOTIA-ID is a comprehensive, highly accurate end-to-end diagnostic assay with notable advantages over current culture-based diagnostics.IMPORTANCEUrinary tract infections (UTIs) are among the most common infections, yet current diagnostic methods, including urine culture, often fail to detect pathogens accurately, leading to delayed treatment and inappropriate antimicrobial use. Clinical metagenomics offers a powerful alternative, especially in complicated cases. BIOTIA-ID is a validated, clinical-grade next-generation sequencing (NGS)-based assay that provides highly accurate pathogen identification and antimicrobial resistance profiling. By incorporating machine learning and stringent quality controls, BIOTIA-ID minimizes false positives and enhances diagnostic precision. Our study demonstrates its superior performance over culture, with potential to improve UTI diagnostics, guide targeted therapy, and support antimicrobial stewardship. The implementation of urine metagenomic diagnostics could support recurrent and complicated UTI patient management, providing a more reliable alternative to traditional methods.}, }
@article {pmid42012671, year = {2026}, author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC}, title = {Correction to: Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, doi = {10.1007/s00284-026-04870-w}, pmid = {42012671}, issn = {1432-0991}, }
@article {pmid42012700, year = {2026}, author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J}, title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.}, journal = {Journal of clinical immunology}, volume = {46}, number = {1}, pages = {}, pmid = {42012700}, issn = {1573-2592}, support = {23141901900//the Shanghai Science and Technology Innovation Action Plan&#xff0c;experimental animal research&#xa0;project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; }, abstract = {Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4+ T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4+ T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.}, }
@article {pmid42012708, year = {2026}, author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P}, title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.}, journal = {European journal of nutrition}, volume = {65}, number = {4}, pages = {}, pmid = {42012708}, issn = {1436-6215}, abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood.<br><br>OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions.<br><br>METHODS: Screening participants with a positive faecal immunochemical test at ages 55&#x2013;77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis.<br><br>RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend&#x2009;=&#x2009;0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10&#xa0;g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in &#x3b1;- and &#x3b2;-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria.<br><br>CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00394-026-03960-6.}, }
@article {pmid42012901, year = {2026}, author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T}, title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {17}, pages = {13990-13997}, pmid = {42012901}, issn = {1520-5118}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sweetening Agents/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Thiazines/metabolism ; Intestinal Barrier Function ; Caco-2 Cells ; Butyrates/metabolism ; Child ; }, abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.}, }
@article {pmid42013836, year = {2026}, author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and ,  and ,  and Korten, I and Xavier, RJ}, title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {925-941.e6}, doi = {10.1016/j.chom.2026.03.019}, pmid = {42013836}, issn = {1934-6069}, mesh = {Humans ; *Microbiota/genetics/drug effects ; Infant ; Haemophilus influenzae/genetics/growth &amp; development/drug effects ; *Cystic Fibrosis/microbiology/therapy ; Metagenomics ; *Nose/microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Saline Solution, Hypertonic/pharmacology ; }, abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.}, }
@article {pmid42013844, year = {2026}, author = {Bargheet, A and Bø, GH and Hetland, MAK and Justine, M and Moyo, SJ and Löhr, IH and Blomberg, B and Langeland, N and Klingenberg, C and Pettersen, VK}, title = {Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102752}, pmid = {42013844}, issn = {2666-3791}, mesh = {Humans ; *Probiotics/pharmacology/administration &amp; dosage ; *Bifidobacterium/metabolism/drug effects/physiology ; Infant ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metabolome ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; Male ; Female ; Infant, Newborn ; }, abstract = {Early-life probiotics that strengthen gut resilience in infants are a promising strategy to combat the global emergency of antibiotic resistance. Still, their effects on antibiotic-resistant opportunistic pathogens, i.e., pathobionts, remain unclear. We evaluate the effects of probiotic supplementation in 152 full-term Tanzanian infants enrolled in the ProRIDE trial. Oral probiotics during the first 4 weeks of life increase gut colonization by Bifidobacterium species, while suppressing pathobionts, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Integrated metagenomics and metabolomics show that probiotics reduce resistome load and mobilome richness at 6 weeks, accompanied by concurrent shifts in the fecal metabolome. Specifically, the intervention increases lactate and pyruvate and reduces cross-feeding pathways that lead to propionate and butyrate, which partly explains the reduction in ESBL-E carriage. Our study documents putative pathways by which probiotic-driven Bifidobacterium colonization modulates the infant gut toward a lower level of antibiotic resistance.}, }
@article {pmid42013850, year = {2026}, author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB}, title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102761}, pmid = {42013850}, issn = {2666-3791}, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Saliva/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; *Mouth/microbiology ; Male ; Metagenome ; Middle Aged ; *Microbiota ; Dysbiosis/microbiology ; Aged ; }, abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.}, }
@article {pmid42013936, year = {2026}, author = {Nie, Z and Wang, Y and Ya, T and Dang, T and Wang, X and Liu, C and Hu, Z and Wang, X}, title = {Rapid recovery from starvation stress in low-temperature anammox system: extracellular polymeric substances protection and dissimilatory nitrate reduction to ammonium synergistically promote nitrogen metabolism recovery.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134677}, doi = {10.1016/j.biortech.2026.134677}, pmid = {42013936}, issn = {1873-2976}, mesh = {*Nitrogen/metabolism ; *Nitrates/metabolism ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Stress, Physiological ; *Cold Temperature ; *Extracellular Polymeric Substance Matrix/metabolism ; }, abstract = {Understanding the response of the anammox system to starvation disturbances under low-temperature conditions is of great importance. In this study, we explored the performance, microbial community structure, and microbial metabolic in a low-temperature anammox system following a 15-day starvation period with the aim of identifying their response and recovery mechanisms after starvation stress. It was found that the low-temperature anammox system was able to regain its initial performance within 5 days. After system stabilization, the total nitrogen removal efficiency increased from 85% to 88%. The upregulation of hydrazine synthase (hzs) and hydrazine dehydrogenase (hdh) genes involved in anammox process was identified as part of a response mechanism of anammox bacteria. During the starvation period, the increased secretion of extracellular polymeric substances (EPS) served as a protective mechanism. Additionally, the synergistic interaction between dissimilatory nitrate reduction to ammonium (DNRA) bacteria and anammox bacteria contributed to the enhancement of nitrogen removal efficiency. The EPS-mediated synergistic interaction between anammox bacteria and heterotrophic bacteria was conducive to the survival of microorganisms during starvation and their prompt recovery upon the restoration of substrate supply.}, }
@article {pmid42013937, year = {2026}, author = {Zhu, Y and Hou, Q and Hu, F and Zhuang, G and Ma, A}, title = {Functional activators-facilitated FeS transformation enhances petroleum hydrocarbon degradation by promoting functional microbial proliferation.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134631}, doi = {10.1016/j.biortech.2026.134631}, pmid = {42013937}, issn = {1873-2976}, mesh = {*Petroleum/metabolism ; Biodegradation, Environmental/drug effects ; *Hydrocarbons/metabolism ; *Ferrous Compounds/metabolism ; *Bacteria/metabolism/growth &amp; development ; Reactive Oxygen Species/metabolism ; }, abstract = {Bioremediation of total petroleum hydrocarbon (TPH)-contaminated sites often faces a major challenge in sulfur-rich environments, where ferrous sulfide (FeS) immobilizes pollutants and sharply reduces their bioavailability, thereby stalling remediation. This study demonstrates that the bottleneck can be overcome by applying a composite functional activator to induce a targeted shift of the site microenvironment. The activator first selectively suppresses competing iron- and sulfur-reducing bacteria, reducing their relative abundance by 92%, thereby shifting the microbial community structure. Concurrently, a controlled decrease in local pH converts FeS from a pollutant sink into an active catalyst. The transformed FeS then activates molecular oxygen (O2) to generate reactive oxygen species (•OH and SO4[•-]), which chemically mobilize and pre-oxidize TPH, producing a "priming effect". This priming effect subsequently restructures the indigenous microbial community. Consequently, under optimized niche conditions and increased nutrient availability, TPH-degrading Bacillus populations expand significantly in the remediation environment: their relative abundance increases by 57%, and their niche breadth widens by 34%. Metagenomic analysis confirms upregulation of genes related to pollutant degradation, substance transport, and energy metabolism, strengthening the metabolic network. Ultimately, the integrated chemical-biological process achieves 90% TPH degradation. This study realizes the functional shift of FeS from remediation barrier to degradation booster, offering an innovative chemo-biological synergistic strategy and engineering paradigm for long-term stable remediation of TPH-contaminated sites.}, }
@article {pmid42014006, year = {2026}, author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W}, title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.}, journal = {International journal of biological macromolecules}, volume = {362}, number = {}, pages = {152109}, doi = {10.1016/j.ijbiomac.2026.152109}, pmid = {42014006}, issn = {1879-0003}, mesh = {Animals ; *Spleen/metabolism/drug effects/immunology ; *Polysaccharides/pharmacology ; *Cyclophosphamide/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Metabolomics/methods ; Cytokines/metabolism ; Immunosuppression Therapy ; Male ; *Immunologic Factors/pharmacology ; *Metabolome/drug effects ; Immunosuppressive Agents ; }, abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.}, }
@article {pmid42014453, year = {2026}, author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T}, title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1233-1244}, pmid = {42014453}, issn = {2058-5276}, support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, mesh = {*Metagenomics/methods/standards ; *Shotgun Sequencing ; *Bacteria/genetics/classification ; *Benchmarking ; Computational Biology/methods ; Metagenome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.}, }
@article {pmid42014512, year = {2026}, author = {Vijayasimha, M and Srikanth, M and Trivedi, NS}, title = {From Diagnostic Accuracy to Decision-Grade Respiratory Nanopore Metagenomics: Minimum Standards, Stewardship Endpoints, and Equitable Implementation.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42014512}, issn = {1432-0991}, }
@article {pmid42014682, year = {2026}, author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI}, title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42014682}, issn = {2041-1723}, support = {F30 DK142304/DK/NIDDK NIH HHS/United States ; DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Transcriptome ; *Gene Expression Profiling/methods ; Bacteria/genetics/classification ; *Metagenomics/methods ; Germ-Free Life ; }, abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.}, }
@article {pmid42014730, year = {2026}, author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W}, title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42014730}, issn = {2052-4463}, support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; }, mesh = {*Kelp/microbiology ; Aquaculture ; *Microbiota ; *Metagenome ; Phylogeny ; Bacteria/classification/genetics ; Archaea/genetics/classification ; }, abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.}, }
@article {pmid42014993, year = {2026}, author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C}, title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42014993}, issn = {1471-2180}, abstract = {UNLABELLED: Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05043-2.}, }
@article {pmid42015023, year = {2026}, author = {Peng, Z and He, H and Zhou, S and Qiao, L and Wang, Q and Li, M and Zhao, Y}, title = {Rhino-orbito-cerebral Rhizopus delemar infection in a patient with anti-melanoma differentiation-associated-5-positive dermatomyositis diagnosed by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42015023}, issn = {1471-2334}, abstract = {BACKGROUND: Rhino-orbito-cerebral mucormycosis, caused by pathogens such as Rhizopus delemar, is a life-threatening opportunistic infection primarily affecting immunosuppressed individuals. Anti-melanoma differentiation-associated protein 5-positive dermatomyositis (MDA5+ DM) is a distinct subtype of DM associated with interstitial lung disease (ILD) and high mortality. Fungal co-infections in anti-MDA5+ DM, particularly mucormycosis, are rarely reported. CASE PRESENTATION: We report a case of rhino-orbito-cerebral mucormycosis caused by Rhizopus delemar in a patient with anti-MDA5+ DM. The patient was receiving high-dose glucocorticoids and immunosuppressive therapy for rapidly progressive ILD, and later she developed progressive neurological symptoms, palatal ulceration with black eschar, and periorbital swelling. Metagenomic next-generation sequencing (mNGS) of blood subsequently identified Rhizopus delemar, and the diagnosis was further supported by cerebrospinal fluid mNGS. Antifungal therapy was adjusted promptly after pathogen identification. Despite aggressive treatment, the infection progressed rapidly with central nervous system involvement. CONCLUSIONS: This case highlights the heightened susceptibility to invasive mucormycosis in patients with anti-MDA5+ DM, likely exacerbated by immunosuppressive therapy. Early diagnosis using mNGS and prompt initiation of targeted antifungal therapy are critical in managing such co-infections. Clinicians should maintain a high index of suspicion for invasive fungal infections in immunosuppressed anti-MDA5+ DM patients presenting with non-specific neurological or sinus symptoms.}, }
@article {pmid42015434, year = {2026}, author = {Wang, S and Deng, F}, title = {Clinical Features and Coinfection Factors of Severe Community-Acquired Pneumonia with &lt;em&gt;Mycoplasma Pneumoniae&lt;/em&gt; in Children.}, journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP}, volume = {36}, number = {4}, pages = {483-488}, doi = {10.29271/jcpsp.2026.04.483}, pmid = {42015434}, issn = {1681-7168}, mesh = {Humans ; Male ; *Community-Acquired Pneumonia/microbiology ; Female ; *Coinfection/microbiology/epidemiology/diagnosis ; Retrospective Studies ; Child, Preschool ; Child ; *Pneumonia, Mycoplasma/diagnosis/epidemiology/microbiology ; *Mycoplasma pneumoniae/isolation &amp; purification ; China/epidemiology ; *Community-Acquired Infections/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Adolescent ; Infant ; }, abstract = {OBJECTIVE: To characterise the clinical features of children with severe community-acquired pneumonia (CAP) associated with Mycoplasma pneumoniae (Mp) infection and to identify factors influencing polymicrobial coinfections.<br><br>STUDY DESIGN: A descriptive study. Place and Duration of the Study: Department of Internal Medicine, Anhui Provincial Children's Hospital, Anhui, China, from January to December 2023.<br><br>METHODOLOGY: A retrospective cohort study was conducted on 207 hospitalised children aged <16 years with confirmed CAP who underwent BALF testing due to severe symptoms, antibiotic-unresponsive fever, or unclear aetiology. Those with chronic comorbidities were excluded. BALF pathogens were detected via multiplex PCR and metagenomic next-generation sequencing (mNGS). Patients were divided into Mp mono-infection and coinfection groups; demographic, clinical, and laboratory data were compared, and logistic regression analysis was performed to identify factors associated with coinfection.<br><br>RESULTS: The coinfection group was significantly younger (4.12 &#xb1; 2.83 vs. 6.56 &#xb1; 2.47 years, p = 0.013) and had longer hospital stays (11.21 &#xb1; 4.26 vs. 9.90 &#xb1; 3.68 days, p = 0.049) than the mono-infection group. Inflammatory markers differed significantly: the coinfection group had higher IL-6 (28.64 &#xb1; 8.03 vs. 15.86 &#xb1; 14.21 pg/mL, p <0.001), but lower IL-2R (1774.15 &#xb1; 104.18 vs. 2157.39 &#xb1; 382.76 U/mL, p <0.001) and ESR (30.31 &#xb1; 14.79 vs. 40.08 &#xb1; 13.66 mm/h, p <0.001). Logistic regression confirmed IL-6 (p <0.001), IL-2R (p <0.001), and complications (p = 0.0281) as independent factors associated with coinfections, while chest CT findings showed no correlation (p >0.05).<br><br>CONCLUSION: Younger age, elevated IL-6 levels, reduced IL-2R levels, and the presence of complications are closely correlated with polymicrobial coinfections in children with severe Mp-associated CAP.<br><br>KEY WORDS: Pneumonia, Mycoplasma pneumoniae, Paediatrics, Coinfection, Metagenomic sequencing, Clinical characteristics.}, }
@article {pmid42015472, year = {2026}, author = {Song, M and Zhang, Z and Huang, H and Zou, Z and Wen, S and Cui, Y and Liu, S}, title = {Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951840}, pmid = {42015472}, issn = {1941-5923}, mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Spinal/diagnosis ; *Renal Dialysis ; *Metagenomics/methods ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Antitubercular Agents/therapeutic use ; }, abstract = {BACKGROUND Spinal tuberculosis is difficult to diagnose in patients undergoing maintenance hemodialysis (MHD) because of immunosuppression, atypical clinical manifestations, and the limited sensitivity of conventional microbiological assays. Rapid and accurate pathogen identification is essential to distinguish spinal tuberculosis from other causes of vertebral destruction, including metastatic malignancy and bacterial spondylitis. This report aims to illustrate the diagnostic value of capture-based targeted sequencing for detecting Mycobacterium tuberculosis in extrapulmonary infection when routine tests and metagenomic next-generation sequencing (mNGS) yield inconclusive or misleading results. CASE REPORT A 64-year-old woman with end-stage renal disease secondary to IgA nephropathy, receiving long-term MHD, presented with progressive low back pain. Imaging revealed multilevel vertebral involvement with pathological fractures, raising suspicion of metastatic disease or infectious spondylitis. Histopathological examination demonstrated granulomatous inflammation, while acid-fast staining and routine cultures were negative. Initial mNGS of spinal tissue identified Staphylococcus aureus, leading to targeted antibacterial therapy. Although inflammatory markers declined, the patient's symptoms worsened and pancytopenia developed. Subsequent analysis of spinal pus using metagenomic capture (MetaCAP)-based targeted sequencing detected the Mycobacterium tuberculosis complex with high confidence. Anti-tuberculosis therapy was promptly initiated, resulting in rapid clinical improvement and radiological resolution. CONCLUSIONS This case shows the limitations of conventional microbiological methods and unbiased mNGS in diagnosing extrapulmonary tuberculosis in immunocompromised patients. Capture-based targeted sequencing offers enhanced sensitivity for Mycobacterium tuberculosis detection and may facilitate timely diagnosis and appropriate treatment of spinal tuberculosis in patients undergoing MHD.}, }
@article {pmid42016528, year = {2026}, author = {Xu, H and Guo, J and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H and Shao, X}, title = {Metagenomics reveals the functional profiles of soil microorganisms and nutrient cycling under long-term grass vegetation cropping.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100583}, pmid = {42016528}, issn = {2666-5174}, abstract = {Soil microbes are crucial for biogeochemical cycles and their functional potential is greatly affected by ecosystem management. Yet, how does grass vegetation affect the composition of soil microbial communities and the abundance of key nutrient-cycling functional genes? In this study, based on an experimental plot built for 7 years, the long - term influence of two grass vegetation types (Carex breviculmis and Festuca arundinacea Schreb) on soil microbial community structure and C, N, P, and S cycles were explored by metagenomics. The results showed that both plants significantly increased the diversity and richness of soil bacteria and fungi, and the abundance of Pseudomonadota and Ascomycota in Carex breviculmis increased significantly, while those of Actinomycetota and Mucoromycota decreased. Microbial network analysis shows that Carex breviculmis forms a highly modular, low - complexity microbial interaction network, indicating specialized and stable microbial community functions. Conversely, Festuca arundinacea Schreb has a more complex and less modular network, suggesting enhanced microbial interactions. Carex breviculmis significantly increased the abundance of genes related to carbon fixation (fumA/B, pps, ppc) and phosphorus mineralization (phoR/P/B, phnF/P), and also enhanced soil denitrification potential. In contrast, Festuca arundinacea Schreb showed a enrichment of soil nitrogen fixation genes (nifh). Additionally, growing Carex breviculmis and Festuca arundinacea Schreb induced the growth of sulfur - oxidizing bacteria (e.g., Thiobacillus), enriching the abundance of sulfur - metabolism - related genes (apr, sox). Genes related to microbial C, N, P, and S cycles are positively correlated with soil pH, available P, and alkali-hydrolyzed nitrogen. Overall, this study reveals how different grass vegetation types regulate microbial community structure and functional gene abundance to drive nutrient cycling differentiation in grassland ecosystems, thereby providing a theoretical basis for optimizing grass vegetation configuration in managed and restored grasslands to enhance soil ecological functions.}, }
@article {pmid42016568, year = {2026}, author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ}, title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101401}, pmid = {42016568}, issn = {2665-9271}, abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.}, }
@article {pmid42016597, year = {2026}, author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG}, title = {Investigating the role of bacterial raw milk community members in chlorate reduction.}, journal = {Access microbiology}, volume = {8}, number = {4}, pages = {}, pmid = {42016597}, issn = {2516-8290}, abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.}, }
@article {pmid42016660, year = {2026}, author = {Qu, Y and Liu, Y and Zhou, X and Xu, P and Wang, L}, title = {Polymicrobial Pasteurella multocida-Anaerobic Coinfection Followhing a Cat Bite: Limb Salvage Through Metagenomic Next-Generation Sequencing-Guided Diagnosis and Multidisciplinary Management.}, journal = {Clinical case reports}, volume = {14}, number = {3}, pages = {e72304}, pmid = {42016660}, issn = {2050-0904}, abstract = {Successful management of a Pasteurella multocida and polymicrobial infection following a cat bite on the left leg entailed debridement, split-thickness skin grafting with vacuum-sealing drainage, and targeted antibiotic treatment. This approach enabled successful incorporation of the skin graft, preserving the limb and eliminating the necessity for amputation.}, }
@article {pmid42016731, year = {2026}, author = {Chen, G and Tang, S and Wang, H and Liang, Z and Lv, X and Han, J and Ni, L}, title = {Integration of volatile flavor metabolomics and metagenomics reveals microbial-enzymatic pathways governing key aromatic volatile compound biosynthesis in Hongqujiu fermentation.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103811}, pmid = {42016731}, issn = {2590-1575}, abstract = {The anabolic pathways of key volatile flavor compounds (VFCs) in Hongqujiu (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an integrated multi-omics strategy combining metabolomics, flavoromics and metagenomics. The results demonstrated that the ethanol content, titratable acidity, amino nitrogen and higher alcohols increased progressively throughout fermentation. Quantitative flavor metabolomic profiling identified 18 key VFCs, maining comprising ethyl esters, acetate esters and higher alcohols. Metagenomic sequencing revealed that Weissella, Lactobacillus, Saccharomyces, Aspergillus, Talaromyces and Monascus were the predominant microbal genera throughout HQJ fermentation. Functional gene annotation further indicated that key enzymes involved in flavor metabolism are primarily associated with Lactobacillus, Aspergillus, Talaromyces, Saccharomyces, Cyberlindnera and Monascus. Overall, this study elucidates the microbial-enzymatic basis of VFC biosynthesis and establishes a comprehensive flavor metabolic framework for HQJ fermentation, providing a theoretical foundation for aroma quality improvement.}, }
@article {pmid42016742, year = {2026}, author = {Funada Barbosa, MR and Ramos, EDSF and Villanova, F and Oliveira Silva, RL and Garcia, SC and de Araújo, RS and Mendes-Correa, MC and Tozetto-Mendoza, TR and Zhang, W and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E}, title = {Exploring the Genomics of Marnaviridae Family: Identification, Characterization, and Taxonomic Implications.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {7188239}, pmid = {42016742}, issn = {1687-918X}, abstract = {In this study, we characterized sequences similar to Marnaviridae obtained from water samples in the state of São Paulo, Brazil. Sixteen complete or nearly complete genomes were determined, all of them positive-sense single-stranded RNA, with lengths between 7074 and 10,198 base pairs, containing one or two open reading frames (ORFs). The amino acid sequences derived from the ORFs showed similarity and protein domains typical of the Marnaviridae family. Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) revealed clusters closely related to viruses that have not yet been classified by the International Committee on Taxonomy of Viruses (ICTV). Some sequences showed proximity to established genera such as Salicharnavirus, Locarnavirus, and Labynarvirus, while others formed three distinct clades, suggesting the presence of new genera. Furthermore, one sequence displayed an RdRp identity of less than 90% and a capsid identity of less than 75%, indicating that it represents a novel species related to Marnaviridae. These findings expand current knowledge of Marnaviridae diversity, contributing to a better understanding of evolutionary relationships and emphasizing the need for taxonomic reorganization.}, }
@article {pmid42016964, year = {2026}, author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X}, title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73260}, pmid = {42016964}, issn = {2045-7758}, abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.}, }
@article {pmid42016980, year = {2026}, author = {De Panis, D and Priotto, O and Padró, J}, title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73262}, pmid = {42016980}, issn = {2045-7758}, abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.}, }
@article {pmid42017035, year = {2026}, author = {Yang, Y and Ren, Y and Ma, T and An, J and Jin, S and Dong, Y}, title = {Research advances in the role of circulating microorganisms in gastrointestinal tumors (Review).}, journal = {Molecular and clinical oncology}, volume = {24}, number = {6}, pages = {40}, pmid = {42017035}, issn = {2049-9469}, abstract = {Gastrointestinal tumors are common malignant tumors of the digestive system, which globally threaten human health. Notably, it has been discovered that blood and other circulating body fluids are not completely sterile; instead, they harbor complex and dynamic microbial DNA and signatures [circulating microorganisms (CM)]. These microorganisms primarily originate from the microbial translocation (including bacterial fragments, DNA and metabolites) through a compromised intestinal barrier, and are closely associated with the initiation and progression of gastrointestinal tumors, thus providing novel perspectives for early tumor diagnosis and prognosis. Although there is currently no evidence that CM can directly cause cancer, their metabolites and exosomes may contribute to tumor microenvironment remodeling. On one hand, they activate pattern recognition and inflammatory signaling pathways, such as Toll-like receptor/signal transducer and activator of transcription, potentially inducing and maintaining low-grade chronic inflammation. On the other hand, they may facilitate immune evasion, potentially promoting the 'inflammation-cancer' transition. With the development of metagenomic technologies and the maturation of next-generation high-throughput sequencing technologies, CM have shown potential as liquid biopsy biomarkers for the early diagnosis of gastrointestinal tumors. Interventions targeting specific CMs have also shown prospects for enhancing efficacy in early clinical trials. However, the field still faces numerous challenges, including insufficient depth of mechanistic validation and a lack of standardized detection protocols. Future efforts should aim to conduct further systematic research to clarify the biological functions and clinical translational value of CM in gastrointestinal tumors.}, }
@article {pmid42017731, year = {2026}, author = {Su, DM and Ni, T and Yu, XL}, title = {Invasive streptococcus pneumoniae infection in the hip joint and thigh muscle group of an adult diagnosed by Q-mNGS: a case report.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {76}, number = {3}, pages = {451-454}, doi = {10.47391/JPMA.22494}, pmid = {42017731}, issn = {0030-9982}, mesh = {Humans ; Male ; Adult ; *Hip Joint/microbiology/diagnostic imaging ; Thigh ; *Abscess/microbiology/therapy/diagnosis ; *Pneumococcal Infections/diagnosis/therapy/complications ; *Streptococcus pneumoniae/isolation &amp; purification/genetics ; *Soft Tissue Infections/microbiology/therapy/diagnosis ; *Arthritis, Infectious/therapy/microbiology/diagnosis ; Debridement ; Anti-Bacterial Agents/therapeutic use ; Drainage ; *Myositis/therapy/microbiology ; }, abstract = {Joint infections and myositis due to S. pneumoniae are rare. We report the case of a young adult male presenting with right hip joint infection complicated by thigh muscle abscess, successfully treated by surgical debridement, drainage tube placement, and aggressive antimicrobial therapy. A 38-year-old male presented with right buttock and thigh swelling, pain, night sweats, and limited mobility for 45 days. Imaging examination indicated soft tissue infection around the right hip joint with abscess formation. Quantitative meta-genomic next-generation sequencing (Q-mNGS) of joint fluid confirmed S. pneumoniae as the pathogen. Surgical intervention was performed due to lack of significant improvement after six days of anti-inflammatory therapy. The patient recovered well post-operatively and was discharged with medication after a total hospital stay of 31 days. This case highlights the importance of considering S. pneumoniae as a potential pathogen in joint and soft tissue infections in adults.}, }
@article {pmid42018084, year = {2026}, author = {Han, D and Pan, X and Pan, F and Han, B and Wu, Q and Zhou, Y and Liu, H and Xu, H and Sun, W and Cheng, H and Liu, W and Wan, R and Weng, W and Zhang, H}, title = {Translating Host-Derived Signals from Cerebrospinal Fluid Metagenomic Sequencing into a Diagnostic Tool for Autoimmune Encephalitis in Children.}, journal = {Journal of clinical immunology}, volume = {46}, number = {1}, pages = {}, pmid = {42018084}, issn = {1573-2592}, support = {82471882//National Natural Science Foundation of China/ ; 21ZR1452900//Natural Science Foundation of Shanghai Municipality/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; shslczdzk06902//Shanghai Municipal Key Specialty/ ; }, abstract = {BACKGROUND: The rapid differentiation between autoimmune and infectious encephalitis in children is a critical clinical decision that dramatically impacts treatment and outcome. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is a powerful but often underutilized tool, as its host-derived RNA component is typically discarded. We hypothesized that this host response data could be translated into a diagnostic tool for autoimmune encephalitis (AE). METHODS: We enrolled 180 pediatric patients with suspected encephalitis to evaluate the clinical performance of CSF mNGS against conventional methods. Host transcriptomic analysis was performed on CSF cells from 88 patients (autoimmune, bacterial, and viral encephalitis). A novel biomarker was validated using RT-qPCR in an independent cohort, and its functional role was investigated in neuronal cultures challenged with NMDAR1 antibodies. A diagnostic model was developed and validated. RESULTS: mNGS demonstrated a significantly higher pathogen detection rate than conventional methods (29.4% vs. 16.7%). Host transcriptomic profiling revealed that AE shared a hyperinflammatory signature with viral encephalitis but was uniquely associated with dysregulation of receptor tyrosine kinase and heme signaling pathways. Furthermore, memory B cells and activated mast cells were specifically elevated in AE. We identified and validated RAD54B as a novel biomarker specifically upregulated in AE. Functionally, RAD54B upregulation protected neurons from DNA damage stress induced by NMDAR1 antibodies. A multi-gene diagnostic model based on host-response genes robustly differentiated AE from infectious encephalitis (AUC > 0.923) in a validation set. CONCLUSIONS: We present a validated translational pipeline that repurposes routine CSF mNGS data into a dual-purpose diagnostic tool. By leveraging the host RNA data inherent in CSF mNGS, clinicians can now simultaneously investigate infectious and autoimmune etiologies in a single, rapid test. This strategy has the immediate potential to reduce diagnostic delay, guide timely therapy, and improve outcomes in children with encephalitis.}, }
@article {pmid42018438, year = {2026}, author = {Sun, X and Jiang, X and Zhang, L and Li, M}, title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117284}, doi = {10.1016/j.celrep.2026.117284}, pmid = {42018438}, issn = {2211-1247}, mesh = {Humans ; *Circadian Rhythm/physiology ; *Microbiota/genetics ; Female ; Adult ; Male ; *Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.}, }
@article {pmid42018637, year = {2026}, author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM}, title = {Defining metabolic niches for marine microbial heterotrophs.}, journal = {Science advances}, volume = {12}, number = {17}, pages = {eadz0537}, pmid = {42018637}, issn = {2375-2548}, mesh = {Ecosystem ; *Heterotrophic Processes ; Phytoplankton/metabolism ; Carbon Cycle ; *Microbiota ; *Seawater/microbiology ; Oceans and Seas ; *Aquatic Organisms/metabolism ; Biomass ; Metagenomics ; }, abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.}, }
@article {pmid42019101, year = {2026}, author = {Ramírez-Arenas, PJ and López-Cortés, A and Martínez-Mercado, MA}, title = {Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126716}, doi = {10.1016/j.syapm.2026.126716}, pmid = {42019101}, issn = {1618-0984}, mesh = {*Methanosarcinaceae/classification/genetics/isolation &amp; purification ; *Phylogeny ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; Genome, Archaeal/genetics ; Metagenome ; }, abstract = {The Methanosarcinaceae family is the most versatile among methanogenic archaea, utilizing a wide variety of substrates for methanogenesis. It includes all known halophilic, methylotrophic methanogens. Despite evidence of their presence and even dominance over other methanogenic taxa in Guerrero Negro hypersaline microbial mats, no archaeal species have been cultured or described to date. Consequently, a significant gap remains in our understanding of their metabolic potential and diversity. In this study, seven high-quality metagenome-assembled genomes (MAGs) affiliated with the Methanosarcinaceae family were reconstructed. Three MAGs (E22BA4_117[TS], E22_A5_bin58[TS], and E22bin_1538[TS]) serve as the nomenclatural type for the novel proposed species Methanohalophilus methylutens, Methanolobus methylotrophicus, and Methanococcoides guerreronegronense, according to the SeqCode rules and representing the first Methanosarcinaceae species described from microbial mats of Guerrero Negro. Based on genomic content and phylogenetic features, we infer that these MAGs are cytochrome-containing methanogens supported by the presence of core methanogenesis genes (fwd/fmd, ftr, mch, mtd, mer, mtr and mcr). They exhibit distinct metabolic strategies: E22BA4_117[TS] is a generalist with broad substrate versatility, E22_A5_bin58[TS] is an expanded methylotrophic specialist, and E22bin_1538[TS] is a narrow-range methylotroph. All three MAGs encode the complete set of genes for the methylotrophic pathway, multiple Na[+]/H[+] antiporters and both transport and biosynthesis genes for compatible solutes, collectively indicative of their adaptations to hypersaline conditions. These novel species enrich the phylogenomic resolution of Methanosarcinaceae and expand current understanding of the diversity and ecological relevance of these methanogenic archaea in hypersaline ecosystems, while providing genomic evidence that clarifies their metabolic potential and adaptations.}, }
@article {pmid42019198, year = {2026}, author = {Zhang, C and Geng, H and Li, X and Dai, X and Xu, Y}, title = {Magnetically controlled non-conductive microbial carrier-mediated anaerobic digestion of sewage sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125963}, doi = {10.1016/j.watres.2026.125963}, pmid = {42019198}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; Microspheres ; *Waste Disposal, Fluid/methods ; Biofuels ; }, abstract = {Magnetic porous microspheres (MPMs) have been used to enhance the anaerobic digestion (AD) of sludge. However, the feasibility of using MPMs as magnetically controlled microbial carriers in long-term AD remains unclear. Herein, without replenishment of MPMs, the methanogenic performance, main physicochemical properties of sludge and methanogenic metabolomics in 150-day MPM-mediated AD were comprehensively investigated. A substantial highly active anaerobes were found to adhere to MPMs, which maintained strong magnetic controllability and structural stability and significantly enhanced methane production (P < 0.001) and the methane proportion in biogas (P < 0.05) from AD at different hydraulic retention times (HRTs). The significant positive correlations between the interfacial Lewis acid-base (AB) interaction (R[2] > 0.79, P < 0.01) and daily methane production (R[2] > 0.52, P < 0.01) with water-mediated proton-coupled electron transfer (PCET) indicate that MPM-enhanced AB interactions can accelerate electron transfer by promoting proton movement in interfacial water molecules, thus enhancing methanogenesis during AD. Statistical analyses of variations in activities or contents of key bioenergetic substances on and within anaerobic cell membranes in AD confirmed this observation and simultaneously indicated that MPMs significantly enhanced the bioenergetics of CO2-reduction methanogenesis by promoting intracellular water-mediated PCET. Microbial community changes show that during the AD under different HRTs, MPMs significantly enriched bacteria capable of decomposing complex organics into acetate and hydrogen in an attached state, as well as free acetotrophic methanogens and attached hydrogenotrophic and hydrogen-dependent methylotrophic methanogens, thereby optimising the spatial distribution of methanogenic consortia. Metagenomics and genome-centric metagenomic analyses confirmed that MPMs significantly enhanced the hydrogen-dependent methanogenesis pathways of the attached methanogenic consortia and promoted energy-conserving metabolic cooperation between free and attached methanogenic consortia, reducing resource competition. Basic economic and environmental analyses revealed that the annual economic benefit increased by 112.2% and carbon emissions decreased by approximately 1.34 × 10[5] tons CO2/year with MPM-mediated AD relative to conventional AD. These findings can provide an important reference for the development of exogenous material-mediated AD technology.}, }
@article {pmid42019199, year = {2026}, author = {Liu, S and Wei, W and Wang, C and Ni, BJ and Zhu, S}, title = {Persulfate-driven sludge biorefinery toward value-added medium-chain fatty acids.}, journal = {Water research}, volume = {300}, number = {}, pages = {125935}, doi = {10.1016/j.watres.2026.125935}, pmid = {42019199}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Fatty Acids ; Biofuels ; Fermentation ; Waste Disposal, Fluid ; }, abstract = {Transforming waste activated sludge (WAS) into high-value biofuels is a key pathway toward sustainable waste management and carbon neutrality, yet the recalcitrance of extracellular polymeric substances (EPS) and microbial cell walls severely limits medium-chain fatty acids (MCFAs) production during anaerobic fermentation. Here, we propose a persulfate (PDS)-based pretreatment strategy that enhances MCFAs synthesis by driving sludge disintegration and substrate transformation. Treatment with 7.5 mM PDS increased MCFAs yield by ∼50%, reaching 13,341.4 mg COD/L. Mechanistic investigations reveal that SO4·[-] and ·OH radicals preferentially degrade tightly bound EPS, reducing protein and polysaccharide content by 38% and 46%, respectively, and increasing soluble chemical oxygen demand (SCOD) 5.05-fold. This transformation produces nitrogen-rich, low-molecular-weight dissolved organic matter (DOM). The resulting DOM exhibited high H/C ratios, low O/C ratios, and low aromaticity indices (AImod), significantly enhancing its bioavailability during anaerobic fermentation. Integrated metagenomic functional annotation and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that EPS-derived DOM reshaped the microbial metabolic network, stimulating glycolysis, amino acid metabolism, and carbon chain elongation. Moreover, the formation of unsaturated and aromatic-like fermentation products indicated enhanced DOM humification, which facilitated carbon chain elongation and microbial metabolic activity. Life cycle assessment and techno-economic analysis confirmed the environmental sustainability and economic feasibility of this radical-driven strategy. By elucidating the radical-EPS-DOM-metabolism cascade, this study provides mechanism-guided strategies for efficient sludge biorefinery, advancing the field from empirical operation toward targeted, high-efficiency design.}, }
@article {pmid42019232, year = {2026}, author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X}, title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.}, journal = {International journal of food microbiology}, volume = {456}, number = {}, pages = {111785}, doi = {10.1016/j.ijfoodmicro.2026.111785}, pmid = {42019232}, issn = {1879-3460}, mesh = {*Quorum Sensing ; *Homoserine/analogs &amp; derivatives/metabolism ; *Lactones/metabolism ; Bacterial Proteins/metabolism/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Fermentation ; *Food Storage ; *Microbiota ; Food Microbiology ; Carbon-Sulfur Lyases/metabolism/genetics ; }, abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.}, }
@article {pmid42019335, year = {2026}, author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A}, title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129718}, doi = {10.1016/j.jenvman.2026.129718}, pmid = {42019335}, issn = {1095-8630}, mesh = {*Drinking Water/microbiology ; *Lakes/microbiology ; *Fisheries ; *Bacteria ; RNA, Ribosomal, 16S/genetics ; Water Supply ; Water Quality ; }, abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.}, }
@article {pmid42019341, year = {2026}, author = {Zhao, Y and Chen, Y and Dang, Z and Li, K and Zhu, Y and Xu, C and Wan, X and Jia, B and Cao, G and Shen, Q and Zhao, Z}, title = {Metagenomic and transcriptomic insights into microbial activity maintenance strategies in a pilot-scale biosorption-biodegradation system for in situ sewer overflow treatment.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129750}, doi = {10.1016/j.jenvman.2026.129750}, pmid = {42019341}, issn = {1095-8630}, mesh = {*Sewage ; Biodegradation, Environmental ; *Waste Disposal, Fluid ; Transcriptome ; Metagenomics ; }, abstract = {Sewer overflow is a widely recognized issue in urban water environment pollution. Traditional in situ treatment technologies based on filtration and flocculation often fail to remove soluble pollutants effectively. Conventional in situ biological systems also struggle to maintain activity under fluctuating and nutrient-imbalanced influent conditions. Here, a compact in situ biological treatment process based on biosorption-biodegradation technology with a shortened hydraulic retention time (HRT) is proposed. During a 180-day pilot-scale experiment integrating ballasted flocculation, the system achieved average removal efficiencies of 75-94% for CODCr, NH4[+]-N, TP, BOD5, and SS. Effluent concentrations met Chinese surface water quality standards. The system maintained stable performance during wet weather events and after multiple dry periods of up to 30 days, demonstrating effective microbial activity maintenance. Based on the metagenomic and transcriptomic analyses, this stability is potentially related to nutrient supplementation through carbon metabolism of mixotrophic organisms and pollutant adsorption by biosorption sludge. Additionally, the reduced HRT prevents endogenous respiration and sludge degradation. The compact biosorption-biodegradation process offers an efficient and space-saving strategy for maintaining microbial activity during dry periods. It provides a promising solution for mitigating sewer overflow pollution in high-density urban areas.}, }
@article {pmid42019423, year = {2026}, author = {Xu, C and Feng, Y and He, S and Wu, M and Hu, S}, title = {Mining of FDRs-carrying microbes involved in aflatoxin B1 degradation.}, journal = {Food chemistry}, volume = {515}, number = {}, pages = {149316}, doi = {10.1016/j.foodchem.2026.149316}, pmid = {42019423}, issn = {1873-7072}, mesh = {*Aflatoxin B1/metabolism ; Biotransformation ; *Bacterial Proteins/metabolism/genetics ; *Mycobacterium/metabolism/genetics/isolation &amp; purification/classification/enzymology ; *Oxidoreductases/metabolism/genetics ; Biodegradation, Environmental ; Animal Feed/microbiology/analysis ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Aflatoxin B1 (AFB1), a potent hepatocarcinogenic mycotoxin commonly found in food and feed, poses significant threats to food safety and public health. Microbes reduce AFB1 via biotransformation, so mining degrading strains is key. In this study, a novel AFB1 degrader, Mycobacterium sp. strain HM-7, was isolated from an AFB1-degrading bacterial consortium (designated A-2). Genomic analysis of the reconstructed metagenome-assembled genome (MAG) 12 and strain HM-7 revealed six putative F420H2-dependent reductases (FDRs), which are essential for the biotransformation of AFB1. When strain HM-7 was applied to animal feed, it achieved a significant reduction in AFB1 levels. Furthermore, bioinformatics mining based on the Genome Taxonomy Database (GTDB) identified a wide diversity of FDRs-carrying microbes involved in AFB1 degradation, mainly those belonging to the phylum Actinomycetota, highlighting their potential for bioremediation applications. This study provides valuable insights into the diversity of FDRs-carrying microbes involved in AFB1 degradation.}, }
@article {pmid42019451, year = {2026}, author = {Wei, ZW and Li, HQ and Wang, XH and Yang, XR and Su, JQ}, title = {Non-biodegradable microplastics amplify antibiotic resistance and pathogen spread in bay plastisphere.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142147}, doi = {10.1016/j.jhazmat.2026.142147}, pmid = {42019451}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Bacteria/genetics/drug effects ; Humans ; Virulence Factors/genetics ; }, abstract = {Microplastics (MPs) serve as reservoirs that facilitate the dissemination of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), posing significant threats to public health. However, quantitative evaluations of high-risk ARGs in the plastisphere and comprehensive assessments of their associated health implications are still scarce. In this study, we employed in-situ incubation combined with high-throughput quantitative PCR and metagenomic sequencing to systematically compare the prevalence of ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and HBPs between biodegradable and non-biodegradable MPs. Our findings revealed a marked enrichment of ARGs, VFGs, MGEs, and HBPs in non-biodegradable MPs (polypropylene, polyethylene, and polystyrene) relative to the biodegradable MPs (polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate). Furthermore, an integrated risk assessment combining high-risk ARGs quantification with a Projection Pursuit Regression model revealed significantly elevated microbial risks associated with non-biodegradable MPs. Taxonomic analysis further indicated that Pseudomonas and Aeromonas act as key HBP vectors carrying ARGs and VFGs in the plastisphere, underscoring their role in facilitating the spread of antimicrobial resistance and virulence. These results highlight how plastic properties mediate microbial colonization patterns under complex field conditions, providing a robust framework for environmental risk evaluation and the targeted management of plastic-associated biological hazards.}, }
@article {pmid42019469, year = {2026}, author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH}, title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106914}, pmid = {42019469}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/growth &amp; development/physiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Signal Transduction ; *Taurine/metabolism/analogs &amp; derivatives ; p38 Mitogen-Activated Protein Kinases/metabolism/genetics ; *Avian Proteins/metabolism/genetics ; *Muscle Fibers, Skeletal/physiology ; Pectoralis Muscles/growth &amp; development/physiology ; Male ; *Muscle Development ; }, abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.}, }
@article {pmid42019695, year = {2026}, author = {Liu, X and Wang, H and Zhou, S and Xie, Y and Wang, J and Wang, X and Xu, S and Wang, L and Jiang, C and Zhuang, X}, title = {Nanobubbles drive advanced anaerobic treatment of swine wastewater for efficient methane recovery: Performance gains and multi-pathway enhancement.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134692}, doi = {10.1016/j.biortech.2026.134692}, pmid = {42019695}, issn = {1873-2976}, mesh = {Animals ; *Methane/isolation &amp; purification/biosynthesis ; Anaerobiosis ; *Wastewater/chemistry/microbiology ; Swine ; *Water Purification/methods ; Oxygen ; }, abstract = {Swine wastewater contains recoverable energy, but anaerobic digestion is often limited by complex organics and slow hydrolysis. To overcome this limitation, this study introduced nanobubble technology using three gas media (air, O2, and O3) and systematically studied their effects on methane recovery during the anaerobic digestion of swine wastewater. Batch experiments showed that O3 nanobubbles achieved the strongest enhancement, increasing cumulative methane production by 87.5% compared with the control. This improvement may result from the strong oxidative capacity of O3 nanobubbles to degrade recalcitrant organics, as indicated by the second methane production peak observed only in the O3 nanobubbles. In contrast, O2 nanobubbles provided the weakest improvement, potentially because excess dissolved oxygen stimulated facultative aerobic respiration, converting substrates to CO2 and lowering availability for methanogenesis. Further analysis revealed that all nanobubble treatments accelerated volatile fatty acid turnover and enriched key hydrolytic and acidogenic microbes, particularly under O3 nanobubbles. The enrichment of Methanothrix and downregulation of the energy-intensive PilA gene suggest promoted electron transfer. Negatively charged nanobubbles may act as abiotic mediators that facilitate direct interspecies electron transfer. Metabolic analysis indicated enhanced hydrogenotrophic, methylotrophic, and acetoclastic methanogenesis, implying strengthened synergy among pathways. Overall, O3 nanobubbles show promise for resource recovery from organic waste.}, }
@article {pmid42019770, year = {2026}, author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J}, title = {Atopic dermatitis: Multi-omics insights into microbiota-driven modulation of the gut-skin axis.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108504}, doi = {10.1016/j.micpath.2026.108504}, pmid = {42019770}, issn = {1096-1208}, mesh = {Humans ; *Dermatitis, Atopic/microbiology/therapy/genetics/immunology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; Fecal Microbiota Transplantation ; Animals ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Receptors, Aryl Hydrocarbon/metabolism ; Skin Microbiome ; }, abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.}, }
@article {pmid42020064, year = {2026}, author = {Peters, BA}, title = {Evidence grows for the gut-kidney axis, but questions still remain.}, journal = {Kidney international}, volume = {109}, number = {5}, pages = {832-834}, doi = {10.1016/j.kint.2026.02.015}, pmid = {42020064}, issn = {1523-1755}, mesh = {Humans ; *Kidney/physiology/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Kidney Diseases/microbiology ; }, abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.}, }
@article {pmid42020421, year = {2026}, author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T}, title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020421}, issn = {2041-1723}, support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.}, }
@article {pmid42020426, year = {2026}, author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ}, title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020426}, issn = {2041-1723}, support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Escherichia coli/genetics/metabolism/growth &amp; development/physiology ; *Oligosaccharides/metabolism ; *Bifidobacterium bifidum/genetics/physiology/metabolism/growth &amp; development ; *Symbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/physiology ; Trisaccharides/metabolism ; Infant ; Infant, Newborn ; Breast Feeding ; }, abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.}, }
@article {pmid42020430, year = {2026}, author = {Zhou, L and Li, D and Huang, Y and Kang, J and Lu, Y and Zhang, L and Liu, SQ}, title = {Lactiplantibacillus plantarum-mediated modulation of volatile flavor and quality in low-salt spontaneously fermented yellow capsicum sauce.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00854-z}, pmid = {42020430}, issn = {2396-8370}, support = {32302036//National Natural Science Foundation of China/ ; NHXXRCXM202312//'Nan Hai Xin Xing' Science and Technology Innovation Talent Platform Project Funding of Hainan Province, China/ ; 202407560053//China Scholarship Council/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University, China/ ; }, abstract = {Yellow capsicum sauce (YCS) is a special fermented condiment in Hainan province, China, and its fermentation typically occurs in a high-salt environment. In this study, the effects of different salt contents (5, 10, 15, and 20%, w/w) on microbial communities and volatile flavor profiles in YCS were systematically investigated by metagenomic approach and HS-SPME-GC-MS. The results revealed that Lactiplantibacillus (54.66%) was the dominant genus in low-salt samples (SF5), while its abundance was less than 6% in higher salinity levels (SF15 and SF20). A total of 48 volatile flavor compounds (VFCs) were detected in the naturally fermented YCS, with alcohols and esters being the primary VFCs. Low-salt fermentation facilitated the accumulation of VFCs, and the total VFCs content in SF5 was the highest. Aroma compounds showed a strong correlation with Lactiplantibacillus plantarum. To further validate the findings, L. plantarum MA1 isolated from SF5 was inoculated into the low-salt YCS substrate for bioaugmented fermentation. This strain significantly increased key aroma components, such as cis-3-hexenyl isovalerate, hexyl 3-methylbutanoate, and ethyl acetate. Moreover, it significantly increased the lactic acid content while reducing the nitrite content, thereby more effectively preserving the fresh yellow color of capsicum sauce and the stability of its spiciness.}, }
@article {pmid42020464, year = {2026}, author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH}, title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42020464}, issn = {2045-2322}, support = {5850.0109317.18.9 and 21167-2//Petr&#xf3;leo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Atlantic Ocean ; *Microbiota/genetics ; *Ecosystem ; Metagenomics/methods ; *Seawater/microbiology ; *Bacteria/genetics/classification ; Metagenome ; Water Microbiology ; }, abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.}, }
@article {pmid42020676, year = {2026}, author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR}, title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020676}, issn = {1867-1314}, abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.}, }
@article {pmid42020750, year = {2026}, author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS}, title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.}, journal = {Nature}, volume = {653}, number = {8116}, pages = {1139-1147}, pmid = {42020750}, issn = {1476-4687}, mesh = {*Enterococcus faecium/genetics/pathogenicity/isolation &amp; purification ; *DNA Transposable Elements/genetics ; Humans ; Genome, Bacterial/genetics ; *Adaptation, Physiological/genetics ; Metagenome/genetics ; Promoter Regions, Genetic/genetics ; Feces/microbiology ; }, abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.}, }
@article {pmid42020953, year = {2026}, author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL}, title = {Metabolic potential structures gill symbiont communities in two common shipworm species.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42020953}, issn = {1751-7370}, mesh = {Animals ; *Symbiosis ; *Gills/microbiology ; Phylogeny ; *Bivalvia/microbiology ; *Bacteria/genetics/classification/metabolism/enzymology ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes representing seven distinct symbiont species. The metagenome of each host specimen contained between one and five symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.}, }
@article {pmid42021075, year = {2026}, author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K}, title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.}, journal = {The journal of medical investigation : JMI}, volume = {73}, number = {1.2}, pages = {186-207}, doi = {10.2152/jmi.73.186}, pmid = {42021075}, issn = {1349-6867}, mesh = {Animals ; *Ampicillin/adverse effects ; *Diet, Western/adverse effects ; Female ; *Fatty Liver/etiology ; Mice, Inbred C57BL ; Mice ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Dysbiosis ; Male ; Feces/microbiology ; }, abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.}, }
@article {pmid42021418, year = {2026}, author = {Ravi, A and Shestivska, V and Thiago Dobbler, P and Sechovcová, H and Maixnerová, M and Semerád, J and Nehasilová, A and Vadroňová, M and Odriozola, I and Šubrtová Salmonová, H and Větrovský, T and Musilová, &#x160; and Cajthaml, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42021418}, issn = {2524-4671}, abstract = {BACKGROUND: Antibiotic resistance poses a major threat to human health, with antibiotic use in livestock contributing to the selection and spread of resistance genes. The genus Acinetobacter includes human- and animal-associated species capable of acquiring resistance, yet their diversity and resistance potential in livestock remain far less explored than in humans. In this study, we investigated Acinetobacter in cattle feces from 28 Czech farms with contrasting antibiotic use, aiming to assess species composition, resistance profiles, and the potential for resistance dissemination. We applied an integrative approach combining strain isolation and characterization, enrichment cultures, metabarcoding, and shotgun metagenomics.<br><br>RESULTS: Cattle feces harbored diverse Acinetobacter species with A. indicus and A. pseudolwoffii being the core species based on both isolated strains and metabarcoding, while A. baumannii was less common. Acinetobacter species occurrence determined by metabarcoding was driven by multiple factors, including production type, herd size, and per-head antibiotic use, while their abundance was mostly influenced by sample type (higher in feces from the farm floor than in rectal samples) and production type (higher in dairy than in beef cattle). Remarkably, 37% of the 284 isolated strains could not be assigned to validly named species and represent at least 19 putative novel species. Decreased susceptibility due to acquired resistance was observed in 57 strains; notably, A. indicus and A. pseudolwoffii from antibiotic-using farms were less susceptible to streptomycin than those from antibiotic-free farms. Shotgun metagenomics revealed a greater richness of acquired resistance genes in antibiotic-using farms, including the clinically relevant carbapenemase gene blaOXA-58. This gene was located on putative plasmid contigs alongside streptomycin resistance determinants strA-strB, suggesting horizontal dissemination under streptomycin selection pressure. Strain analysis confirmed the co-localization of blaOXA-58 and strA-strB on a large plasmid in A. pseudolwoffii.<br><br>CONCLUSIONS: Despite relatively strict regulations, Czech cattle farms constitute a reservoir of antibiotic-resistant Acinetobacter carrying mobile resistance genes of clinical concern. Commonly applied antibiotics likely co-select for such genes, posing an ongoing public health risk. Our findings reveal an unexpectedly high diversity of Acinetobacter spp. in cattle, highlighting the research bias toward human-associated species and underscoring the need for integrated One Health monitoring approaches.}, }
@article {pmid42021724, year = {2026}, author = {Batra, N and Rout, PR and Dey, P}, title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.}, journal = {Food &amp; function}, volume = {17}, number = {9}, pages = {4245-4261}, doi = {10.1039/d5fo04976h}, pmid = {42021724}, issn = {2042-650X}, mesh = {*Probiotics/pharmacology ; Humans ; *Butyrates/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Lactiplantibacillus plantarum/physiology ; Anaerobiosis ; *Colon/microbiology/metabolism ; Amino Acids/metabolism ; }, abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.}, }
@article {pmid42021875, year = {2026}, author = {Li, H and Song, Z and Zhao, Y and Li, M}, title = {[Advances in the Application of Artificial Intelligence in Clinical Microbiological Testing].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {313-318}, pmid = {42021875}, issn = {1672-173X}, mesh = {*Artificial Intelligence ; Humans ; *Microbiological Techniques/methods ; Algorithms ; Machine Learning ; }, abstract = {Traditional microbiological detection methods have inherent limitations in detection speed, sensitivity, and specificity, making them increasingly unable to meet growing clinical demands. In recent years, artificial intelligence (AI) has been rapidly integrated into clinical microbiological testing, with numerous studies demonstrating its significant potential to enhance pathogen identification, predict antimicrobial susceptibility testing, and advance laboratory automation. This article systematically reviews classical AI algorithms and their latest advancements in this field. For visual data applications, deep learning-based models are used to automatically analyze microscopy images or colony morphology, significantly improving recognition efficiency and diagnostic accuracy. For non-visual data, AI has achieved breakthroughs in analyzing multi-omics data such as genomics, transcriptomics, and metagenomics, and is widely used for rapid pathogen identification and prediction of antimicrobial resistance. Despite its promising prospects, the application of AI in clinical microbiological testing remains in the early stages of transitioning from scientific research to clinical practice. This paper further discusses the key challenges and opportunities encountered during this technological translation, aiming to help clinical professionals comprehensively understand the current status, future trends, and potential impact of AI in this field, thereby promoting its development into reliable and scalable routine diagnostic methods.}, }
@article {pmid42021890, year = {2026}, author = {Zhang, W and Zhong, S and Lu, S and Xiao, X and Xie, Y}, title = {[Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {411-418}, pmid = {42021890}, issn = {1672-173X}, mesh = {*Mucormycosis/diagnosis/microbiology ; Humans ; Retrospective Studies ; *Mucorales/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Sensitivity and Specificity ; ROC Curve ; Middle Aged ; Adult ; }, abstract = {OBJECTIVE: Mucormycosis is a life-threatening invasive fungal infection with high mortality, yet traditional diagnostic methods are limited by low positivity rates. This study aims to evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in mucormycosis.<br><br>METHODS: A retrospective analysis was conducted on 135 patients with mNGS results positive for Mucorales fungi at West China Hospital of Sichuan University from November 1, 2022, to October 31, 2024. Based on comprehensive clinical diagnostic criteria (including proven and probable cases), patients were classified into a confirmed mucormycosis group and a non-mucormycosis group. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of normalized read counts (lgRPM) from different specimen types. Fungal species distribution and laboratory parameters were compared between the two groups.<br><br>RESULTS: Among the 135 patients with positive mNGS results for Mucorales, 100 (74.1%) were ultimately diagnosed with mucormycosis. ROC curve analysis revealed that the diagnostic performance of mNGS varied by specimen type. For blood specimens, the area under the curve (AUC) was 0.772, with a specificity of 87.5% at the optimal cutoff value of 0.11 RPM. For bronchoalveolar lavage fluid specimens, the AUC was 0.717, with a sensitivity of 76.5% at the optimal cutoff value of 0.02 RPM. Combined analysis of all specimens showed that at the optimal cutoff value of 0.08 RPM (approximately 8 reads/100M), the sensitivity and specificity were 62.0% and 71.4%, respectively. Species distribution analysis showed that the proportions of Cunninghamella elegans (11.0% vs. 2.9%) and Rhizomucor pusillus (9.0% vs. 2.9%) were significantly higher in the confirmed group than in the non-mucormycosis group (P < 0.05). Levels of C-reactive protein and interleukin-6 were also significantly higher in the confirmed group (P < 0.05). Notably, all seven renal perfusion fluid samples yielded false-positive mNGS results.<br><br>CONCLUSION: mNGS technology can effectively improve the diagnostic yield for mucormycosis. However, results should be interpreted in conjunction with specimen type, read count, and clinical characteristics. BALF specimens offer high sensitivity, making them suitable for screening, while blood specimens demonstrate high specificity, making them valuable for confirmation. Positive results from low-biomass samples such as renal perfusion fluid warrant caution against false positivity. Fungal species identification and inflammatory markers may serve as adjunctive evidence for clinical diagnosis.}, }
@article {pmid42022012, year = {2026}, author = {Conrad, RE and Rodriguez-R, LM and Lindner, BG and Gerhardt, K and Konstantinidis, KT}, title = {An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag068}, pmid = {42022012}, issn = {2730-6151}, abstract = {Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, Alteromonas macleodii [97% average amino-acid identity (AAI) to the type genome] and Prochlorococcus marinus (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.}, }
@article {pmid42022013, year = {2026}, author = {Franco, MEE and Singer, E and Roux, S and Meredith, LK and U'Ren, JM}, title = {Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome specificity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag054}, pmid = {42022013}, issn = {2730-6151}, abstract = {Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications.}, }
@article {pmid42022196, year = {2026}, author = {Yan, Z and Xie, J and Jin, L and He, T and Zhang, X and Li, X}, title = {Steam Cooking Methods Promote the Transfer of Viable Antibiotic-Resistant Pathogens from Water into Air.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {4}, pages = {730-741}, pmid = {42022196}, issn = {2833-8278}, abstract = {Steam cooking is an ancient and widely used method for sterilizing water and food globally. However, its effectiveness may be compromised by the ubiquitous presence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in these media. Here, we combined metagenomic sequencing, quantitative PCR analysis, plate culture, and Sanger sequencing to examine the effects of steam cooking on the profiles of antibiotic resistance in cooked fish, tap water, and indoor air in real cooking environments (i.e., a canteen and a home kitchen) and a laboratory chamber. We found that while steam cooking eliminated over 92.0% of bacteria and ARGs in both tap water and fish, it significantly increased the absolute abundance of bacteria and ARGs in indoor fine particulate matter (PM2.5) across all settings. Tap water was identified as the primary contributor to the increase, transferring 14.6% of bacteria and 33.2% of ARGs into indoor PM2.5 during steam cooking. This process also elevated the relative abundance of certain putative human pathogens in indoor PM2.5, containing ARGs and heat shock proteins and mainly originating from tap water. To test if these transferred ARGs hosts were viable, we conducted plate culture experiments and identified a viable heat-resistant ARB, Bacillus cereus, transferred from water to indoor PM2.5 via water vapor. Our results highlight the cross-medium transport of ARB and ARGs via steam cooking and underscore the potential microbial safety issues to cooking personnel through inhalational exposure.}, }
@article {pmid42022320, year = {2026}, author = {Zhang, W and Huang, R and Yuan, J}, title = {Case Report: HHV8-positive multicentric Castleman disease in an HIV-positive patient :diagnostic challenges arising from atypical histology and the role of metagenomic sequencing.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1779973}, pmid = {42022320}, issn = {2234-943X}, abstract = {BACKGROUND: Multicentric Castleman disease (MCD), especially the HHV8-positive subtype, is a rare lymphoproliferative disorder that presents considerable diagnostic and therapeutic difficulties, particularly among HIV-positive patients. The co-occurrence of other infections, such as syphilis, may further complicate its clinical picture and management.<br><br>CASE DESCRIPTION: A 65-year-old man with well-controlled HIV presented with persistent fever, fatigue, and disseminated lymphadenopathy,. Through histopathological examination, molecular testing (including mNGS for HHV8), and PET-CT imaging, HHV8-positive MCD was diagnosed, along with latent syphilis. The patient was successfully treated with R-VP16 (rituximab and etoposide) for MCD and benzathine penicillin for syphilis, showing a positive clinical response. Throughout 36 months of continuous monitoring, the patient has maintained sustained complete remission with no evidence of disease recurrence.<br><br>CONCLUSION: This case underscores the importance of considering HHV8-driven lymphoproliferative disorders in HIV patients with unexplained lymphadenopathy and systemic symptoms, particularly in HHV8-endemic regions. It also highlights the essential roles of advanced diagnostics and multidisciplinary management in such complex presentations. The favorable outcome demonstrates the effectiveness of timely and targeted treatment, though long-term follow-up remains necessary due to the potential for relapse or progression.}, }
@article {pmid42022392, year = {2026}, author = {Abedien, ZU and Lean, IJ and Djordjevic, SP and Hick, PM and Westman, ME and Mckay-Demeler, J and Webster, J and Brito, BP}, title = {Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1788101}, pmid = {42022392}, issn = {2297-1769}, abstract = {Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.}, }
@article {pmid42022531, year = {2026}, author = {Wang, Y and Fu, J and Zhan, J and Liang, Y and Chen, R and Su, L and Zhou, Q and Zhang, Y and Cong, W and Xu, F}, title = {Panax ginseng-Polygonum cuspidatum is beneficial for alleviating atherosclerosis in ApoE[-/-] mice by modulating the composition of gut microbiota and related metabolites.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1773819}, pmid = {42022531}, issn = {2297-055X}, abstract = {BACKGROUND: Atherosclerosis (AS) is a central pathological driver underlying most cardiovascular diseases. Gut microbiota and related metabolites participate in regulating atherosclerosis. Panax ginseng and Polygonum cuspidatum (GP) herb pair has traditionally been used for cardiovascular diseases. Some active compounds in GP have shown anti-atherosclerotic effects and the effects of GP still needs more evidence-based supports. Therefore, this study aims to investigate the potential effects of GP on atherosclerosis and explore the underlying mechanisms.<br><br>METHODS: Fifty C57BL/6J ApoE[-/-] mice were randomly assigned to five groups: model, statin, low-dose GP, medium-dose GP and high-dose GP. They were fed a high-fat diet (HFD) to induce atherosclerosis. Ten wild-type C57BL/6J mice were given chow diet and served as controls. After 12-week intervention, their aortic tissues were collected for Oil Red O staining, colon tissues for Alcian staining and immunofluorescence, and serum samples for measurement of lipid levels and inflammatory cytokines. Then, their fecal DNA was extracted for metagenomic sequencing, while cecum and ileocecal valves were for untargeted metabolomics. Finally, fecal microbiota transplantation was performed to assess the contribution of gut microbiota to observed effects. Twenty additional ApoE[-/-] mice were randomized to two groups: FMT-Mod and FMT-GPH, given feces from the model or high-dose GP group.<br><br>RESULTS: Atherosclerotic plaques accumulated in the aorta and aortic sinus after HFD, while statin and high-dose GP alleviated this burden. TC, TG, LDL-C, MCP-1, MCP-3 and IL-2 showed significant increase after HFD, while statin and GP decreased LDL-C, MCP-1 and MCP-3. The goblet cells, ZO-1 and Occludin decreased after HFD, while statin and GP increased them, indicating that the intestinal barrier integrity was improved. Additionally, the composition of gut microbiota was modulated by GP. Some candidate taxa were identified, such as Bifidobacteriales, Bacteroidetes and Escherichia coli. Twenty-two metabolites were differentially abundant among the control, model and GP groups. Nineteen of them were modulated by HFD and reversed by GP, including 1-methylnicotinamide, dopamine and lysoPA (0:0/18:0). Mice given fecal transplants from the high-dose GP group showed less aortic plaques, lower levels of some lipid and inflammatory cytokines, more goblet cells, more expression of ZO-1 and Occludin, and more 1-methylnicotinamide than those given fecal transplants from the model group.<br><br>CONCLUSION: This study suggests that GP is beneficial for alleviating atherosclerosis in HFD-induced ApoE[-/-] mice, potentially by modulating the composition of gut microbiota and related metabolites.}, }
@article {pmid42022543, year = {2026}, author = {Yang, P and Meng, Y and Ma, Y and Xu, M and Zhang, X}, title = {Fermented cotton stalks preserve colonic epithelial integrity in Hu sheep via the microbiota-metabolite-NF-κB/MLCK axis and mitigate the adverse effects of direct feeding.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1777023}, pmid = {42022543}, issn = {2296-861X}, abstract = {BACKGROUND: This study aimed to compare three cotton-stalk processing strategies-grinding (FS), steam explosion (PH), and microbial fermentation (FJ)-and to clarify whether fermented cotton stalks preserve colonic epithelial integrity through a microbiota-metabolite-NF‑κB/MLCK axis in Hu sheep.<br><br>METHODS: Fifteen clinically healthy Hu sheep (26.7 &#xb1; 1.76 kg body weight; 115 &#xb1; 4 days of age) were used after a 14&#x2011;day adaptation period and randomly assigned to one of three diets (n&#x202f;= 5 per treatment) containing 40% processed cotton stalks (FS, PH, or FJ) for 8 weeks.<br><br>RESULTS: PH and FJ increased final body weight compared with FS, and average daily gain increased progressively from FS to PH to FJ (206.07, 282.50, and 322.14 g/d, respectively; p&#x202f;< 0.05). Colonic fermentation profiles were markedly improved by FJ, evidenced by lower pH, ammonia nitrogen, free gossypol, and acetate (p&#x202f;< 0.05), alongside higher total VFAs with elevated propionate and butyrate (p&#x202f;< 0.05), whereas LPS was not different among treatments (p&#x202f;> 0.05). Histology and scanning electron microscopy indicated that FJ maintained intact crypt architecture and epithelial surface continuity, while FS exhibited epithelial detachment and surface erosion. Metagenomic analysis revealed distinct community structures among groups, with FJ showing higher richness and enrichment of taxa associated with carbohydrate utilization and butyrate&#x2011;producing guilds (e.g., Lachnospiraceae&#x2011;related genera such as Anaerostipes, Blautia, and Coprococcus). Consistently, FJ suppressed colonic mucosal inflammation, as reflected by reduced IL&#x2011;1&#x3b2;, IL&#x2011;6, IL&#x2011;8, and TNF-&#x3b1; at both mRNA and protein levels (p&#x202f;< 0.05). Mechanistically, FJ attenuated NF&#x2011;&#x3ba;B activation and downstream MLCK signaling, shown by decreased p&#x2011;p65/p65, p&#x2011;I&#x3ba;B/I&#x3ba;B, MLCK abundance, and p&#x2011;MLC/MLC ratio (p&#x202f;< 0.05), while upregulating tight&#x2011;junction proteins (ZO&#x2011;1, occludin, claudin&#x2011;1, and claudin&#x2011;4; (p&#x202f;< 0.05).<br><br>CONCLUSION: Fermentation&#x2011;based processing of cotton stalks enhanced growth performance and promoted a favorable hindgut fermentation and microbial-metabolic milieu, thereby reinforcing colonic barrier integrity via inhibition of NF&#x2011;&#x3ba;B/MLCK&#x2011;associated inflammatory signaling, supporting fermented cotton stalk as a practical strategy to valorize cotton residues for ruminant feeding while mitigating gossypol&#x2011;related hindgut stress.}, }
@article {pmid42022809, year = {2026}, author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH}, title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799859}, pmid = {42022809}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; Multiomics ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; *Infant, Premature ; Male ; Infant, Newborn ; Feces/microbiology ; Infant ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Biomarkers ; Metabolomics ; Dysbiosis/microbiology ; }, abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.}, }
@article {pmid42022943, year = {2026}, author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z}, title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70318}, pmid = {42022943}, issn = {2397-9070}, abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.}, }
@article {pmid42022944, year = {2026}, author = {Zhao, Z and Ling, J and Chen, J}, title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70390}, pmid = {42022944}, issn = {2397-9070}, abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.<br><br>METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176&#x2009;629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.<br><br>RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR&#x2009;=&#x2009;3.961, 95% CI&#x2009;=&#x2009;1.085-14.453, p&#x2009;=&#x2009;0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR&#x2009;=&#x2009;0.409, 95% CI&#x2009;=&#x2009;0.167-0.999, p&#x2009;=&#x2009;0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR&#x2009;=&#x2009;4.864, 95% CI&#x2009;=&#x2009;1.293-18.302, p&#x2009;=&#x2009;0.019), while Aggregatibacter segnis demonstrated a protective effect (OR&#x2009;=&#x2009;0.400, 95% CI&#x2009;=&#x2009;0.188-0.854, p&#x2009;=&#x2009;0.018).<br><br>CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.}, }
@article {pmid42023092, year = {2026}, author = {Li, X and Chen, D and Xiao, Y and Lei, Z and Yang, X and Zhang, Y and Li, L and Zheng, Y and Zhang, Y and Huang, Z and Lin, B}, title = {Metagenomic next-generation sequencing improves diagnosis of Talaromyces marneffei and mixed infections in HIV/AIDS patients: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1800314}, pmid = {42023092}, issn = {2296-858X}, abstract = {BACKGROUND: Opportunistic infections remain a leading cause of morbidity in people living with HIV (PLWH). Talaromyces marneffei (T. marneffei) accounts for up to 15% of HIV-related hospitalizations in endemic regions. Metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection; however, its utility in diagnosing HIV-associated coinfections is uncertain.<br><br>METHODS: This retrospective study enrolled 56 hospitalized PLWH with coinfections at the Third Affiliated Hospital of Sun Yat-sen University from March 2022 to October 2024. All patients underwent pathogen detection using both mNGS and CTM, with their diagnostic performance compared. Clinical data, treatment adjustments, and outcomes were analyzed.<br><br>RESULTS: mNGS demonstrated significantly higher detection rate (84.4%, 54/64; 95% CI: 73.1-92.2%) than CTM (28.1%, 18/64; 95% CI: 17.6-40.8%; p&#x202f;<&#x202f;0.0001), especially for T. marneffei detection (100% vs. 45.5%, p&#x202f;<&#x202f;0.0001). mNGS identified T. marneffei in 39.3% (n&#x202f;=&#x202f;22/56) of patients, including two rare cases (urinary and intracranial infections) missed by CTM. mNGS revealed mixed infections in 82.1% (46/56) of patients, substantially higher than the 5.4% detected by CTM. Notably, mNGS-guided therapy adjustments occurred in 74.1% of cases, compared with 22.2% for CTM (p&#x202f;<&#x202f;0.001), correlating with clinical improvement in 90% (36/40) of adjusted regimens.<br><br>CONCLUSION: Our data demonstrated that mNGS had a higher positive detection rate than CTM for detecting coinfections among PLWH, especially for T. marneffei and mixed infections. These results highlight the clinical value of mNGS as a complementary tool for pathogen identification in this vulnerable population.}, }
@article {pmid42023515, year = {2026}, author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y}, title = {PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkag382}, pmid = {42023515}, issn = {1362-4962}, support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; 9667256//Institute of Digital Medicine/ ; 9678241//Institute of Digital Medicine/ ; }, abstract = {Metagenomic sequencing has transformed virus discovery; however, downstream bioinformatic analyses for viral identification, classification, and host prediction remain fragmented across multiple tools. Here, we present PhaBOX2, a major upgrade that extends the platform from a specialized bacteriophage identification tool to a comprehensive and integrated suite for viral sequence analysis. PhaBOX2 broadens its detection, taxonomic, and host prediction scope beyond phages to enable the characterization of archaeal and eukaryotic viruses. The updated workflow incorporates rigorous quality control and quantitative analyses, automatically removes host contamination, clusters sequences into viral operational taxonomic units, and performs phylogenetic analysis based on marker genes. In contrast to traditional "black-box" deep learning approaches, PhaBOX2 combines alignment-based strategies with machine-learning models under a "glass-box" design philosophy, providing interpretable intermediate evidence alongside final predictions to improve transparency and biological interpretability. Powered by a dedicated high-performance computing infrastructure, the server delivers a fully automated, end-to-end workflow, while achieving an ~80% reduction in processing time. PhaBOX2 thus provides a robust and user-friendly ecosystem for viral metagenomic analysis and is freely available at https://phage.ee.cityu.edu.hk/.}, }
@article {pmid42023591, year = {2026}, author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y}, title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662556}, pmid = {42023591}, issn = {1949-0984}, mesh = {Humans ; Animals ; *Energy Metabolism ; *Major Depressive Disorder/metabolism/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation ; Male ; Female ; Mice ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adult ; Middle Aged ; Multiomics ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.}, }
@article {pmid42023670, year = {2026}, author = {Santillan, E and Neshat, SA and Wuertz, S}, title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42023670}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bioreactors/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Wastewater/microbiology/chemistry ; Biomass ; Life History Traits ; Ecosystem ; }, abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.}, }
@article {pmid42023843, year = {2026}, author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.}, journal = {mBio}, volume = {17}, number = {5}, pages = {e0053426}, pmid = {42023843}, issn = {2150-7511}, support = {R01 AI158527/AI/NIAID NIH HHS/United States ; }, mesh = {Ethiopia/epidemiology ; Humans ; *Trachoma/microbiology/epidemiology ; Female ; *Phylogeny ; Male ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; Child, Preschool ; Infant ; Eye/microbiology ; Metagenomics ; Aged ; }, abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.}, }
@article {pmid42023878, year = {2026}, author = {Conte, CA and Rivarola, M and Gonzalez, S and Milla, FH and Soria, C and Giardini, MC and Segura, DF and Handler, AM and Bourtzis, K and Ragoussis, J and Lanzavecchia, SB}, title = {De novo whole-genome assembly of the Wolbachia sp. endosymbiont from Anastrepha fraterculus using long- and short-read metagenomic data.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0042526}, pmid = {42023878}, issn = {2576-098X}, abstract = {A whole-genome assembly and annotation of Wolbachia sp. infecting Anastrepha fraterculus sp. 1 were generated by a metagenomic analysis of sequencing reads from a host genome project. This study contributes to the characterization of this endosymbiotic bacterium and provides valuable insights for research on host-symbiont interactions and pest management strategies.}, }
@article {pmid42024170, year = {2026}, author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y}, title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.}, journal = {Clinical oral investigations}, volume = {30}, number = {5}, pages = {}, pmid = {42024170}, issn = {1436-3771}, support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; }, mesh = {Humans ; *Biofilms ; *Microbiota ; *Dental Caries/microbiology ; Adult ; Microscopy, Electron, Scanning ; Microscopy, Confocal ; Candida albicans ; Streptococcus mutans ; Female ; Male ; Saliva/microbiology ; }, abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.<br><br>MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.<br><br>RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.<br><br>CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.<br><br>CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.}, }
@article {pmid42025071, year = {2026}, author = {Waseem, H and Feng, K and Zhao, B and Yang, X and Liu, M and Wang, J and Li, J and He, Q and Wang, S and Lu, Y and Örmeci, B and Deng, Y}, title = {Diversity and geographic distribution of antibiotic resistance in food waste anaerobic digestion systems.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142168}, doi = {10.1016/j.jhazmat.2026.142168}, pmid = {42025071}, issn = {1873-3336}, mesh = {Food Loss and Waste ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; China ; *Sewage/microbiology ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance genes (ARGs) present in food waste pose a significant environmental and public health challenge, with anaerobic digestion emerging as a promising technology to reduce ARG abundance during waste treatment. In this study, we analyzed the resistomes in 64 anaerobic digestion sludge samples from seven full-scale food waste treatment facilities representing seven Chinese provinces. Across all facilities, a small core set of glycopeptide (van clusters), β-lactamase, aminoglycoside, and macrolide-lincosamide-streptogramin genes accounted for most ARG abundance (70.3%), marking them as critical targets for monitoring and post-treatment at high-risk sites such as Wenzhou. Resistome composition differed significantly among facilities and exhibited moderate correlation with bacterial taxonomic composition, with Firmicutes (Bacillota), Chloroflexota, and Proteobacteria as the major carriers associated with multiple resistance classes. ARG abundance was positively correlated with mobile genetic elements (r = 0.54, p < 0.0001), driven by integrases, transposases, and Tn916. Horizontal gene transfer was largely constrained within phylogenetic boundaries, particularly within Firmicutes (66.67%), limiting cross-phyla ARG dissemination. Resistome variation was driven predominantly by deterministic processes.; these deterministic filters together with regional differences in food-waste composition and MGEs, collectively select for a glycopeptide-dominated, Firmicutes-anchored resistome that is distinct from those in activated sludge and manure digesters.}, }
@article {pmid42025084, year = {2026}, author = {Xu, GL and Tan, S and Hu, Y and Cheng, M and Hou, J and Cui, HL}, title = {Five novel Haloarchaeobius species from coastal tidal flats and saline-alkali soil in China using integrated culture-dependent and culture-independent approaches.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126718}, doi = {10.1016/j.syapm.2026.126718}, pmid = {42025084}, issn = {1618-0984}, mesh = {China ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sequence Analysis, DNA ; DNA, Archaeal/genetics ; Soil/chemistry ; Seashore ; Nucleic Acid Hybridization ; *Halobacteriaceae/classification/genetics/isolation &amp; purification ; Sodium Chloride ; Metagenomics ; Base Composition ; }, abstract = {Six novel halophilic archaeal strains, DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T] were isolated from tidal flats and saline-alkali soil collected from the eastern coastal region of China. Amplicon sequencing and metagenomic analyses indicated that these strains were present at low abundance in their original habitats, with only three strains detected by culture-independent approaches. These six strains constituted an independent clade alongside members of the genus Haloarchaeobius based on the 16S rRNA gene phylogeny. Except for the comparison between strains DYHT-AS-18[T] and TZWSO28, the average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values among these strains and existing members of the genus Haloarchaeobius were 76.60-89.50%, 21.00-38.50%, and 67.99-88.76%, respectively, below the proposed thresholds for species delineation. In contrast, these three values between strains DYHT-AS-18[T] and TZWSO28 were 97.36%, 76.30%, and 97.25%, respectively, exceeding the proposed thresholds. Phylogenomic analysis revealed that the six strains clustered with members of the genus Haloarchaeobius, but formed distinct branches separate from the current species. The optimal growth conditions for these six strains in terms of NaCl, MgCl2, temperature, and pH were 0.9-4.8 M, 0-1 M, 20-50 °C, and 5.0-9.5, respectively. According to phenotypic differences in nutrition and biochemical activity, these six strains can be distinguished from their related species. On the basis of polyphasic taxonomic evidence, five novel species within the genus Haloarchaeobius are proposed to accommodate strains DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T], respectively.}, }
@article {pmid42025086, year = {2026}, author = {Islam, A and Han, Z and Rana, ML and Qiao, W and Guruge, SK and Zhang, Y and Yang, M}, title = {Removal of protozoa, opportunistic pathogens with virulence factors in swine manure using anaerobic digestion: Full-scale investigation and lab-scale optimization.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129728}, doi = {10.1016/j.jenvman.2026.129728}, pmid = {42025086}, issn = {1095-8630}, mesh = {Animals ; *Manure/parasitology/microbiology ; Swine ; *Virulence Factors ; Phylogeny ; Anaerobiosis ; Giardia/isolation &amp; purification ; Cryptosporidium/isolation &amp; purification ; Cryptosporidium parvum/isolation &amp; purification ; }, abstract = {Swine manure serves as a significant reservoir of zoonotic protozoa and opportunistic pathogens, posing environmental and public health risks when inadequately treated. In this study, multiple molecular approaches, including quantitative PCR, nested PCR with gp60-based phylogenetic analysis, virulence factor profiling, and metagenome-assembled genome (MAG) reconstruction, were employed to investigate the abundance, diversity, and treatment responses of Cryptosporidium, Giardia, twelve opportunistic pathogens, and associated virulence factors (VFs) in swine manure. Three full-scale anaerobic digestion (AD) systems were investigated, and thermophilic and hyperthermophilic pretreatments were applied to lab-scale AD systems to evaluate the efficiency of biological risk control. Cryptosporidium parvum was identified as the dominant species, with subtype IIaA17G4R1 and related zoonotic subtypes detected in both lab-scale and full-scale samples. Phylogenetic clustering of swine-derived sequences with human and cattle isolates indicates a potential risk of zoonotic transmission through manure-associated environmental contamination. In lab-scale AD, a significant reduction in Cryptosporidium, particularly under hyperthermophilic conditions, was observed, while Giardia was undetectable in both influent and effluent samples. In full-scale systems, persistence of Escherichia coli, Clostridium perfringens, Enterococcus, Salmonella, and multiple VFs was confirmed in the effluents. The hyperthermophilic-mesophilic (70 °C-37 °C) lab-scale treatments achieved a substantial reduction in overall pathogen abundance from 3.40 × 10[8] to 1.21 × 10[8] copies/g dry weight and in virulence gene loads from 5.24 to 2.35 copies/cell (P < 0.001), along with the significant removal of pathogenic MAGs such as Enterococcus, Escherichia, Pseudomonas, and Streptococcus. These findings demonstrate the effectiveness of AD for reducing microbial risks and underscore the potential of thermophilic phase digestion as a scalable, biologically effective method for reducing microbial risks associated with livestock manure reuse.}, }
@article {pmid42025876, year = {2026}, author = {Stamatopoulou, P and Scarborough, MJ}, title = {Impacts of organic loading rate fluctuations and division of labor on sugar-based chain elongation revealed through metatranscriptomics.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134687}, doi = {10.1016/j.biortech.2026.134687}, pmid = {42025876}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; Caproates/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/metabolism/genetics ; *Metagenomics ; Glucose/metabolism ; *Gene Expression Profiling ; *Sugars/metabolism ; *Transcriptome ; }, abstract = {Medium-chain carboxylates (MCCs) can be produced using open, mixed cultures of microorganisms in a process termed "chain elongation." Chain elongating bacteria can increase ATP yield by producing six-carbon caproate rather than four-carbon butyrate. Therefore, requiring chain elongating bacteria to maximize ATP yield for cell synthesis may be a way to increase production of the more valuable caproate. To test this, duplicate bioreactors were operated, and the impact of organic loading rate (OLR) fluctuations were assessed with glucose and xylose as substrates in media that did not include amino acids, vitamins, or other growth factors. Increasing the OLR did not reliably improve caproate production despite several known caproate-producing bacteria being present. 16S rRNA gene amplicon sequencing and shotgun metagenomics revealed that the same chain-elongating and sugar-degrading species were enriched in both bioreactors, including members of the Caproiciproducens, Caproicibacter, Olegusella, and Tractidigestivibacter genera. Further, metatranscriptomic results suggest a distinct division of labor associated with critical growth factors, including amino acids, folate, and pantothenate. This division of labor, while potentially beneficial to the microbial community, may result in low caproate production.}, }
@article {pmid42026082, year = {2026}, author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P}, title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07163-w}, pmid = {42026082}, issn = {2052-4463}, support = {240859//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; }, abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.}, }
@article {pmid42026126, year = {2026}, author = {Miravet-Verde, S and Cacace, E and Mores, CR and Rutschmann, C and Lin, CW and Ruscheweyh, HJ and Cuénod, A and Barazzone, EC and Marrec, E and Vershynina, K and Schumann, R and Bower, DJ and Schubert, M and Egli, A and Fiebig, T and Slack, E and Sunagawa, S and Keys, TG}, title = {In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1217-1232}, pmid = {42026126}, issn = {2058-5276}, support = {51NF40_225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; CRSK- 3_228959//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 117.143 IP-LS//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; FN24-0000000703//Novartis Stiftung f&#xfc;r Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; 865730//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Escherichia coli/genetics/classification/metabolism ; *Bacterial Capsules/genetics/classification/metabolism/chemistry ; *Serotyping/methods ; Genome, Bacterial ; Computer Simulation ; *Membrane Transport Proteins/metabolism/genetics ; *Escherichia coli Proteins/genetics/metabolism ; Genetic Variation ; Hidden Markov Models ; Genotype ; }, abstract = {Serotyping identifies bacterial variants based on surface antigens, traditionally using antibody-based assays, but has been increasingly replaced by in silico methods that infer serotypes from genomic sequences for faster, scalable and more reproducible analyses. However, traditional Escherichia coli capsule serotyping has largely fallen out of use since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution and epidemiology. As capsules influence bacterial interactions with phages, host immune systems and the environment, this gap limits our understanding of E. coli ecology and pathogenicity as well as vaccine and diagnostic development. Here we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed 37,723 E. coli genomes, cataloguing 85 transporter-dependent capsule types (K-types), including 55 types that were not part of the reference collection. We leveraged this catalogue to develop a hidden Markov model-based in silico serotyping tool, kTYPr, and applied it to curated sets of 24,015 E. coli genomes and 2,762 metagenome-assembled genomes spanning diverse environmental and clinical sources. We found previously uncharacterized K-types enriched in undersampled environments and associated with E. coli disease. This study expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.}, }
@article {pmid42026467, year = {2026}, author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F}, title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42026467}, issn = {1471-2180}, support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Primary idiopathic male infertility (PIMI) is a complex condition with unclear biological mechanisms. Increasing evidence indicates that gut microbiome-derived functional and metabolic alterations can influence host physiological processes, yet microbiome-associated functional changes in PIMI remain poorly characterized.<br><br>METHODS: In this case&#x2013;control study, fecal shotgun metagenomics and untargeted liquid chromatography-tandem mass spectrometry (LC&#x2013;MS/MS) metabolomics were performed in 19 men with PIMI and 12 fertile controls, alongside computer-assisted semen analysis. The study workflow integrated differential analyses, correlation analyses among key microbial species, metabolites, and clinical traits, and Random Forest modeling to derive a microbial-metabolic panel.<br><br>RESULTS: Compared with fertile controls, infertile men exhibited selective functional remodeling of gut microbial pathways and fecal metabolic profiles, accompanied by reduced sperm concentration and progressive motility and increased round cell counts. Although overall microbial diversity was broadly comparable between groups, 23 differentially abundant species and 53 altered Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified by metagenomic profiling. Untargeted metabolomics annotated 4,434 metabolites and identified 780 differential metabolites, with enrichment of 29 KEGG pathways. Eight key microbial species and eight key metabolites mapped to sperm- and testis-related pathways showed coordinated correlations with semen parameters. An integrated Random Forest model incorporating microbial and metabolic features demonstrated robust discrimination between infertile and fertile men, with optimal performance achieved using six top-ranked features.<br><br>CONCLUSIONS: PIMI is associated with selective gut microbial functional shifts and fecal metabolic disturbances that correlate with semen quality. Multi-omics integration highlights coordinated microbiome-metabolome alterations, providing insights into host-associated microbial functional dysregulation in male infertility.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05064-x.}, }
@article {pmid42026490, year = {2026}, author = {Pan, J and Kong, H and Liang, M and Fang, X}, title = {Pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii leading to acute respiratory distress syndrome in an HIV-negative immunocompromised patient: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42026490}, issn = {1471-2334}, abstract = {BACKGROUND: Pulmonary tuberculosis (PTB) and Pneumocystis jirovecii pneumonia (PJP) often occur in immunosuppressed populations, particularly in individuals with human immunodeficiency virus (HIV) infection. However, co-infection with these two pathogens resulting in acute respiratory distress syndrome (ARDS) has been less frequently reported, especially in HIV-negative patients. CASE PRESENTATION: We report the case of a 68-year-old immunosuppressed male patient with pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii, leading to ARDS, who was successfully treated. Following a definitive diagnosis of pemphigus vulgaris and 3 months of glucocorticoid and immunosuppressive therapy, the patient had a sudden onset of fever and dyspnea. He was admitted to the respiratory department of a general hospital with a diagnosis of severe community-acquired pneumonia. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected the presence of M.tuberculosis and P. jirovecii. Owing to the suspected contagious nature of tuberculosis, he was transferred to the tuberculosis department of our hospital. The patient developed severe respiratory distress; chest computed tomography (CT) revealed cavitary lesions and progressive pulmonary exudative changes, and arterial blood gas analysis demonstrated hypoxic respiratory failure. Because of limited respiratory support resources in the tuberculosis department, the patient was then transferred to the Respiratory Intensive Care Unit for endotracheal intubation and invasive mechanical ventilation. The patient received high positive end-expiratory pressure respiratory support therapy and restrictive fluid management strategies. Clindamycin combined with caspofungin was administered for PJP because of a suspected sulfonamide allergy, while standard first-line anti-tuberculosis therapy was initiated concurrently. The patient showed progressive clinical improvement and was successfully extubated on day 7 after intubation. At one-month follow-up, he had recovered well, and chest CT demonstrated substantial resolution of pulmonary lesions. CONCLUSION: The successful management of this patient was attributed to timely etiological diagnosis, targeted anti-infective therapy, effective supportive respiratory care, and fluid management. This case highlights the importance of heightened vigilance and prompt, comprehensive treatment in immunosuppressed patients with severe pneumonia, particularly in non-HIV individuals.}, }
@article {pmid42026803, year = {2026}, author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R}, title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662690}, pmid = {42026803}, issn = {1949-0984}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/genetics/drug effects ; Biomarkers, Tumor/genetics ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Deep Learning ; }, abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.}, }
@article {pmid42027256, year = {2026}, author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J}, title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {581751}, pmid = {42027256}, issn = {1178-7031}, abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.<br><br>MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.<br><br>RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.<br><br>CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.}, }
@article {pmid42027295, year = {2026}, author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR}, title = {Methanotrophy dominated symbiosis in novel species Gigantidas niobengalensis from the cold seeps of Krishna-Godavari basin.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag014}, pmid = {42027295}, issn = {2633-6685}, abstract = {Bathymodiolus mussels, which are prominent invertebrates at cold seeps and hydrothermal vents, are known for hosting symbiotic microbes within their gills. In this study, the microbial communities associated with the gills of novel bathymodioline mussel Gigantidas niobengalensis from an active cold seep site of Krishna-Godavari (K-G) basin was investigated by 16S rRNA amplicon sequencing. The average abundance of culturable methanotrophs in the gill tissues was 3.4 ± 0.9 × 10[4] CFU g[-1] with average methane oxidation rates of 1.71 ± 0.04 to 1.89 ± 0.02 µM g[-1] d[-1] under aerobic and 1.86 ± 0.001 to 1.98 ± 0.005 µM g[-1] d[-1] under anaerobic conditions. Metagenomic analysis revealed dominance of methanotrophs within the microbial communities comprising of >55% bacterial and >28% archaeal methanotrophs; with phyla Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, Euryarchaeota, and Crenarcheaota being prevalent. Functional classification highlighted methane metabolism (20%) and carbon fixation (22%) as major energy metabolism pathways. This study represents the first metagenomic characterization of gill-associated symbionts in the novel cold seep mussel G. niobengalensis from the Indian Ocean. The findings fill a knowledge gap on chemosynthetic symbioses in Indian cold seep ecosystems and provide insights into metabolic adaptation of G. niobengalensis in the cold seep ecosystem.}, }
@article {pmid42027454, year = {2026}, author = {Chen, X and Gong, L and Lu, Y and Liu, W and Liu, F and Li, Q and Wang, L and Qiu, L and Zhang, D and Ye, X}, title = {Epidemiological characteristics and environmental surveillance of human psittacosis in Lishui City, Zhejiang Province, China (2021-2024).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1769696}, pmid = {42027454}, issn = {1664-302X}, abstract = {INTRODUCTION: Psittacosis, caused by Chlamydia psittaci, is an underdiagnosed zoonosis that can lead to severe pneumonia and fatal outcomes. In China, traditional poultry farming poses substantial risks for avian-to-human transmission, yet comprehensive epidemiological evidence is scarce. To address this gap, we aimed to define the local epidemiology, risk factors, and environmental reservoirs of human psittacosis in Lishui City, Zhejiang Province.<br><br>METHODS: We conducted a multi-source epidemiological study (2021-2024) integrating surveillance data, clinical records, contact investigations, and environmental sampling. Cases were confirmed by quantitative polymerase chain reaction (qPCR) or metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: We identified 28 laboratory-confirmed cases, showing annual fluctuations in reported case numbers. Infections, mostly confirmed by mNGS, were predominantly sporadic among elderly agricultural workers (mean age 62.6 years), with 96.4% reporting recent poultry exposure. All patients presented with pneumonia; 64.3% developed severe disease, resulting in three deaths. The median diagnostic delay-from symptom onset to diagnosis-was 12 days. A household cluster of three cases was detected; however, no secondary transmission occurred among 205 close contacts outside the household. C. psittaci DNA was detected in 14.79% (21/142) of environmental samples, with the highest number of cases detected in duck manure samples, with the highest positive rate (26.7%). Phylogenetic analysis of 20 ompA gene sequences revealed a predominantly genotype A and the waterfowl-TW genotype, which are closely related to strains from southern China.<br><br>DISCUSSION: Psittacosis in Lishui presents as a sporadic but clinically severe disease in older rural residents. The high frequency of severe pneumonia and prolonged diagnostic delay underscores an urgent need to improve clinical suspicion and access to molecular diagnostics. Detection of C. psittaci nucleic acid in environmental samples suggests possible environmental contamination; however, viability and transmissibility were not assessed.}, }
@article {pmid42027830, year = {2026}, author = {Chen, L and Ding, Y and Liu, Y and Xie, Q and Hu, J and Wang, M and Zeng, X and Zou, D}, title = {Case Report: Ultrasound guided puncture for type 2 diabetes mellitus combined with psoas abscess-a report of two cases.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1773238}, pmid = {42027830}, issn = {2296-858X}, abstract = {BACKGROUND: Psoas abscess (PA) is a rare infectious disease, with type 2 diabetes mellitus (T2DM) serving as a significant risk factor. The combination of metagenomic next-generation sequencing (mNGS) and ultrasound offers innovative approaches for the rapid and precise treatment of PA.<br><br>CASE PRESENTATION: Case 1: A 77-year-old woman presented with lumbar pain was initially misdiagnosed with lumbar disc herniation based on CT scan. Subsequent CT scan and ultrasound-guided puncture confirmed a left lumbar PA. mNGS detected the presence of Streptococcus agalactiae, which was negative on conventional culture. The patient was successfully treated with vancomycin for 5 weeks, with no recurrence at 3-year follow-up. Case 2: A 56-year-old woman with a 10-year history of T2DM presented with poor appetite and fatigue. CT imaging identified a left lumbar PA along with perirenal infection. Pus from ultrasound-guided puncture for conventional culture and mNGS detected the presence of Staphylococcus aureus. Treatment with oxacillin and vancomycin led to clinical resolution. The follow-up CT scan in 2024 indicated complete resorption of the lesion.<br><br>CONCLUSION: mNGS combined with ultrasound-guided puncture overcomes conventional culture limitations. This approach suggests clinical feasibility.}, }
@article {pmid42028026, year = {2026}, author = {Heinzelmann, D and Reuss, F and Zeh, N and Nilson, R and Walker, E and Fieder, J and Lindner, B and Renner, B and Schulz, P and Fischer, S and Schmidt, M}, title = {Discovery of a chimeric transposase-transposon system for advanced genome engineering.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115548}, pmid = {42028026}, issn = {2589-0042}, abstract = {Transposases have transformed genetic engineering, yet functional systems remain scarce. In response, an unknown transposase system from Acyrthosiphon pisum was identified by metagenomic screening. Through systematic optimization, we enhanced nuclear localization, transposon architecture, and created a hyperactive transposase variant to boost efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein-producing Chinese Hamster Ovary (CHO) cell lines, even surpassing the hyperactive piggyBac system with regard to cell-specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.}, }
@article {pmid42028145, year = {2026}, author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J}, title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.}, journal = {Journal of intensive medicine}, volume = {6}, number = {2}, pages = {157-165}, pmid = {42028145}, issn = {2667-100X}, abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.<br><br>METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/&#xb5;L<CD4[+]T-cell count<500/&#xb5;L), moderate (200 /&#xb5;L<CD4[+]T-cell count &#x2264; 350/&#xb5;L), and severe (CD4[+]T-cell count &#x2264;200/&#xb5;L) groups. Microecological analysis was performed on each group. Intergroup comparisons were conducted for 28-day mortality, hospital length of stay, and ICU length of stay.<br><br>RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.<br><br>CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.}, }
@article {pmid42028191, year = {2026}, author = {Hariharamohan, M and Chindarkar, M and Swain, HS and Rajesh, N and Rajesh, V}, title = {Integrating physicochemical and microbial characterization of red rice broth fermented over an 18-hour period augmented with metagenomic and metabolomic approaches.}, journal = {RSC advances}, volume = {16}, number = {23}, pages = {21129-21141}, pmid = {42028191}, issn = {2046-2069}, abstract = {Fermentation enhances the nutritional properties of foods. Fermented water of Kerala red rice (Oryza sativa L. subsp. indica), traditionally consumed in South India remains underexplored scientifically. This study characterizes the nutritional, microbial, and metabolite profiles of Kerala red rice water (broth) after 18 hours of natural fermentation using biochemical assays, shotgun whole-genome metagenomic sequencing (Illumina NovaSeq X Plus), untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, and a phytase-mediated mineral release assay. Fermentation enhanced nutritional quality with increase in carbohydrates by 22.7%, protein by 163.52%, and free amino acids by 35.47% compared to unfermented controls. Phytase activity rose from negligible levels to 0.12 U mL[-1]. Metagenomics identified 50 taxa, dominated by Proteobacteria (59.63%) and Firmicutes (40.12%), with ∼34% of the community carrying phytase-encoding genes. Dominant genera included Pantoea, Saccharibacillus, and Bacillus. Fermentation also enhanced mineral release, with calcium, iron, and zinc in the fermented rice water showing increases of approximately 1190%, 566%, and 93%, respectively, relative to unfermented controls over a 360 min in vitro digestion period. These findings provide the first integrated insight bridging traditional dietary practice with modern analytical science.}, }
@article {pmid42028978, year = {2026}, author = {Xiao, L and Liu, J and Noyce, GL and Lee, J and Duarte, CM and Zhou, M and Luo, M and Sun, R and Dang, R and Zhou, L and Zhang, L and Fu, C and Tan, Y and Yu, J and Han, G}, title = {Microbial Responses to Warming Reduce Deep Blue Carbon Storage.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70883}, doi = {10.1111/gcb.70883}, pmid = {42028978}, issn = {1365-2486}, support = {U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 42071126//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; XDA23050202//Strategic Priority Research Program of Chinese Academy/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Carbon/metabolism ; Soil/chemistry ; *Carbon Sequestration ; Wetlands ; *Climate Change ; *Global Warming ; }, abstract = {Coastal wetlands are critical blue carbon reservoirs, yet the depth-resolved impacts of warming on belowground carbon dynamics remain poorly understood. Over the course of an 8-year in situ experiment, we investigated plant-derived carbon inputs, soil carbon losses via respiration, and microbially mediated carbon fixation across a 60 cm soil profile under a projected 2°C atmospheric warming scenario. Plant carbon fixation (above- and belowground net primary productivity) and soil respiration exhibited synchronized responses to warming, with an initial increase, followed by a decline in the mid-term, and no significant response in the later stages. Soil and microbial respiration stabilized after prolonged exposure to elevated temperatures, as these processes were constrained by substrate availability. In contrast, phospholipid fatty acid profiling, amino sugar biomarkers, and metagenome-assembled genomes consistently indicated a greater than one-third reduction in microbial carbon fixation within subsoils (40-60 cm). Our fully factorial, depth-stratified warming design reveals the particular vulnerability of deep soil microbial carbon retention to long-term climate warming, independent of shifts in plant input or respiratory carbon loss. This work highlights underappreciated pathways influencing soil blue carbon dynamics in a changing world.}, }
@article {pmid42028995, year = {2026}, author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y}, title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0026826}, pmid = {42028995}, issn = {1098-5336}, mesh = {*Medicago sativa/growth &amp; development/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacillus/physiology ; Soil/chemistry ; *Coal ; Gene Expression Regulation, Bacterial ; }, abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.<br><br>IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.}, }
@article {pmid42029028, year = {2026}, author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M}, title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0030826}, pmid = {42029028}, issn = {1098-5336}, support = {37/1027-1//Deutsche Forschungsgemeinschaft/ ; 503493769//Deutsche Forschungsgemeinschaft/ ; PE501078509-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; }, mesh = {Biodegradation, Environmental ; Mining ; *Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Peru ; Oxidation-Reduction ; Acids/metabolism ; }, abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.}, }
@article {pmid42029155, year = {2026}, author = {Perlas, A and Reska, T and Sánchez-Cano, A and Mejías-Molina, C and Gygax, D and Martínez-Puchol, S and Rusiñol, M and Eger, E and Schaufler, K and Höfle, U and Croville, G and Le Loc'h, G and Guérin, J-L and Urban, L}, title = {Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0254325}, pmid = {42029155}, issn = {1098-5336}, support = {2824HS010//German One Health Platform Pilot Project/ ; PID2020-114060RR-C32//MCIN/AEI/10.13039/501100011033/ ; }, mesh = {*Wetlands ; Animals ; Birds ; Humans ; Host Tropism ; *Water Microbiology ; *Bacteria/genetics/isolation &amp; purification/drug effects ; Influenza A virus/genetics/isolation &amp; purification ; Metagenomics ; Ecosystem ; Viruses/isolation &amp; purification/genetics ; }, abstract = {UNLABELLED: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains.<br><br>IMPORTANCE: Wetlands connect wildlife, livestock, and people, making them key places to watch for pathogens and antibiotic resistance. Yet potentially harmful microbes are easy to miss in water because they represent only a small fraction of the abundant microbial life in water, making them hard to detect. We paired 3D-printed passive torpedo-shaped samplers with a portable genetic sequencer to analyze all microbes captured. We deployed this approach at 12 wetlands in Germany, France, and Spain. It revealed local microbial communities, identified disease-causing bacteria, and linked many antibiotic resistance genes to likely bacterial hosts. By comparing locations, we observed that sites near cities, farms, or wastewater had higher levels of pathogens and resistance than protected natural sites. Our analysis also recovered all viruses present, including those from mammals, birds, fish, insects, and plants. We also specifically looked for the virus that causes avian flu, found it at several sites, and classified it as low pathogenicity. Because our method is non-invasive to wildlife, affordable, and practical to deploy, it can provide early warnings to conservation and public health agencies and guide action where risks are present.}, }
@article {pmid42029954, year = {2026}, author = {Gao, J and Li, HL and Li, MS and Shao, ZJ and Yang, ZF and Li, CJ and Zhang, ZX and Zhu, D and Lv, ZH and Song, RH and Li, JL and Hu, W and Yin, YR}, title = {Cloning, heterologous expression, and characterization of a metagenome-derived GH10 xylanase with salt and alkali tolerance from Xinjiang saline-alkali soil.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {42029954}, issn = {1572-9699}, support = {YWLCYXZX2023300075//the Yunnan Provincial Clinical Medical Center for Emergency Traumatic Diseases/ ; 32560004//the National Natural Science Foundation of China Regional Program/ ; }, mesh = {Cloning, Molecular ; *Metagenome ; *Soil Microbiology ; *Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Alkalies ; China ; Soil/chemistry ; Salt Tolerance ; Recombinant Proteins/genetics/metabolism/chemistry ; Temperature ; Xylans/metabolism ; Escherichia coli/genetics/metabolism ; Amino Acid Sequence ; Substrate Specificity ; Sodium Chloride ; }, abstract = {Xylanases are widely used in baking, seafood processing, and paper production, but their performance is often compromised under high-salt, acidic, or alkaline conditions, limiting broader industrial deployment. Identifying robust xylanases from saline-alkali environments is therefore of practical importance. Here, we report a GH10 xylanase gene, XynE102, mined from a saline-alkali soil metagenome from Karamay, Xinjiang. The deduced amino acid sequence shares 69.17% identity with a xylanase from Cellvibrionaceae bacterium (GenBank accession HEY7885703.1). XynE102 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified by Ni-NTA affinity chromatography. Using beechwood xylan as substrate, XynE102 exhibited optimal activity at 50 °C and pH 7.0. It retained ≥ 50% relative activity between 30 and 55 °C and pH 5.6-8.6, and ≥ 75% activity in 2.0 M NaCl. Notably, after preincubation at 40 °C for 60 and 120 min, its activity increased to 130% and 165% of the initial value, respectively. Following 24 h preincubation at pH 7-10, residual activity remained ≥ 80%, indicating pronounced alkaline stability. At 1 mM, Mn[2+], Co[2+], and Fe[3+] activated the enzyme, whereas Mg[2+], Cu[2+], and Cd[2+] inhibited it; 1% SDS had no measurable effect. XynE102 primarily hydrolyzed xylan to xylobiose and xylotetraose. It also hydrolyzed alkali-treated corn stalk and hot-water-pretreated wheat bran, yielding reducing sugar concentrations of 5.44 mM and 4.18 mM, respectively, after 24 h. Taken together, these results indicate that XynE102 is a neutral-pH xylanase with notable salt and alkali tolerance, supporting its potential for prebiotic XOS production and food-processing applications under moderate temperature conditions.}, }
@article {pmid42030718, year = {2026}, author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L}, title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142145}, doi = {10.1016/j.jhazmat.2026.142145}, pmid = {42030718}, issn = {1873-3336}, mesh = {*Arsenic/analysis/metabolism ; *Estuaries ; *Water Pollutants, Chemical/analysis/metabolism ; Rivers/chemistry/microbiology ; Geologic Sediments/chemistry ; China ; Bacteria/metabolism/genetics ; Seasons ; Metagenome ; Microbiota ; }, abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.}, }
@article {pmid42030844, year = {2026}, author = {Zhao, H and Che, W and Tan, X and Shen, Y and Xu, Y and Man, Y}, title = {Distribution characteristics and potential microbial degradation mechanisms of microplastics in oyster aquaculture areas of southern China.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142136}, doi = {10.1016/j.jhazmat.2026.142136}, pmid = {42030844}, issn = {1873-3336}, mesh = {*Microplastics/metabolism/analysis ; *Aquaculture ; Animals ; China ; *Water Pollutants, Chemical/analysis/metabolism ; Biodegradation, Environmental ; *Ostreidae ; *Bacteria/metabolism/genetics ; Seawater ; Environmental Monitoring ; Geologic Sediments/microbiology ; }, abstract = {Microplastic (MP) pollution in coastal aquaculture is a growing environmental and public health concern. Despite increasing reports, the cross-regional and cross-media pollution patterns, ecological risks, and microbial degradation potentials in aquaculture ecosystems remain poorly understood. We investigated oyster farming systems in South China: Zhanjiang Bay (ZJB, semi-enclosed) and Xuwen (XW, open coast). MP abundances ranged from 20 to 54 items/L in seawater and 950-6483 items/kg in sediment, with particles < 50 μm and granular shapes dominant in both media, as determined by Laser Direct Infrared Imaging. MP spatial patterns differed markedly between regions; XW exhibited higher seawater MP levels attributed to larger farming scales, whereas ZJB showed greater sediment MP accumulation owing to weaker water exchange and a longer farming history. Source apportionment identified aquaculture facilities as the primary source (44.86%). Notably, while the overall pollution load was relatively low, the potential ecological risk index reached 866.51 (classified as "dangerous"), driven predominantly by highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC). The distribution of plastic-degrading genes (PDGs) and their host microbial communities was primarily determined by these aquaculture facilities and the environmental medium (sediment vs. seawater), rather than by localized water-quality conditions. Metagenomic analysis identified sediments as key metabolic hotspots, harboring diverse functional genes involved in polyethylene β-oxidation, polystyrene aromatic ring cleavage, and PU hydrolysis. These findings bridge the gap in understanding MP dynamics between diverse aquaculture habitats and highlight the potential of indigenous microbes in natural attenuation, providing critical insights for MP risk management.}, }
@article {pmid42030878, year = {2026}, author = {Saini, K and Prajapati, A and Kumar, SS and Kumar, V and Bajar, S}, title = {Performance assessment of sulfate-reducing bacterial consortium for the treatment of real landfill leachate under anaerobic conditions.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129743}, doi = {10.1016/j.jenvman.2026.129743}, pmid = {42030878}, issn = {1095-8630}, mesh = {*Water Pollutants, Chemical/metabolism ; *Sulfates/metabolism ; Biodegradation, Environmental ; Anaerobiosis ; Bacteria/metabolism ; RNA, Ribosomal, 16S ; Metals, Heavy/metabolism ; Biological Oxygen Demand Analysis ; Waste Disposal, Fluid/methods ; }, abstract = {Landfill leachate contains complex organic pollutants, ammonia, sulfate, and toxic metals, posing major environmental challenges. This study evaluated a sulfate-reducing bacterial (SRB) consortium isolated from electroplating wastewater for the treatment of real landfill leachate under anaerobic conditions. Physicochemical characterization revealed a Leachate Pollution Index (LPI) of 63.16, confirming the high hazardous nature of the leachate. The acclimatized SRB consortium exhibited strong metabolic activity and rapidly degraded pollutants. Within 10 days of treatment, the system achieved 82.84% removal of chemical oxygen demand (COD) and 97.83% removal of biochemical oxygen demand (BOD5), demonstrating efficient biodegradation of both biodegradable and persistent organic compounds. The concentrations of heavy metals were reduced to below the detection limit (BDL), primarily due to sulfide-mediated precipitation. Thus, SRB provide dual benefits of organic degradation and metal detoxification. Metagenomic profiling (16S rRNA sequencing) revealed dominant sulfate-reducing species, including Desulfovibrio vulgaris, Desulfotomaculum nigrificans, Desulfobulbus propionicus, and Desulfosporosinus orientis. Kyoto Encyclopedia of Genes and Genomes (KEGG) based functional annotation was performed to elucidate the metabolic potential of the SRB consortium. Scanning electron microscopy (SEM) analysis before and after treatment confirmed microbial colonization and sulfide-mediated metal precipitation. Overall, SRB-based anaerobic processes demonstrate significant potential as a sustainable and efficient treatment for high-strength landfill leachate with strong potential for scale-up and integration into waste management systems. Although the treated effluent did not meet CPCB (India) and EPA COD discharge standards, this bioremediation approach provides a cost-effective alternative to conventional physicochemical treatments. Further optimization of operational parameters and microbial activity could enhance treatment efficiency and facilitate regulatory compliance.}, }
@article {pmid42030912, year = {2026}, author = {Hua, Y and Xu, X and Chen, Y and Li, Y and Dai, X}, title = {Making waves: Wastewater sludge holds untapped antimicrobial potential.}, journal = {Water research}, volume = {300}, number = {}, pages = {125989}, doi = {10.1016/j.watres.2026.125989}, pmid = {42030912}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Wastewater ; *Anti-Infective Agents ; Antimicrobial Peptides ; Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants are widely recognized as critical nodes in the environmental dissemination and control of antimicrobial resistance (AMR). This risk-focused view is warranted, but incomplete. Wastewater sludge is one of the largest engineered and repeatedly accessible microbiomes on Earth, continuously shaped by diverse microbial inputs and exposure to antimicrobial compounds and other stressors. These conditions may also harbor underexplored antimicrobial functions. Here we propose framing sludge as a dual-function node within AMR stewardship: a resource for routine surveillance and risk management, and a source material for an offline, containment-first workflow to identify antimicrobial candidates, particularly antimicrobial peptides. We summarize recent advances in metagenomics and machine-learning-enabled peptide prioritization and outline an evidence ladder that links sequence signals to functional validation. A central principle is to decouple discovery from plant operations and to apply explicit decision gates early in the pipeline, including cross-resistance screening and resistance-evolution assays, to prevent inadvertently increasing selection pressure or AMR risks. Finally, we call for shared benchmarks to improve comparability across studies, including curated datasets, standardized validation panels, and routine reporting of negative findings and resistance-related outcomes. Together, these steps can help translate sludge-enabled discovery into environmentally responsible innovation aligned with AMR stewardship.}, }
@article {pmid42030968, year = {2026}, author = {Brown, JR and Chiu, CY and López-Labrador, FX and de Vries, JJC}, title = {The impact of clinical metagenomic testing on patient management: facts versus fantasy.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00106-4}, pmid = {42030968}, issn = {1474-4457}, abstract = {Clinical metagenomic testing by agnostic, unbiased next-generation sequencing is a diagnostic approach with the broad-based capacity to detect all known and novel pathogens in a single assay. After the discovery of this potentially transformative method decades ago, the availability of clinical metagenomic testing in the daily practice of the infectious disease specialist is accelerating. Prospective metagenomic studies have supplemented the substantial existing body of retrospective, exploratory literature, and these reports offer us a glimpse into the real-world use of clinical metagenomic testing for the diagnosis of infections in patients. In this Review, we examine the evidence collected from the prospective reports published to date, focusing on their impact on patient management, treatment, and outcomes.}, }
@article {pmid42031746, year = {2026}, author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q}, title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031746}, issn = {2041-1723}, support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Nitrous Oxide/metabolism/analysis ; *Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Methane/metabolism ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism ; }, abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.}, }
@article {pmid42031750, year = {2026}, author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K}, title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031750}, issn = {2041-1723}, }
@article {pmid42032005, year = {2026}, author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG}, title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42032005}, issn = {2045-2322}, support = {N. 24-45-20005//RSF grant/ ; }, mesh = {Animals ; *Ixodes/virology ; Russia ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; *Virome/genetics ; Genetic Variation ; }, abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.}, }
@article {pmid42032049, year = {2026}, author = {Zhang, X and Li, W and Wu, H and Cai, T and Chen, H and Zeng, S}, title = {Enhanced pathogen identification in fungal endophthalmitis by metagenomic next-generation sequencing: a retrospective clinical evaluation.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42032049}, issn = {2045-2322}, support = {LHGJ20220091//Henan Province Medical Science and Technology Key Project/ ; 2023A1515012220//Guangdong Basic and Applied Basic Research Foundation/ ; 2024ZDJS120//Guangdong Province Research Capability Improvement Project for Key Construction Disciplines/ ; 2025XSJ013&#xff1b;2024XK003&#xff1b;2021BQ011//Nanfang College Guangzhou/ ; }, mesh = {*Endophthalmitis/microbiology/diagnosis ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; *Eye Infections, Fungal/microbiology/diagnosis ; Aqueous Humor/microbiology ; Vitreous Body/microbiology ; *Fungi/genetics/isolation &amp; purification/classification ; Aspergillus flavus/genetics ; }, abstract = {Fungal endophthalmitis (FE) is a vision-threatening emergency that requires rapid pathogen identification. Conventional microbial culture demonstrates limited sensitivity in FE, warranting improved diagnostic approaches. We evaluated the detection performance of unbiased metagenomic next-generation sequencing (mNGS) in 31 clinically diagnosed FE cases, including 16 vitreous humor (VH) and 15 aqueous humor (AH) specimens. mNGS showed a positivity rate of 90.3% (28/31, 95% CI: 74.2%-98%), outperforming culture (9.1%, 2/22, 95% CI: 1.1%-29.2%). The positivity rates were 100% for endogenous FE and 85% for exogenous FE, while VH and AH specimens achieved 100% and 80% positivity, respectively. mNGS identified polymicrobial infections in 5 exogenous cases, and a total of 15 fungal species across 9 genera, dominated by Aspergillus flavus, Candida albicans, and Aspergillus niger. Candida albicans and Aspergillus flavus were the predominant pathogens in endogenous and exogenous FE, respectively. Notably, mNGS enabled detection of rare fungal species including Aspergillus niger, Aspergillus welwitschiae, Fusarium oxysporum, Memnoniella echinata, Rhizopus oryzae, Rhizopus microsporus, Chaetomium globosum, and Debaryomyces fabryi. Sequencing results were supported or supplemented by culture, beta-D-glucan, and galactomannan testing in selected cases. Among mNGS-positive cases, 82.1% (23/28) experienced clinical management changes guided by fungal identification. We further propose a laboratory workflow integrating mNGS with conventional assays, tailored to the obtained specimen volume of intraocular fluids.}, }
@article {pmid42032279, year = {2026}, author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G}, title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1739-1753}, pmid = {42032279}, issn = {2058-5276}, support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics/classification ; *Metagenomics/methods ; Colorectal Neoplasms/microbiology ; Substrate Specificity ; Carbohydrate Metabolism ; Mucins/metabolism ; }, abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .}, }
@article {pmid42032281, year = {2026}, author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J}, title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1626-1638}, pmid = {42032281}, issn = {2058-5276}, support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Metagenomics/methods ; Algorithms ; Polymorphism, Single Nucleotide ; Streptococcus pneumoniae/genetics ; Plasmodium falciparum/genetics ; Feces/microbiology ; COVID-19/transmission ; Malaria, Falciparum/transmission ; Gastrointestinal Microbiome/genetics ; Metagenome ; Infant ; High-Throughput Nucleotide Sequencing ; }, abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.}, }
@article {pmid42032282, year = {2026}, author = {}, title = {Benchmarking shotgun metagenomics.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1149-1150}, pmid = {42032282}, issn = {2058-5276}, }
@article {pmid42032888, year = {2026}, author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z}, title = {Rhizosphere microbiome influences fruit quality in citrus.}, journal = {The New phytologist}, volume = {250}, number = {6}, pages = {3914-3931}, doi = {10.1111/nph.71159}, pmid = {42032888}, issn = {1469-8137}, support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; }, mesh = {*Rhizosphere ; *Microbiota/genetics ; *Fruit/microbiology ; *Citrus/microbiology ; Iron/metabolism ; Bacteria/genetics/metabolism ; Siderophores/metabolism ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.}, }
@article {pmid42032992, year = {2025}, author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M}, title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {12}, pages = {2312-2324}, pmid = {42032992}, issn = {1672-7347}, support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *RNA, Ribosomal, 16S/genetics ; Child ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.<br><br>METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. &#x3b1;-diversity, &#x3b2;-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.<br><br>RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). &#x3b1;-diversity analysis showed that in the overall population, the Shannon index (5.49&#xb1;1.11) and Chao1 index (1 843.04&#xb1;580.78) in the V3 to V4 region were higher than the Shannon index (4.98&#xb1;0.65) and Chao1 index (379.59&#xb1;47.27) in the V4 region (all P<0.001). &#x3b2;-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41&#xb1;1.62) was not significantly different from that of metagenomic sequencing (6.39&#xb1;0.42) (P=0.169), while the Chao1 index (1 889.92&#xb1;781.73) was lower than that of metagenomic sequencing (3 092.71&#xb1;505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89&#xb1;0.94 vs 6.39&#xb1;0.42, 362.41&#xb1;35.22 vs 3 092.71&#xb1;505.89, respectively, both P<0.01).<br><br>CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of &#x3b1;-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.}, }
@article {pmid42033828, year = {2026}, author = {Liu, X and Li, N and Wu, WM and Ambrosini, R and Zhong, B and Mei, X and Liu, R and Zhou, L and Yi, S and He, Y}, title = {Freeze-thaw aging and microbial colonization converts microplastics into nitrogen cycling hotspots.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142170}, doi = {10.1016/j.jhazmat.2026.142170}, pmid = {42033828}, issn = {1873-3336}, mesh = {*Microplastics/metabolism/chemistry ; *Freezing ; *Nitrogen Cycle ; *Nitrogen/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {As global warming intensifies, the frequency of freeze-thaw events increases, significantly impacting microbial metabolism and biogeochemical cycling. However, the synergistic effects of freeze-thaw cycles (FTCs) and pervasive microplastics (MPs) on microbial community assembly and nitrogen cycling remain poorly understood. Here, we conducted a microcosm experiment integrating metagenomic and random forest model to elucidate the co-regulatory mechanisms of FTCs and MPs on plastisphere microbial communities and nitrogen metabolism. Results revealed that FTCs accelerated the environmental aging of MPs, inducing surface cracking and oxidation, thereby creating microenvironments favorable for microbial colonization. In the experimental microcosms, the combined effects of FTCs and presence of MPs increased microbial richness and diversity, promoted community differentiation between sediment and plastisphere, and increased microbial niche specialization. Functional analyses showed that FTCs induced a functional reconfiguration of the plastisphere nitrogen metabolism, with a selective enrichment of key enzyme genes, such as nitrite reductase, which may enhance nitrite redox activity and N2O emission capacity. In the plastisphere, the contribution of Acinetobacter to nitrogen cycling increased, whereas Nitrospira declined, possibly due to oxygen limitation. Overall, our findings suggested that FTCs may facilitate transformation of MPs from inert pollutants into potentially metabolically active microhabitats, providing critical insights for assessing emerging pollutants and climate change.}, }
@article {pmid42033834, year = {2026}, author = {Su, S and Lin, M and Li, K and Lin, J and Chen, Z}, title = {Soil aggregates as functional units for cadmium sequestration: Differential regulation by nitrogen enrichment and labile carbon inputs.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142196}, doi = {10.1016/j.jhazmat.2026.142196}, pmid = {42033834}, issn = {1873-3336}, mesh = {*Cadmium/chemistry ; *Nitrogen/chemistry ; *Soil Pollutants/chemistry ; *Carbon/chemistry ; *Soil/chemistry ; Soil Microbiology ; Glucose/chemistry ; }, abstract = {While cadmium (Cd) speciation in soil is known to control its environmental risk, how nitrogen (N) enrichment and labile organic carbon (LOC) inputs redistribute Cd fractions within soil aggregates remains unclear. This study examined how ammonium enrichment (AT), nitrate enrichment (NT), and glucose input (CT) altered carbonate-bound Cd (CB-Cd) and organic matter-bound Cd (OM-Cd) within soil aggregates. Both N enrichment and glucose input enhanced CB-Cd formation, with CT increasing CB-Cd by 39.19% via stimulated microbial activity and carbonate precipitation. Different sources of enriched N regulated OM-Cd, with AT decreasing OM-Cd by 15.55%, and NT increasing OM-Cd by 24.61%. This was attributed to competitive adsorption and suppressed microbial decomposition of recalcitrant organic matter. Aggregate hierarchy was also crucial in determining Cd speciation, where macroaggregates, with higher LOC and genes involved in carbonate precipitation, favored CB-Cd partitioning, whereas microaggregates, with greater surface area and enriched alkyl/aromatic C, served as the major OM-Cd sink. Microbial community analysis revealed that glucose reshaped communities, enriching r-strategists like Amycolatopsis and Trichoderma, which were positively correlated with CB-Cd and OM-Cd. Metagenomic data indicated that glucose stimulated genes for labile C degradation, reinforcing CB-Cd formation, while N addition suppressed C-degradation genes. Random forest and PLS path models identified alkyl C, O-alkyl C, and polysaccharide derivatives as primary SOC components regulating CB-Cd, while alkyl C, phenolic, and aromatic compounds regulating OM-Cd. These findings reveal a mechanism for stabilizing Cd in less bioavailable fractions via SOC and N management, leveraging soil aggregates' role in long-term metal sequestration.}, }
@article {pmid42033969, year = {2026}, author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C}, title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108068}, doi = {10.1016/j.marenvres.2026.108068}, pmid = {42033969}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; China ; *Environmental Monitoring ; *Microbiota ; Bacteria ; }, abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.}, }
@article {pmid42033990, year = {2026}, author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W}, title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.}, journal = {Biomaterials}, volume = {333}, number = {}, pages = {124234}, doi = {10.1016/j.biomaterials.2026.124234}, pmid = {42033990}, issn = {1878-5905}, mesh = {*Biofilms/drug effects ; Molybdenum/chemistry ; *Oxygen/chemistry ; *Periodontitis/microbiology/drug therapy/therapy ; *Microbiota/drug effects ; Humans ; Indocyanine Green/chemistry/pharmacology ; Animals ; *Nanoparticles/chemistry ; Photochemotherapy ; Photosensitizing Agents/chemistry/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.}, }
@article {pmid42034087, year = {2026}, author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z}, title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.}, journal = {Food chemistry}, volume = {516}, number = {}, pages = {149287}, doi = {10.1016/j.foodchem.2026.149287}, pmid = {42034087}, issn = {1873-7072}, mesh = {*Biogenic Amines/metabolism ; Fermentation ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Sodium Chloride/metabolism/analysis ; *Wine/microbiology/analysis ; Microbiota ; }, abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.}, }
@article {pmid42034426, year = {2026}, author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H}, title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107059}, doi = {10.1016/j.pestbp.2026.107059}, pmid = {42034426}, issn = {1095-9939}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Metagenome ; Interspersed Repetitive Sequences ; }, abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.}, }
@article {pmid42034448, year = {2026}, author = {Zhang, Y and Zhao, L and Zhang, P and Yang, Y and Wang, A and Xue, C and Yao, Y and Zhang, J and Zhao, M}, title = {Paenibacillus polymyxa EP-4 can effectively control southern corn leaf blight and affect the selectivity of Spodoptera frugiperda to corn.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107047}, doi = {10.1016/j.pestbp.2026.107047}, pmid = {42034448}, issn = {1095-9939}, mesh = {Animals ; *Zea mays/microbiology/parasitology ; *Spodoptera/physiology ; *Paenibacillus polymyxa/physiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Pest Control, Biological/methods ; *Ascomycota/physiology ; }, abstract = {Southern corn leaf blight (SCLB) and Spodoptera frugiperda pose serious threats to corn yield. In recent years, an increasing number of studies have investigated biological control agents to control plant diseases and insect pests. However, research on the use of one biocontrol bacterium to control plant diseases and insect pests simultaneously is very limited. In this study, the bacterium EP-4, which can significantly inhibit the growth of Bipolaris maydis, was identified as Paenibacillus polymyxa. EP-4 metabolites inhibited hyphal growth, caused hyphal deformities, significantly reduced the spore germination of B. maydis, and damaged cell membranes, leading to DNA leakage. In the greenhouse, EP-4 significantly reduced the disease index of SCLB and the feeding and oviposition preferences of S. frugiperda to corn. Metabolite analysis revealed that inoculation with B. maydis and S. frugiperda after EP-4 pretreatment affected the production of corn resistance-related substances such as brassinolide, quercetin, 2-undecanone and naringin. Metagenomic analysis revealed that EP-4 pretreatment and subsequent inoculation with pests and diseases could induce the recruitment of Pseudomonas, Burkholderia, Azotobacter and Mesorhizobium in corn. EP-4 could significantly reduce the occurrence of SCLB and significantly affect the feeding and oviposition of S. frugiperda on corn. The mechanism of action of EP-4 on pests and diseases has been shown to differ. This strain has great application potential in corn.}, }
@article {pmid42034850, year = {2026}, author = {Gupta, E and Sharma, S and Dash, PK and Parida, M}, title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42034850}, issn = {2045-2322}, abstract = {UNLABELLED: Several arboviruses including Dengue, Chikungunya, Zika, West Nile and Japanese encephalitis viruses are emerging and re-emerging in many parts of the world over last two decades. Thus, environmental surveillance of the mosquito borne viruses employing latest next generation sequencing technology could enhance our comprehension about an impending outbreak, thereby, providing opportunity for timely intervention. In this study, Aedes larvae were collected from different locations of Gwalior, Central India, cultured and grown to adult and were screened utilizing metagenomic workflow in Oxford Nanopore platform. The results produced sufficient and valuable insights through demonstration of divergence of these mosquitoes’ virome. Viral families associated with Myoviridae, Mimiviridae, Iridoviridae, Bunyaviridae, Flaviviridae, Mesonivirdae etc. were prevailing across the pools, varying in relative abundance. Viruses like Betabaculovirus, Mimivirus, Shamonda virus were reported in most pools in high abundance. Viral analysis leads to Phasi Charoen-like virus (PCLV), Nam Dinh virus (NDiV), Hubei mosquito virus (HMV), Wenzhou sobemo-like virus 4 (WSLV) findings across samples. This work reports the first successful metagenomic profiling of field-collected mosquitoes from Gwalior, Central India. Consequently, this technique might be employed to wide spectrum investigation of field mosquitoes, aiding in public health awareness about currently circulating viruses as a preparedness against future epidemic.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-49112-y.}, }
@article {pmid42034975, year = {2026}, author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K}, title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04999-5}, pmid = {42034975}, issn = {1471-2180}, support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; }, }
@article {pmid42034994, year = {2026}, author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B}, title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42034994}, issn = {1471-2334}, support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; }, abstract = {INTRODUCTION: The incidence of Mycobacterium abscessus complex (MABC) infections is rising, becoming a major pathogen of nontuberculous mycobacteria responsible for pulmonary disease (PD) and extrapulmonary disease (ED). However, studies on the clinical characteristics of MABC-ED remain limited. METHODS: A 7-year retrospective analysis was conducted on MABC-ED cases at Zhongshan Hospital in Shanghai, China. We analyzed predisposing factors, clinical features, metagenomic sequencing (MS) results, drug susceptibility testing (DST), and genomic characteristics of MABC-ED patients, comparing the data with those of PD cases. RESULTS: Among 17 MABC-ED patients, 15 had predisposing risk factors and underlying conditions, with 2 of 3 patients with rheumatic disease showing poor prognosis. The diagnostic performance of metagenomic sequencing for MABC-ED was comparable to that for MABC-PD. However, MABC-ED samples exhibited distinct microbiome features and a more diverse mycobacterial community structure compared to PD. Resistance rates among extrapulmonary MABC isolates were observed as follows: 0% (amikacin), 20% (macrolides), 30% (linezolid), and 40% (cefoxitin). One case showed paradoxical results between erm (41) T28 sequevar and susceptibility phenotype. Genomic analysis revealed no specific dominant circulating clones (DCC) for MABC-ED isolates. CONCLUSION: MABC-ED patients commonly present with risk factors and underlying diseases. Metagenomic sequencing diagnosis of MABC-ED poses challenges, and DST and whole genome sequencing data indicate diversity among MABC-ED isolates. Our study provides detailed data on MABC-ED, contributing to a better understanding of its disease characteristics.}, }
@article {pmid42035444, year = {2026}, author = {Lopez, C and Banker, A and Venkatasamy, V and Garcia, J and Mattiazzi, A and Eidam, L and Preczewski, L and Anjan, S and Nasrallah, A and Vianna, R and Morsi, M and Natori, Y}, title = {Diagnosing Hyperammonemia Syndrome in Non-Lung Solid Organ Transplant Recipients With Metagenomic Next-Generation Sequencing: Utility and Limitations From Two Clinical Cases.}, journal = {Clinical transplantation}, volume = {40}, number = {4}, pages = {e70550}, doi = {10.1111/ctr.70550}, pmid = {42035444}, issn = {1399-0012}, }
@article {pmid42035799, year = {2026}, author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K}, title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.}, journal = {Journal of affective disorders}, volume = {408}, number = {}, pages = {121858}, doi = {10.1016/j.jad.2026.121858}, pmid = {42035799}, issn = {1573-2517}, mesh = {Humans ; *Major Depressive Disorder/microbiology/psychology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Young Adult ; Adult ; Metagenomics ; Machine Learning ; Case-Control Studies ; }, abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.<br><br>METHODS: Fecal samples were collected from 121 first-episode, drug-na&#xef;ve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.<br><br>RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.<br><br>CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.}, }
@article {pmid42035921, year = {2026}, author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X}, title = {Molecular traces of microbial cross-kingdom migration: from the gut ecosystem to the intervertebral disc microenvironment.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2026.04.027}, pmid = {42035921}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.<br><br>PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multiomics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.<br><br>STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.<br><br>PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.<br><br>OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).<br><br>METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multiomics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.<br><br>RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter 3 nonchondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-&#x3b2; pathway for pro-fibrotic remodeling.<br><br>CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.}, }
@article {pmid42036057, year = {2026}, author = {Stem, AD and Alayyoub, M and Aalizadeh, R and Nikolopoulou, V and Lisgara, A and Shvartsman, A and Anitha, M and Patterson, A and Coble, R and Rushing, B and Sumner, S and Vasiliou, V}, title = {Integrated Multi-Omics Reveals Synergistic Hepatotoxicity of Ethanol and PFOS Co-Exposure.}, journal = {Chemico-biological interactions}, volume = {434}, number = {}, pages = {112101}, doi = {10.1016/j.cbi.2026.112101}, pmid = {42036057}, issn = {1872-7786}, mesh = {Animals ; *Ethanol/toxicity ; *Alkanesulfonic Acids/toxicity ; *Fluorocarbons/toxicity ; *Liver/drug effects/metabolism/pathology ; Multiomics ; Mice ; Male ; Mice, Inbred C57BL ; Metabolomics ; Lipidomics ; }, abstract = {Alcohol-associated liver disease (ALD) and exposure to per- and polyfluoroalkyl substances (PFAS) share key mechanisms of hepatotoxicity, yet their combined effects remain poorly characterized. We evaluated the impact of concurrent ethanol and perfluorooctanesulfonic acid (PFOS) exposure using a murine Lieber-DeCarli model characterized via multi-omic, spatial lipidomic, and metagenomic analyses. Exposure to PFOS resulted in rapid weight loss, while co-exposure led to decreased survival and pronounced hepatomegaly exceeding the effects of either exposure alone despite reduced cumulative ethanol intake. Histological analysis revealed enhanced hepatocellular injury with combined macrovesicular and microvesicular steatosis, consistent with impaired lipid handling and mitochondrial dysfunction. Transcriptomic and metabolomic profiling demonstrated disruption of xenobiotic metabolism, fatty acid β-oxidation, mitochondrial function, and bile acid transport, with PFOS acting as a dominant driver of metabolic stress and ethanol amplifying injury-related responses. Spatial lipidomics revealed hepatocyte-scale remodeling of membrane phospholipids, characterized by increased phosphatidic acid and depletion of phosphatidylinositol and phosphatidylserine under PFOS-containing conditions. Plasma metabolomics indicated systemic metabolic disturbance, including altered amino acid and redox pathways and depletion of microbiome-derived indole metabolites. Metagenomic analysis revealed reduced bacterial load and severe dysbiosis characterized by loss of commensal anaerobes, expansion of opportunistic taxa, and decreased microbial biosynthetic capacity. These findings indicate that PFOS increases susceptibility to alcohol-induced liver injury potentially through coordinated disruption of hepatic metabolism and gut-liver crosstalk, highlighting environmental PFAS exposure as a potential modifier of ALD severity.}, }
@article {pmid42036452, year = {2026}, author = {Byun, HR and Ji, SR and Frank, LE and Kipp, EJ and Larsen, PA and Chae, JS}, title = {Application of nanopore adaptive sampling for metagenomic detection of tick-borne RNA viruses.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42036452}, issn = {2045-2322}, support = {550-20250009//Seoul National University/ ; }, mesh = {Animals ; *Metagenomics/methods ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; *RNA Viruses/genetics/isolation &amp; purification/classification ; *Nanopores ; *Haemaphysalis longicornis/virology ; *Ticks/virology ; Republic of Korea ; *Nanopore Sequencing/methods ; }, abstract = {Nanopore sequencing is a powerful tool for real-time pathogen detection and genomic characterization; however, its application to individual ticks is limited by abundant host-derived nucleic acids and low viral RNA levels. In this study, we applied nanopore adaptive sampling (NAS) to sequence viral RNA from individual Haemaphysalis (H.) ticks collected in the Republic of Korea (ROK). By combining NAS with long-read sequencing, high-resolution genome assembly can be achieved from samples containing low-abundance viral RNA and relatively short complementary DNA (cDNA) fragments generated during library preparation. These results indicate that NAS remains effective under suboptimal fragment-size conditions and improves genome assembly compared to conventional nanopore workflows. Phylogenetic analyses revealed that the detected Dabieshan tick virus (DTV) sequences were clustered with isolates from China and Japan, suggesting regional circulation facilitated by the widespread distribution of H. longicornis. Unlike previous studies relying on pooled samples without selective sequencing, NAS allowed high-resolution viral genome assembly from single ticks. These findings confirm the presence and genotypes of DTV for the first time in the ROK and demonstrate NAS as a practical, scalable approach for tick-borne RNA virus surveillance in single ticks, improving genomic assembly and supporting the monitoring of emerging tick-borne viruses in endemic regions.}, }
@article {pmid42036496, year = {2026}, author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U}, title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {42036496}, issn = {1432-0614}, mesh = {Animals ; *Coumarins/metabolism ; *Feces/microbiology ; Rats, Sprague-Dawley ; Rats ; Hydrolyzable Tannins/metabolism ; *Plant Extracts/metabolism ; Ellagic Acid/metabolism ; Metagenomics ; Fermentation ; Male ; *Gastrointestinal Microbiome ; *Bacteria/metabolism/genetics/classification ; *Sapindaceae/chemistry ; }, abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.}, }
@article {pmid42036837, year = {2026}, author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L}, title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70359}, pmid = {42036837}, issn = {1751-7915}, support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; }, mesh = {*Microbiota/genetics ; Phenotype ; Soil Microbiology ; Chitin/metabolism ; *Chitinases/genetics/metabolism ; *Bacteria/enzymology/genetics/classification ; }, abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.}, }
@article {pmid42037322, year = {2026}, author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP}, title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {9}, pages = {e71828}, pmid = {42037322}, issn = {1530-6860}, support = {APIDOM-BACTERIOB//CHU de La R&#xe9;union/ ; //Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (Inserm)/ ; //University of La R&#xe9;union/ ; }, mesh = {Humans ; *Periodontitis/microbiology/metabolism/complications/pathology ; Female ; Male ; *Intra-Abdominal Fat/metabolism/pathology/microbiology ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/microbiology/pathology/metabolism ; *Metabolic Diseases/microbiology/metabolism/pathology ; Porphyromonas gingivalis ; Dysbiosis/microbiology ; *Mouth/microbiology ; }, abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.}, }
@article {pmid42037351, year = {2026}, author = {Chakraborty, S and Mukherjee, D and Sar, P}, title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0005926}, pmid = {42037351}, issn = {2576-098X}, abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.}, }
@article {pmid42037384, year = {2026}, author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ}, title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0358725}, pmid = {42037384}, issn = {2165-0497}, support = {K08 AI159384/AI/NIAID NIH HHS/United States ; K08AI159384/NH/NIH HHS/United States ; }, mesh = {Humans ; *Severe Acute Malnutrition/microbiology ; South Sudan ; Recurrence ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Infant ; Child, Preschool ; }, abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.}, }
@article {pmid42037401, year = {2026}, author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q}, title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0248125}, pmid = {42037401}, issn = {1098-5336}, mesh = {*Polyphosphates/metabolism ; *Phosphates/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics ; Geologic Sediments/microbiology/virology ; China ; *Viruses/genetics/metabolism ; Phosphorus/metabolism ; Rivers/microbiology/virology ; }, abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.}, }
@article {pmid42037579, year = {2026}, author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F}, title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70144}, pmid = {42037579}, issn = {1755-0998}, support = {//Wageningen University and Research/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; }, abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.}, }
@article {pmid42038227, year = {2026}, author = {Fu, L and Zhang, Y and Wang, L and Li, X}, title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1801355}, pmid = {42038227}, issn = {2296-2360}, abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.<br><br>CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072&#x2009;&#xd7;&#x2009;10[6]/L, markedly elevated protein (3,667.6&#x2005;mg/L), and significantly decreased glucose (0.08&#x2005;mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11&#x2005;h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3&#x2009;&#xd7;&#x2009;10[5]&#x2005;copies/mL), establishing the diagnosis of PAM.<br><br>CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.}, }
@article {pmid42038247, year = {2026}, author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W}, title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1763281}, pmid = {42038247}, issn = {2296-2360}, abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.}, }
@article {pmid42038299, year = {2026}, author = {Liu, HJ and Wang, LF and Li, XY and Li, L}, title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1805920}, pmid = {42038299}, issn = {1663-9812}, abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.<br><br>METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.<br><br>RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48&#xa0;h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1]-11.25&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1], with maintenance at 7.5&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.<br><br>CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.}, }
@article {pmid42038409, year = {2026}, author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ}, title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {2}, pages = {lqag040}, pmid = {42038409}, issn = {2631-9268}, mesh = {Animals ; *Biodiversity ; *Rivers/microbiology ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Shotgun Sequencing ; Humans ; DNA, Environmental ; *Nanopore Sequencing/methods ; Metagenome ; Animals, Wild/genetics ; }, abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.}, }
@article {pmid42038418, year = {2026}, author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Müller, CL}, title = {Sparse regression, classification, and microbial network estimation in QIIME 2 with q2-classo and q2-gglasso.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {42038418}, issn = {2331-8422}, abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.<br><br>RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.<br><br>AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.<br><br>CONTACT: oleg.vlasovets@helmholtz-munich.de.}, }
@article {pmid42038553, year = {2026}, author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, M&#xc1; and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ}, title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {3219583}, pmid = {42038553}, issn = {1687-918X}, abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.}, }
@article {pmid42038636, year = {2026}, author = {Ryder, JH and Turbett, SE}, title = {Mindful diagnostics: a central nervous system infection case study.}, journal = {Antimicrobial stewardship &amp; healthcare epidemiology : ASHE}, volume = {6}, number = {1}, pages = {e96}, pmid = {42038636}, issn = {2732-494X}, abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.}, }
@article {pmid42039195, year = {2026}, author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H}, title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1749584}, pmid = {42039195}, issn = {1664-3224}, mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/virology ; *Virome ; *Mycobiome ; *Genitalia, Female/microbiology/virology ; Microbiota ; Papillomavirus Infections/microbiology/virology ; *Reproductive Health ; Vagina/microbiology/virology ; }, abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.<br><br>METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.<br><br>RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.<br><br>CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.}, }
@article {pmid42039480, year = {2026}, author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y}, title = {16S rRNA sequence captures microbial functional potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42039480}, issn = {2692-8205}, abstract = {16S rRNA amplicon sequencing is widely used for microbiome profiling, but most methods rely on reference databases of characterized organisms, limiting its accuracy in function prediction for underrepresented environments. We discovered that 16S rRNA k-mer composition carries substantial functional signal: (i) whole-genome k-mer profiles predict genome-encoded functions, and (ii) 16S rRNA k-mer profiles reflect their source genome's composition. Building on these relationships, we developed embeRNA, a neural network framework that predicts functions directly from 16S rRNA k-mer embeddings without requiring taxonomy assignment or phylogenetic placement. embeRNA outputs per-function probability scores, enabling users to tune decision thresholds to balance precision and recall or account for community novelty. In a stringent "novel microbes" benchmark - where all test sequences shared <97% identity with training data - embeRNA outperformed reference-based methods, particularly for hard-to-label functions. Applied to soil metagenomes with paired 16S and whole metagenome shotgun sequencing (WMS) data, embeRNA recovered most WMS-inferred functions and produced abundance profiles strongly correlated with WMS results, attaining better performance than a reference-based approach. Our findings demonstrate that 16S rRNA directly captures functional potential, and 16S amplicon sequencing data can complement WMS-based inference to broaden functional characterization of microbiomes, especially in understudied environments.}, }
@article {pmid42039609, year = {2026}, author = {Maldonado-Pereira, L and Mutawi, TM and Singh, A and Sanderson, BJ and Rekowski, MJ and Barnaba, C and Medina Meza, IG}, title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42039609}, issn = {2692-8205}, abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.}, }
@article {pmid42039751, year = {2026}, author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT}, title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1786413}, pmid = {42039751}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation &amp; purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.<br><br>METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.<br><br>RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly &#x3b2;-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.<br><br>CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.}, }
@article {pmid42039753, year = {2026}, author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G}, title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771148}, pmid = {42039753}, issn = {2235-2988}, mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Male ; *Metagenomics/methods ; Middle Aged ; Antimicrobial Stewardship ; Aged ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; }, abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.<br><br>OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.<br><br>METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.<br><br>RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.<br><br>CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.}, }
@article {pmid42039757, year = {2026}, author = {Wu, Y and Zhang, J and Su, W and Zhang, Z}, title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1791903}, pmid = {42039757}, issn = {2235-2988}, mesh = {Animals ; Phylogeny ; *Rhabdoviridae/classification/genetics/isolation &amp; purification ; *Ticks/virology ; Humans ; *Rhabdoviridae Infections/epidemiology/virology ; *Tick-Borne Diseases/epidemiology/virology ; }, abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.<br><br>METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.<br><br>RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.<br><br>DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.}, }
@article {pmid42039802, year = {2026}, author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P}, title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1780132}, pmid = {42039802}, issn = {1664-302X}, abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.}, }
@article {pmid42039826, year = {2026}, author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C}, title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797687}, pmid = {42039826}, issn = {1664-302X}, abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.<br><br>METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.<br><br>RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 &#xd7; 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.<br><br>CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.}, }
@article {pmid42039832, year = {2026}, author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M}, title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761627}, pmid = {42039832}, issn = {1664-302X}, abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.<br><br>METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.<br><br>RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.<br><br>CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.}, }
@article {pmid42040306, year = {2026}, author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q}, title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1782544}, pmid = {42040306}, issn = {1664-462X}, abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.<br><br>METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.<br><br>RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.<br><br>DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.}, }
@article {pmid42040505, year = {2026}, author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R}, title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag072}, pmid = {42040505}, issn = {2730-6151}, abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.}, }
@article {pmid42040506, year = {2026}, author = {Zhang, T and Pan, J and Palomo, A and Ouyang, Z and Wen, X and Li, J and Wang, C and Zheng, M}, title = {Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag070}, pmid = {42040506}, issn = {2730-6151}, abstract = {Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox Nitrospira to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox Nitrospira was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox Nitrospira demonstrated that this species was phylogenetically novel, named Candidatus Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox Nitrospira and acid-tolerant ammonia-oxidizing bacteria (AOB), Candidatus Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient K m of 0.50 ± 0.05 μM NH3 and an apparent ammonium inhibition constant K i of 241.43 ± 45.64 μM NH3. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.}, }
@article {pmid42040549, year = {2026}, author = {Chen, Q and Yang, Z and Ren, D and Bao, C and Zhao, Y and Shi, Z}, title = {Case Report: Pulmonary tuberculosis with pneumocystis jirovecii colonization in a non-HIV patient: a cautionary tale on interpreting mNGS results.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1782843}, pmid = {42040549}, issn = {2296-858X}, abstract = {The diagnosis and treatment process of this case highlights that mNGS, as a powerful pathogen detection tool, provides a rapid method for the early detection of Pneumocystis jirovecii. However, mNGS testing of lavage specimens alone cannot distinguish between colonization and infection by the pathogen, particularly when a high number of sequences are present. Clinicians should therefore interpret laboratory results with caution to avoid unnecessary treatment that may cause adverse effects to the patient. CT scans offer strong evidence for differentiating between Pneumocystis jirovecii infection and/or Mycobacterium tuberculosis infection. Performing a biopsy at the site of infection, collecting pathological samples, and submitting them for mNGS testing can further assist clinicians in making a definitive diagnosis.}, }
@article {pmid42040584, year = {2026}, author = {Li, CB and Tang, S and Wen, Y}, title = {Case Report: The complete radiological resolution of diffuse cholangitis in a HIV-positive patient with cryptosporidium infection after anti-retroviral therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1686336}, pmid = {42040584}, issn = {2296-858X}, abstract = {We present a case of an HIV-positive patient with AIDS cholangiopathy secondary to Cryptosporidium infection. Imaging examination showed intrahepatic and extrahepatic cholangitis without papillary stenosis and extrahepatic bile duct strictures, indicating mild bile duct disease. However, it failed to obtain positive results in fecal microscopy examinations. Alternatively, metagenomic next-generation sequencing (mNGS) of a blood sample identified Cryptosporidium infection. The diagnostic power of mNGS is highly sensitive and can simultaneously identify various pathogens. To avoid irreversible damage to the biliary system, the rapid initiation of anti-HIV therapy restored the function of the immune system and led to the clinical resolution of cryptosporidiosis.}, }
@article {pmid42040837, year = {2026}, author = {Sander, MM and Stoof-Leichsenring, KR and Liu, S and Shen, W and Lisovski, S and Herzschuh, U}, title = {Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.}, journal = {Ecology and evolution}, volume = {16}, number = {4}, pages = {e72064}, pmid = {42040837}, issn = {2045-7758}, abstract = {The transition from the Last Glacial to the Holocene was marked by significant warming. This forced a compositional turnover of terrestrial plant and mammal communities discovered by diverse palaeoecological techniques. In this study, we analysed ancient environmental DNA with shotgun metagenomics from eight lake sediment cores, collected in northern Eurasia and Alaska, to elucidate the relationship of past bird communities and vegetation structure across the last 21,000 years. We leveraged all DNA reads assigned to the class 'Aves' to characterise the compositional changes of the bird community. The dominance of chicken birds (Galliformes, mainly ptarmigans) during the Last Glacial Maximum turned into a higher taxonomic bird diversity with increased numbers of songbird, raptor and waterfowl abundances and genera. This went along with the late glacial loss of the steppe-tundra and the increase of shrub and tree cover. Compared to the northern boreal areas, vegetation and bird communities were more stable in the northern tundra sites, where open landscapes prevailed throughout. Metagenomics significantly contribute to the reconstruction of past avian community changes and thus have high potential to support the predictions of distribution changes in the course of future ecosystem change.}, }
@article {pmid42041249, year = {2026}, author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS}, title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0286825}, pmid = {42041249}, issn = {2150-7511}, support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; R01AI153332,R21AI186346//National Institute of Allergy and Infectious Diseases/ ; F32AI186285//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Female ; *Streptococcus agalactiae/genetics/growth &amp; development/physiology ; *Vagina/microbiology ; Humans ; *Streptococcal Infections/microbiology ; Pregnancy ; Epithelial Cells/microbiology ; Animals ; Bacterial Adhesion ; Microbiota ; Akkermansia ; Mice ; }, abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.}, }
@article {pmid42041251, year = {2026}, author = {Gador-Whyte, AP and Sherry, NL and Brischetto, A and Andersson, P and Bond, KA and van Hal, SJ and Harris, PNA and Howden, BP and , }, title = {Implementation of pathogen genomics in clinical microbiology laboratories.}, journal = {Clinical microbiology reviews}, volume = {39}, number = {2}, pages = {e0017725}, pmid = {42041251}, issn = {1098-6618}, support = {FSPGN00049//Australian Government Medical Research Future Fund/ ; GNT1196103//National Health and Medical Research Council/ ; GNT2033851//National Health and Medical Research Council/ ; GNT2033803//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Genomics/methods ; *Laboratories, Clinical ; Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.}, }
@article {pmid42041878, year = {2026}, author = {Carlone, J and Ribeiro, &#xc1;CDS and Parisi, A and Giampaoli, S and Fasano, A}, title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, pmid = {42041878}, issn = {2079-7737}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; }, abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.}, }
@article {pmid42041929, year = {2026}, author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J}, title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, pmid = {42041929}, issn = {2079-7737}, abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.}, }
@article {pmid42043232, year = {2026}, author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S}, title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.}, journal = {Viruses}, volume = {18}, number = {4}, pages = {}, pmid = {42043232}, issn = {1999-4915}, support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; }, mesh = {Animals ; China ; Phylogeny ; *Virome ; Haemaphysalis longicornis/virology ; *Ticks/virology ; Genome, Viral ; Dermacentor/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Metagenomics ; Genetic Variation ; Transcriptome ; }, abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.}, }
@article {pmid42043279, year = {2026}, author = {Rūmnieks, J and Baltā, I and Šišovs, M and Tārs, K}, title = {ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {5}, pages = {e70582}, pmid = {42043279}, issn = {1469-896X}, support = {5.2.1.1.i.0/2/24/I/CFLA/001//European Commission/ ; }, mesh = {Open Reading Frames ; *Viral Proteins/genetics/chemistry/metabolism ; *Genome, Viral ; *Metagenome ; *Bacteriophages/genetics ; *RNA, Viral/genetics ; }, abstract = {The bacteriophages with single-stranded RNA (ssRNA) genomes (class Leviviricetes) are among the simplest known viruses that encode only three core proteins: a receptor-binding protein, a capsid protein, and an RNA-dependent RNA polymerase. The number of isolated ssRNA phages has remained very low, but the accumulating RNA metagenome data have uncovered a large variety of these viruses in many environments. Besides the core proteins, many of these genomes putatively encode additional proteins, which up to now have remained uncharacterized. We looked for non-conserved open reading frames (ORFs) in Leviviricetes sequences from the IMG/VR virus metagenome database and used sequence- and structure-based clustering to organize them into similarity groups. Potential ORFs were found throughout the ssRNA phage genomes but almost exclusively on the positive-sense RNA strand, suggestive of their protein-coding potential. The prevalence of the non-conserved ORFs varied in various phage lineages, and their distribution among different genome positions was markedly uneven. Most of the identified ORFs encode all-α proteins, a portion of which contain transmembrane segments that resemble a group of known ssRNA phage lysis proteins, while many others represent previously uncharacterized families of globular or semi-globular α-helical proteins. We additionally uncovered a major class of globular α/β proteins and experimentally determined the structure of a representative protein of this group. These results pave the way for further functional studies of novel ssRNA phage proteins for a better understanding of this diverse virus group.}, }
@article {pmid42043563, year = {2026}, author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W}, title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42043563}, issn = {1432-072X}, support = {Intramural Faculty Grant//Bose Institute/ ; }, abstract = {A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of copiotrophic psychrophiles having potentials for substantive carbon remineralization under natural and/or anthropogenically-influenced conditions of high organic matter delivery to the environment. Overall 27 bacterial species were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lake on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth (LB), all isolates grew at 4 °C and 15 °C; at -10 °C, 13 could grow while others remained only metabolically-active. Catabolizing different complex-organic-compounds, all isolates achieved considerable growth at 4 °C; 20 accomplished low growth at -10 °C. LB-based growth dwindled with rising temperature: 23, 11, and none of the isolates grew at 28 °C, 37 °C, and 42 °C respectively. In agar-overlay assays, most actinobacterial isolates inhibited other mesophilic bacteria. The isolates’ genomes, and their habitats’ metagenomes, encompassed diverse genes for extreme-temperature adaptation, carbohydrate catabolism, antibiosis and antibiotic-resistance. All in-vitro findings collectively engender the following hypothesis, via contextual inferences pending field-study-based validations. Warming-induced cessation of organotrophic growth, within high-altitude cryospheres, would curb the production of simple-fatty-acids, CO2 and N2O. Short-supply of acetate and CO2 would, in turn, cut-back methanogenesis. Such negative-feedback control of greenhouse gas production at the micro-habitat level can add-up in the biome-scale to mitigate broader environmental warming; it, however, endangers the ecosystem from thermally-better-adapted foreign microbes that can usher positive-feedback cycles of warming. In the latter scenario, antibiosis potentials of native actinobacteria become pivotal to microbiome protection.}, }
@article {pmid42043697, year = {2026}, author = {Lomelí-Álvarez, MF and Escamilla-Montes, R and Diarte-Plata, G and Guo, X and Fierro-Coronado, JA and Rubio-Luque, AM and Vega-Carranza, AS and González, AL}, title = {Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42043697}, issn = {1678-4405}, abstract = {This study evaluated the effects of Bacillus licheniformis and Pediococcus pentosaceus administered in both culture water and feed to Penaeus vannamei over a 47-day experiment. Treatments in triplicate were as follows: (I) Commercial Feed (CF); (II) CF + P. pentosaceus in the water (3 × 10[6] CFU/L); (III) CF + B. licheniformis in the water (3 × 10[6] CFU/L); (IV) P. pentosaceus in fermented feed (51 × 10[5] CFU/g); (V) B. licheniformis in fermented feed (147 × 10[6] CFU/g); (VI) Mix of P. pentosaceus (140 × 10[5] CFU/g) + B. licheniformis (180 × 10[5] CFU/g) in fermented feed + Mix of P. pentosaceus + B. licheniformis (3 × 10[6] CFU/L) in the water. Growth, immune effectors (phenoloxidase and superoxide anion), and gut bacterial profiles via 16S metagenomic sequencing were assessed. Survival was determined after a challenge with Vibrio parahaemolyticus. Probiotics did not affect growth. Only B. licheniformis in water and fermented feed elicited a significant immunostimulatory response, increasing superoxide anion production and phenoloxidase activity, respectively. Probiotic administration also modulated the gut microbiota, significantly increasing the relative abundance of beneficial genera like Ruegeria and Haloferula. Measures of both alpha and beta diversity indicated a significant restructuring of the microbial community in response to probiotics. Most major bacterial groups showed predominantly positive intra-group interactions, while Psychromonadaceae solely exhibited negative interactions with other families. Shrimp survival was significantly higher in shrimp treated with probiotics, excluding treatment II. These results demonstrate that probiotics strengthen innate immunity and improves disease resistance in shrimp by enhancing immunocompetence and enriching beneficial gut microbes, offering a viable strategy for sustainable aquaculture health management.}, }
@article {pmid42044527, year = {2026}, author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ}, title = {Identify contaminants with decontam on the QIIME 2 Framework.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0126125}, pmid = {42044527}, issn = {2576-098X}, support = {EEC-2133504//National Science Foundation/ ; R35GM133745/NH/NIH HHS/United States ; 1U24CA248454/NH/NIH HHS/United States ; }, abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.}, }
@article {pmid42044543, year = {2026}, author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y}, title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129734}, doi = {10.1016/j.jenvman.2026.129734}, pmid = {42044543}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Geologic Sediments/microbiology ; Kinetics ; Aerobiosis ; *Thiazines/metabolism ; }, abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.}, }
@article {pmid42044779, year = {2026}, author = {Zhang, Y and Zeng, M and Guo, P and Zhang, Z and Chen, X and Li, X and Hao, F and Jiao, X and Wu, Y and Feng, W and Zheng, X}, title = {Effects of Rehmannia glutinosa Libosch. Rhizome water extract and Rehmapicrogenin on pulmonary hypertension: Multi-omics insights into epidermal growth factor receptor/pyruvate kinase M2 pathway and metabolic regulation.}, journal = {Journal of ethnopharmacology}, volume = {367}, number = {}, pages = {121775}, doi = {10.1016/j.jep.2026.121775}, pmid = {42044779}, issn = {1872-7573}, mesh = {Animals ; ErbB Receptors/metabolism ; *Rehmannia/chemistry ; Mice ; *Hypertension, Pulmonary/drug therapy/metabolism ; Male ; *Plant Extracts/pharmacology/therapeutic use ; Mice, Inbred C57BL ; *Pyruvate Kinase/metabolism ; Disease Models, Animal ; Myocytes, Smooth Muscle/drug effects ; Signal Transduction/drug effects ; Cell Proliferation/drug effects ; *Drugs, Chinese Herbal/pharmacology ; Multiomics ; }, abstract = {Rehmannia glutinosa Libosch. (RG), as one of the 'Four Famous Chinese Medicinal Herbs', has a long history of medicinal use and is classified as belonging to the meridians of the heart, liver, and kidney. RG has the effects of clearing heat and cooling blood, nourishing yin, and generating fluids. Pulmonary hypertension (PH) is a cardiovascular disease, and its pathogenesis can be summarized as 'yin deficiency', 'blood stasis', and 'qi deficiency'. The efficacy of RG is highly compatible with this disease, and the compounds isolated from RG can significantly inhibit the proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the mechanism by which it intervenes in PH remains unclear.<br><br>OBJECTIVE: In this study, the mechanisms and active components of RG were investigated for treating PH by using multi-omics analysis and surface plasmon resonance (SPR) technology, providing experimental support for clinical application.<br><br>METHODS: A PH mouse model was established through 5 weeks of hypoxia, with RG administration starting in week four. Cardiorespiratory function was evaluated after treatment. The therapeutic targets of RG were identified via 16S rDNA sequencing, metagenomics, and metabolomics. SPR ligand fishing was performed to isolate rehmapicrogenin (Reh), an RG-derived compound that targets the epidermal growth factor receptor (EGFR). The effects and mechanisms of Reh were assessed by measuring cardiac and pulmonary function, oxidative stress, apoptosis, immune cell activity, and glycolysis. An in vitro model of hypoxia-induced PASMCs proliferation was used to validate Reh's mechanism with an EGFR agonist (NSC).<br><br>RESULTS: RG extracts improved cardiorespiratory function and regulated gut microbiota, correcting the Firmicutes/Bacteroidetes (F/B) ratio in PH mice. RG also mitigated metabolic disturbances and inhibited glycolysis through pyruvate kinase M2 (PKM2) regulation, as confirmed using immunofluorescence analysis, western blotting, and PCR. SPR identified Reh as the active ingredient, which improved cardiorespiratory function, reduced oxidative stress and apoptosis, and suppressed EGFR and PKM2 expression and glycolysis. In vitro, Reh inhibited PASMC migration and proliferation, alleviated oxidative stress, and reduced mitochondrial damage. These effects were reversed upon NSC addition, confirming the role of EGFR in the mechanism.<br><br>CONCLUSION: RG and its active compound Reh mitigate hypoxia-induced PH by targeting the EGFR/PKM2 pathway, reducing glycolysis, and regulating gut microbiota dysbiosis.}, }
@article {pmid42044791, year = {2026}, author = {Dai, Y and Li, J and Wang, X and Xia, F and Zheng, J and Shen, C}, title = {Synergistic mechanisms of bacteria and fungi in the biodegradation of Benzo[a]pyrene: Insights from metagenomic and metabolomic analyses.}, journal = {Environmental research}, volume = {301}, number = {}, pages = {124602}, doi = {10.1016/j.envres.2026.124602}, pmid = {42044791}, issn = {1096-0953}, mesh = {*Benzo(a)pyrene/metabolism ; Biodegradation, Environmental ; Soil Microbiology ; *Soil Pollutants/metabolism ; Metagenomics ; *Fungi/metabolism ; *Bacteria/metabolism ; Metabolomics ; *Ascomycota/metabolism ; *Pseudomonas/metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants, with benzo[a]pyrene (BaP), a prominent heavy-weight PAH, drawing considerable attention due to its high toxicity and resistance to degradation. While both bacteria and fungi have been demonstrated to effectively remediate BaP, their synergistic mechanisms remain poorly understood. In this study, we employed Pseudomonas nicosulfuronedens DY-8 (bacterium) and Arthrinium acutiapicum DL-5 (fungus) to explore the mechanisms underlying PAH bioaugmentation using metagenomic and metabolomic approaches. Although both strains individually enhanced BaP degradation, their combined application significantly reduced BaP residuals. qPCR analysis revealed that the bacteria promote BaP dissipation by stimulating the abundance of PAH-RHD GP genes in the soil. Correlations between metabolite abundance, enriched microbial populations, functional gene abundance, and fungal growth suggest that fungi enhance the growth of indigenous bacteria, further boosting the degradation of BaP metabolites. Additionally, the synergistic treatment of bacteria and fungi further altered the diversity of soil functional microorganisms, metabolic products, and functional genes. These findings provide insights into potential synergistic mechanisms by which bacterial-fungal interactions drive the degradation of high-molecular-weight PAHs, underscoring the potential of microbial consortia in the bioremediation of persistent organic pollutants in soil environments.}, }
@article {pmid42044793, year = {2026}, author = {Zhou, Y and Hu, X and Du, L and Gu, Y and Li, J and Jia, M and Zhang, G and Wang, Y}, title = {Antibiotic resistance genes across divergent wetland types: Profiles, driving mechanisms, and risk assessment.}, journal = {Environmental research}, volume = {302}, number = {}, pages = {124601}, doi = {10.1016/j.envres.2026.124601}, pmid = {42044793}, issn = {1096-0953}, mesh = {*Wetlands ; *Drug Resistance, Microbial/genetics ; Risk Assessment ; Soil Microbiology ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; }, abstract = {Wetlands are critical reservoirs and hotspots of antibiotic resistance genes (ARGs). Metagenomic sequencing was employed to profile the ARG and mobile genetic element (MGE) abundance and diversity in coastal (B), constructed (R), and swampy (W) wetlands. In total, 560 ARGs were detected across all sites, primarily conferring resistance to cephalosporins and tetracyclines, with antibiotic efflux being the dominant mechanism of resistance. ARG richness was significantly higher in wetlands R and W than in wetland B (p < 0.001). Non-metric multidimensional scaling (NMDS) further indicated significant differences in ARG β-diversity among the wetlands. Pseudomonadota were identified as the primary hosts of both ARGs and MGEs. Soil salinity and Cr content were the key environmental factors regulating ARG profiles, with salinity exhibiting the broadest influence and linearly correlating with multiple ARG types. In addition, plasmid and insertion sequence (IS) richness positively correlated with ARG richness, showing the strongest explanatory power for ARG richness variation. Risk assessment revealed that rank I and II ARGs were significantly enriched in wetland W (p < 0.05), whereas rank IV ARGs were dominant across most sites. This study demonstrated that soil physicochemical properties, plasmids, and ISs jointly and differentially shaped ARG abundance and diversity in wetlands, accompanied by an assessment of their risk. These findings support the development of targeted strategies to mitigate ARG dissemination in wetland ecosystems.}, }
@article {pmid42044853, year = {2026}, author = {Weng, H and Wang, H and Zhang, Q and Li, X and Zhang, L and Peng, Y}, title = {Enrichment of comammox Nitrospira with urea: comparative genomics reveals divergent urea response mechanisms among ammonia-oxidizing microorganisms.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134722}, doi = {10.1016/j.biortech.2026.134722}, pmid = {42044853}, issn = {1873-2976}, mesh = {*Urea/metabolism ; *Ammonia/metabolism ; *Genomics/methods ; Nitrification ; *Bacteria/metabolism/genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genome, Bacterial ; }, abstract = {Urea is a major nitrogen form in natural and engineered ecosystems, yet the traits driving niche partitioning among nitrifiers during urea nitrification remain poorly understood. In this work, a stable urea nitrification microbial community was successfully established over prolonged cultivation characterized using 16S rRNA gene amplicon sequencing, qPCR and genome-resolved metagenomics coupled with comparative genomics. A clade A comammox Nitrospira closely related to Candidatus Nitrospira nitrosa became dominant (OTU330, 13.9%) and yielded the most abundant nitrifier metagenome-assembled genome (MAG). Genomes indicate comammox Nitrospira couples ATP-dependent urea ABC uptake to a streamlined urease-only module characterized by slow substrate turnover, whereas Nitrosomonas relies on passive urea channels and redundant urease/urea-amidolyase pathways, enabling rapid urea metabolism. These contrasting urea acquisition strategies suggest an affinity-capacity trade-off that underpins niche partitioning in urea-fed, oligotrophic nitrifying systems and provide targets for enhancing urea-based wastewater treatment processes.}, }
@article {pmid42045408, year = {2026}, author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S}, title = {Improving metagenome binning by integrating intrinsic features and taxonomy.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42045408}, issn = {1546-1696}, support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; }, abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.}, }
@article {pmid42045553, year = {2026}, author = {Wei, D and Xing, C and Zeng, S and Hou, D and Deng, Z and Long, X and Wang, H and Zhou, R and Yu, L and Shu, N and Tao, Z and Zhou, X and Weng, S and He, J and Huang, Z}, title = {The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.}, journal = {Advanced biotechnology}, volume = {4}, number = {2}, pages = {}, pmid = {42045553}, issn = {2948-2801}, support = {2023YFD2401705//National Key Research and Development Program of China/ ; 2024YFD2401202//National Key Research and Development Program of China/ ; AA23062047//Earmarked Fund for CARS-48-20; Guangxi Science and Technology Major Special Project/ ; SML2021SP203//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, abstract = {Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.}, }
@article {pmid42045683, year = {2026}, author = {Boppana, LKT and Bag, R}, title = {Metagenomic Microbial Next-Generation Gene Sequencing as a Noninvasive Diagnostic Tool in Adult Lung Transplantation: A Retrospective Case Series.}, journal = {Lung}, volume = {204}, number = {1}, pages = {}, pmid = {42045683}, issn = {1432-1750}, }
@article {pmid42045813, year = {2026}, author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , }, title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42045813}, issn = {1471-2180}, abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome.<br><br>METHODS: Fecal samples from 16 Crohn&#x2019;s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy.<br><br>RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the &#x201c;pyrazinamide resistant rpsA&#x201d; gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan).<br><br>CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05101-9.}, }
@article {pmid42046064, year = {2026}, author = {Tang, S and Cai, L and Hao, Y and Jiang, Q and Luan, X and Fang, X and Li, Z and Zhu, J}, title = {SCFAs inhibited NETosis to alleviate lung inflammation in COPD: a potential role for GPR43.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03688-1}, pmid = {42046064}, issn = {1465-993X}, support = {82575021//the National Natural Science Foundation of China/ ; 2408085MH230//Anhui Provincial Natural Science Foundation/ ; 2022AH020044//the Science Fund for Distinguished Young Scholars in Universities of Anhui Province/ ; 2024AKLCMF04//the Foundation of Anhui Provincial Key Laboratory of Chinese Medicinal Formula/ ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, and poses a significant socioeconomic burden attributable to its high mortality and morbidity. Short-chain fatty acids (SCFAs), as the key metabolites produced by gut microbiota, have been considered to be involved in the regulation of pulmonary inflammation. However, the underlying bridging mechanisms through the gut-lung axis remain elusive. METHODS: To delineate cellular heterogeneity during COPD progression, we profiled lung tissues from rats at distinct stages (Days 0, 7, 14, and 28) using scRNA-seq, followed by bulk transcriptomic analysis to pinpoint critical dysregulated pathways. Gas chromatography-mass spectrometry (GC-MS) was employed to quantify the differential SCFA levels. The protective effects of SCFAs against pulmonary inflammation in COPD were evaluated via pulmonary function testing, HE staining, and ELISA. Flow cytometry, Western blotting, immunofluorescence and scanning electron microscopy were employed to explore the mechanism of SCFAs regulating neutrophil extracellular trap (NET) formation in vitro and in vivo. Finally, metagenomic sequencing was applied to investigate the impact of SCFAs on gut microbial communities. RESULTS: ScRNA-seq demonstrated the intense immune activation during the progress of COPD, characterized by neutrophil accumulation exceeding 50% of cellular composition on the 14th day in the lung tissue. Transcriptomic analysis further pinpointed neutrophil-driven NETosis as the key pathogenic pathway. The results of GC-MS showed the significant downregulation of SCFAs represented by acetic acid and propionic acid in COPD. Exogenous supplementation with SCFAs (acetic acid and propionic acid) activated the key receptor GPR43, suppressed the expression of NETs marker proteins (NE, MPO, and CitH3) and attenuated inflammatory cytokine levels in COPD rats. Rescue experiments with NETs inducers/inhibitors and GPR43 agonists/antagonists further elucidated the regulatory mechanisms of SCFAs/GPR43 axis in COPD inflammation. Furthermore, metagenomic sequencing revealed that SCFAs reshaped the intestinal flora in COPD by enriching the abundance of beneficial bacteria. CONCLUSION: As one of the key receptors for gut microbiota-derived SCFAs, GPR43 may be involved in the process by which SCFAs alleviate pulmonary inflammation in COPD through regulating NET formation. These findings provide valuable experimental evidence for promoting the clinical translation of therapeutic strategies characterized by gut microbiota and their metabolites.}, }
@article {pmid42046358, year = {2026}, author = {Chen, K and Huang, L}, title = {[Metagenomic next - generation sequencing for diagnosis of infection of unknown origin in intensive care units: a bibliometric analysis].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {38}, number = {1}, pages = {79-83}, doi = {10.16250/j.32.1915.2026077}, pmid = {42046358}, issn = {1005-6661}, mesh = {*Bibliometrics ; *High-Throughput Nucleotide Sequencing/methods ; *Intensive Care Units ; Humans ; *Metagenomics/methods ; }, abstract = {OBJECTIVE: To investigate the scientific outputs of metagenomic next-generation sequencing (mNGS) for diagnosis of infection of unknown origin in intensive care units (ICUs), and to decipher the latest advances, frontier trends and spatiotemporal evolution of research hotpots in mNGS for diagnosis of infection of unknown origin in ICUs.<br><br>METHODS: Publications pertaining to the application of mNGS in diagnosis of infection of unknown origin in ICUs were retrieved from Web of Science Core Collection (WOSCC) from January 1, 2015 to December 31, 2024. The software Scimago Graphica 1.0.30 was employed to generate the network maps of collaboration relationships between countries, international collaborative relationships, author collaborations, institutional collaborative relationships, and a heatmap of journals, and the software VOSviewer 1.6.18 was used to create a heatmap of keywords, and maps of keyword co-occurrence clustering and keyword clustering timelines. In addition, the keyword burst map was created using the software CiteSpace 6.3.R3.<br><br>RESULTS: A total of 1 707 publications were included in the final analysis, and the number of publications appeared an overall tendency towards a rise from 2015 to 2024, with the largest number of publications seen in 2024 (545 publications). The largest number of publications was recorded in China (1 390 publications), followed by in USA (190 publications) and United Kingdom (31 publications), and China led the global research in this field, with 81% of global related researches linked with China. Frontiers in Cellular and Infection and Microbiology published the largest number of articles (212 publications, 12.42%), and Joseph Derisi was the most productive author (33 publications). Author collaborations occurred within groups; however, there was a lack of close inter-group collaborations, with University of California, San Francisco and Chan Zuckerberg Biohub-based group seen as the largest collaborative group. High-frequency co-occurrence keywords included mNGS, infection, diagnosis, case report, community-acquired pneumonia and bronchoalveolar lavage fluid, and the 100 most common high-frequency co-occurrence keywords were assigned into four clusters. Keyword clustering timeline analysis revealed that the research hotspots in this field shifted from virus sequencing and sequence alignment to severe pulmonary infections, and keyword burst analysis showed identification, mNGS and virus as top three keywords with the highest burst intensity.<br><br>CONCLUSIONS: mNGS was mainly used for identification of viruses among patients with infections of unknown origins in ICUs from 2015 to 2024, and future research priority shifted to pathogen detection for severe pulmonary infections.}, }
@article {pmid42046871, year = {2026}, author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q}, title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.}, journal = {Journal of Zhejiang University. Science. B}, volume = {27}, number = {4}, pages = {375-389}, pmid = {42046871}, issn = {1862-1783}, support = {2021YFA0805904//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; Humans ; Mice ; Germ-Free Life ; *Gastrointestinal Microbiome/genetics ; *Fecal Microbiota Transplantation/methods ; *Metagenomics ; *Metagenome ; Reproducibility of Results ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Male ; Mice, Inbred C57BL ; }, abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.}, }
@article {pmid42047611, year = {2026}, author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C}, title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.}, journal = {Pediatric dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/pde.70219}, pmid = {42047611}, issn = {1525-1470}, support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson &amp; Johnson Consumer Inc./ ; }, abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.<br><br>METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.<br><br>RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.<br><br>CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.}, }
@article {pmid42047812, year = {2026}, author = {Zhu, R and Zhang, J and Shen, HL}, title = {Hip joint infection by Prevotella denticola in rheumatoid arthritis : A case diagnosed with metagenomic sequencing.}, journal = {Wiener klinische Wochenschrift}, volume = {}, number = {}, pages = {}, pmid = {42047812}, issn = {1613-7671}, abstract = {BACKGROUND: Infection, as a complication of rheumatoid arthritis (RA), has attracted increasing attention from rheumatologists. Here, we present the first case of RA with hip joint infection, which was driven by infection with Prevotella denticola. Anaerobic bacterial infection was identified by metagenomic next-generation sequencing (mNGS).<br><br>METHODS: We describe the case of a&#xa0;56-year-old woman with a&#xa0;history of RA who was admitted for intense hip joint pain and intermittent fever following long-term oral glucocorticoid (GC) treatment.<br><br>RESULTS: Although blood and hip joint effusion cultures for aerobic and anaerobic organisms were negative, we considered the possibility of a&#xa0;clinical diagnosis of hip joint infection; therefore, empirical antibiotic treatment was initiated but it was ineffective in this case. Prevotella denticola was identified by mNGS from the hip joint effusion obtained via ultrasound-guided puncture and the organism was resistant to the initial antimicrobial treatment. Finally, the adjustment of antimicrobial treatment led to successful treatment.<br><br>CONCLUSION: Patients with RA have a&#xa0;significantly greater risk of infections than the general population; however, Prevotella denticola infection of the hip joint has not been previously reported. The combination of ultrasound-guided puncture and mNGS to accurately recognize and treat joint infection in patients with RA in a&#xa0;timely manner is necessary to prevent the development of complications, a&#xa0;strategy worthy of further clinical application.}, }
@article {pmid42048337, year = {2026}, author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM}, title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347959}, pmid = {42048337}, issn = {1932-6203}, mesh = {Colombia ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Metagenomics/methods ; *Mangifera/microbiology ; *Air Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Phylogeny ; }, abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.}, }
@article {pmid42048878, year = {2026}, author = {Shi, W and Qin, Y and Li, W and Xu, J and Xu, H and Liu, Y}, title = {The dual role of phosphorus regeneration in controlling arsenic speciation: Iron-reducing bacteria in a seasonally ice-covered lake.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142206}, doi = {10.1016/j.jhazmat.2026.142206}, pmid = {42048878}, issn = {1873-3336}, mesh = {*Phosphorus/metabolism/chemistry ; *Lakes/microbiology/chemistry ; *Arsenic/chemistry/metabolism ; *Iron/metabolism ; Seasons ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism/chemistry ; Oxidation-Reduction ; Ice Cover ; Geologic Sediments/microbiology/chemistry ; }, abstract = {While the reductive dissolution of iron (hydro)oxides by dissimilatory iron‑reducing bacteria (DFeRB) can mobilize sediment bound arsenic (As), the role of concomitant phosphorus (P) regeneration in actively governing As speciation transformation, rather than mere release, remains mechanistically unclear, especially under seasonally contrasting redox regimes of ice-covered lakes. This study demonstrated that DFeRB mediated P regeneration exerts a dual, season‑dependent control over As speciation in lacustrine sediments. Through microcosm experiments simulating ice‑bound and summer periods, combined with sequential extraction, X‑ray diffraction, metagenomics, and structural equation modeling (SEM), and partial least-squares path modeling (PLS-PM), resolved that regenerated P not only promote As desorption via competitive adsorption but also redirect a substantial speciation of released As into a stable, pyrite‑coprecipitated pool (As‑S7). This sequestration pathway was particularly pronounced under ice‑bound anoxia, where DFeRB sustained a low‑rate, long‑duration reduction mode, as evidenced by persistent iron‑reduction gene (K02650, K17230) abundance and delayed As(III) peak release. SEM/PLS-PM quantified the seasonal shift in dominant mechanisms: summer release was driven by intensive P competition (including organic phosphorus), whereas ice‑bound conditions favored Fe‑S‑As co‑precipitation, effectively coupling prolonged microbial iron reduction to long‑term As immobilization. These findings establish P regeneration as a decisive switch between As mobility and stability in anaerobic sediments and define the seasonal microbial‑mineral feedbacks that modulate this switch. This work provides a predictive basis for assessing As fate in seasonally stratified water bodies under changing climatic conditions and a process-based basis for risk assessment and eutrophication management.}, }
@article {pmid42049031, year = {2026}, author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q}, title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102780}, pmid = {42049031}, issn = {2666-3791}, mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/microbiology ; *Biomarkers/metabolism ; Prognosis ; *Gastrointestinal Microbiome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.}, }
@article {pmid42049067, year = {2026}, author = {Khandelwal, S and Mishra, A and Pandey, SK}, title = {Integrating microbial bioremediation, multi-omics, and emerging technologies for polycyclic aromatic hydrocarbon (PAHs) detoxification.}, journal = {Journal of microbiological methods}, volume = {245}, number = {}, pages = {107519}, doi = {10.1016/j.mimet.2026.107519}, pmid = {42049067}, issn = {1872-8359}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism/toxicity ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; Multiomics ; *Environmental Pollutants/metabolism ; Fungi/metabolism/genetics ; Genomics/methods ; Archaea/metabolism/genetics ; Metagenomics/methods ; }, abstract = {Environmental organic pollutants, identified as Polycyclic Aromatic Hydrocarbons (PAHs), are widespread and toxic. These hydrocarbons are commonly produced by industrial activities, burning fossil fuels, and crude oil discharges. Their high hydrophobicity, tendency to bioaccumulate, and mutagenic, carcinogenic, teratogenic, and genotoxic properties lead to significant environmental and human health risks. Additionally, their low bioavailability and chemical stability complicate PAHs remediation. In recent years, various methods have been explored to reduce their impact, including conventional physical and chemical treatments; however, these often face issues such as inadequate removal, high costs, lengthy processes, and environmental concerns. Bioremediation has emerged as a promising, environmentally friendly solution. This approach involves microorganisms such as bacteria, fungi, algae, and archaea utilizing specific enzymatic pathways-like dioxygenases, monooxygenases, peroxidases, and laccases-to transform PAHs into less toxic substances. Advances in genomics and metagenomics have identified key catabolic genes (e.g., nah, Phn, nid, pah) and regulatory mechanisms that enhance microbial resistance in PAH-contaminated environments. Since PAHs' low bioavailability and solubility often limit bioremediation alone, integrated strategies are gaining prominence. In-situ and ex-situ methods-including bioaugmentation, bio-stimulation, composting, and phytoremediation-boost microbial degradation of PAHs. Furthermore, advanced technologies such as multi-omics platforms, CRISPR-based genetic engineering, and artificial intelligence (AI) are transforming the field by enabling the development of targeted microbial strains, improving bioremediation efficiency, and creating predictive models. This review offers a recent, comprehensive outline by unifying PAHs toxicity, microbial degradation, traditional remediation, and advanced biotechnological tools into a single framework. A comprehensive and recent update of microbial and biotechnological approaches for sustainable PAHs bioremediation is offered by this review.}, }
@article {pmid42049248, year = {2026}, author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM}, title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70161}, pmid = {42049248}, issn = {2040-4603}, support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; }, mesh = {Humans ; Prospective Studies ; Male ; *Lactobacillus/physiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Hypertension, Pulmonary/microbiology ; Adult ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Hemodynamics ; }, abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.<br><br>METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.<br><br>RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.<br><br>CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.}, }
@article {pmid42049488, year = {2026}, author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ}, title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338223}, pmid = {42049488}, issn = {1468-3288}, abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.<br><br>OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.<br><br>DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.<br><br>RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.<br><br>CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.}, }
@article {pmid42049592, year = {2026}, author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , }, title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.04.005}, pmid = {42049592}, issn = {1873-5010}, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.}, }
@article {pmid42049781, year = {2026}, author = {Manohar, CS and Ghose, M and Parab, AS}, title = {Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46393-1}, pmid = {42049781}, issn = {2045-2322}, support = {MLP2019//Council of Scientific and Industrial Research, India/ ; }, }
@article {pmid42050358, year = {2026}, author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y}, title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70567}, pmid = {42050358}, issn = {1365-3040}, support = {2024CXPT072//Key R&amp;D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; }, abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.}, }
@article {pmid42050656, year = {2026}, author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K}, title = {Correction: Bacteriophages in gut metagenomes: from analysis to application.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42050656}, issn = {1743-422X}, }
@article {pmid42050727, year = {2026}, author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S}, title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42050727}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces.<br><br>RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71&#x2013;96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected.<br><br>CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00577-2.}, }
@article {pmid42050730, year = {2026}, author = {Seppey, M and Benavides, A and Berkeley, MR and Manni, M and Zdobnov, EM}, title = {LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {42050730}, issn = {1474-760X}, support = {ESKAS No. 2022.0531//Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship/ ; 310030_189062//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; Benchmarking ; *RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.}, }
@article {pmid42051014, year = {2026}, author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L}, title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70280}, pmid = {42051014}, issn = {1744-7917}, support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; }, abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.}, }
@article {pmid42051699, year = {2026}, author = {Du, Y and Guo, Z and Yao, D and Wang, Y}, title = {Hemophagocytic lymphohistiocytosis secondary to Pneumocystis jirovecii pneumonia: a rare case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1795567}, pmid = {42051699}, issn = {2296-858X}, abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Pneumocystis jirovecii pneumonia (PJP) is extremely rare in children. We present the case of a 10-year-old girl with a history of idiopathic thrombocytopenic purpura (ITP) on long-term oral prednisone, who was admitted for progressive fever, cough, and dyspnea. Metagenomic next-generation sequencing of blood and bronchoalveolar lavage fluid confirmed PJP. Despite targeted antifungal therapy and respiratory support, she developed persistent high-grade fever, pancytopenia, hyperferritinemia, hypofibrinogenemia, and hemophagocytosis on bone marrow aspirate by day 10, meeting diagnostic criteria for HLH. Genetic testing was declined by the parents. Management included dexamethasone, continuous renal replacement therapy, and plasmapheresis. Unfortunately, her condition deteriorated, and she was discharged upon parental request on day 22, succumbing on the same day. To our knowledge, this is the first reported pediatric case of HLH secondary to PJP in China. This case highlights that in children with PJP-especially those on immunosuppressive therapy-the development of persistent fever and cytopenia should prompt immediate evaluation for secondary HLH to enable timely intervention.}, }
@article {pmid42052210, year = {2026}, author = {Qu, HL and Li, JN and Gao, Y and Xu, XM and Zhang, XB and Yang, SD}, title = {From microscopy to antimicrobial decisions: a clinically grounded roadmap for critical care infectious diseases.}, journal = {Frontiers in artificial intelligence}, volume = {9}, number = {}, pages = {1807400}, pmid = {42052210}, issn = {2624-8212}, abstract = {In the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or sterile systemic inflammation. Cultures take time and their yield falls after antibiotics. Rapid molecular tests and metagenomics can add actionable information, but they also raise the burden of interpreting complex results. Microscopy is one of the few inputs that can shift management within minutes to hours: Gram-stain patterns from positive blood-culture bottles, respiratory specimens, cerebrospinal fluid, and wound material can reshape initial coverage and support early de-escalation when negative. Tissue and cytology help distinguish invasion from key mimics. The gap is consistency-reads vary across observers, workflows differ, and results do not always translate into reliable bedside actions. This review focuses on infectious-disease artificial intelligence (AI) as ICU bedside decision support, rather than as a survey of models. Using ICU sepsis as the primary use case-and neurocritical care as a challenging setting where sedation, brain injury, and noninfectious inflammation often mimic infection-we separate evidence into pathogen signals and host-response signals. We then map both streams to six decisions over the first 72 hours: start now versus pause, choose initial spectrum, reassess and narrow, escalate diagnostics and source control, act on high-risk resistance or invasive pathogens, and stop safely. We summarize where AI is most credible today (Gram-stain assistance, culture-plate triage, urine-culture screening, infection-focused digital pathology, host-response classifiers, and selected metagenomics) and what makes outputs actionable: calibrated probabilities, explicit confidence with safe deferral when uncertain, validation across hospitals and instruments, and endpoints tied to stewardship and safety (time to appropriate therapy, antibiotic days, de-escalation within 72 hours, missed bacteremia). Evidence was updated through February 28, 2026.}, }
@article {pmid42052392, year = {2026}, author = {Suenaga, H and Fujihara, H}, title = {Molecular basis for adaptive evolution of aromatic degradation enzymes in bacteria revealed by metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1795400}, pmid = {42052392}, issn = {1664-302X}, abstract = {Aromatic hydrocarbons, including persistent polycyclic aromatic hydrocarbons (PAHs), impose strong selective pressures that drive the adaptive evolution of bacterial degradation systems. Metagenomic studies have revealed extensive diversification of key catabolic enzymes, such as ring-hydroxylating and ring-cleavage dioxygenases, through the accumulation of single-nucleotide polymorphisms (SNPs) and structural modifications that increase substrate range and enhance catalytic efficiency in polluted environments. These findings demonstrate that gene mutations that change enzyme properties collectively shape the evolution of aromatic-degrading bacteria. Metagenomics is powerful tools for elucidating these evolutionary processes and advancing applications in bioremediation and industrial biocatalysis.}, }
@article {pmid42052398, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ}, title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794875}, pmid = {42052398}, issn = {1664-302X}, abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.}, }
@article {pmid42052556, year = {2026}, author = {Chu, T and Liu, J and Zhang, Y and Yang, K and Li, S and Yan, Q and Li, Y}, title = {Metagenome-based virome analysis identifies the oral viral signatures for periodontitis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2662091}, pmid = {42052556}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis (PD) is a chronic infectious disease driven by bacterial biofilms, yet the oral virome's role in pathogenesis remains poorly understood.<br><br>OBJECTIVE: This cross-cohort meta-analysis aims to define PD-associated viral signatures, characterize predicted virus-host interactions, and evaluate the diagnostic potential of viral biomarkers.<br><br>METHODS: We integrated 89 saliva (44 PD, 45 healthy) and 86 subgingival plaque (48 PD, 38 healthy) metagenomes from six public cohorts for a unified virome analysis.<br><br>RESULTS: We identified 156 viral operational taxonomic units (vOTUs) significantly associated with PD (105 in saliva, 66 in subgingival plaque and 15 shared). PD-enriched vOTUs were predicted to target periodontal pathogens including Porphyromonas gingivalis, whereas Streptococcus-targeting phages were decreased. PD-associated vOTUs harbored diverse bacterial defense and anti-defense systems, with those enriched in PD overrepresenting lysozyme and replication-associated genes. Diagnostic models based on key viral markers achieved robust performance, with AUCs of 0.95 (saliva) and 0.92 (subgingival plaque) for classifying PD.<br><br>CONCLUSION: This study delineates a distinct oral virome profile in PD, highlights predicted virus-host interactions, and underscores the potential of viral biomarkers for PD diagnosis,providing a basis for future investigations into viral ecology and phage-based interventions.}, }
@article {pmid42052831, year = {2026}, author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S}, title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {4}, pages = {48982}, doi = {10.31083/FBL48982}, pmid = {42052831}, issn = {2768-6698}, support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.<br><br>METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.<br><br>RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 &#xb1; 0.12, suggesting promising discriminatory potential that warrants further validation.<br><br>CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.}, }
@article {pmid42053312, year = {2026}, author = {Chung, B and Wang, S and Hao, Z and Allison, SD and Malik, AA}, title = {Plant litter chemistry and associated changes in microbial decomposition under drought.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0043826}, pmid = {42053312}, issn = {2150-7511}, support = {DE-SC0016410 and DE-SC0020382//US Department of Energy Genomic Science Program/ ; DE-AC02-05CH11231//US Department of Energy Genomic Science Program/ ; }, mesh = {*Droughts ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Fungi/metabolism/genetics ; Ecosystem ; Metagenomics ; *Plants/chemistry ; Poaceae/chemistry ; *Soil/chemistry ; }, abstract = {UNLABELLED: Drought has consequences for microbial decomposition rates, including indirect effects through changes in plant litter chemistry. Here, we studied the impact of a decade-long drought on plant litter chemistry and microbial decomposition traits in a semi-arid ecosystem during an 18-month litter bag experiment. We investigated litter sourced from four conditions: grass and shrub vegetation under ambient and reduced precipitation. We hypothesized that litter chemistry drives microbial decomposition capabilities and enzyme activity due to vegetation differences and drought effects on litter chemistry. We found that carbohydrate-rich grass litter had a higher abundance of decomposition genes detected using metagenomics and enzyme activity than more recalcitrant shrub litter, which was richer in lignin and lipids; these patterns were related to substrate supply. Drought decreased some carbohydrate fractions in grass litter but did not change the lignin fraction in grass and shrub litter, suggesting that drought does not make litter more recalcitrant. Most decomposition genes and enzyme activities were not significantly affected by drought, thereby maintaining decomposition rates. Microbial community succession patterns-decreasing fungal abundance and increasing bacterial abundance with time-corresponded with decreasing chitin gene abundance and increasing peptidoglycan gene abundance over time, indicating microbial necromass recycling. We demonstrate minimal litter chemistry-mediated effects of drought but show significant changes in community composition and their decomposition capabilities over time, highlighting that complex microbial-chemical interactions under climate change can influence ecosystem-scale processes.<br><br>IMPORTANCE: Climate change is causing more severe and frequent droughts in semi-arid ecosystems, affecting soil microbes breaking down plant litter. Our research focuses on understanding the less studied pathway of drought impact on microbes via changes in plant litter chemistry. Drought can alter the plant litter chemistry by changing the composition and physiology of plants, which can alter microbial decomposition and ecosystem-level carbon cycling. We investigated litter decomposition traits of microbial communities in grass and shrub litter under long-term drought. There were significant changes in litter chemistry under drought but no increase in lignin fraction. Despite this, microbial communities maintained their decomposition capabilities under drought, highlighting the ability of microbes to adapt and continue functioning. We also demonstrate unique microbial community succession patterns and dead biomass recycling, which can have implications for carbon cycling rates in the ecosystem. This study sheds light on the complex microbial interactions that affect ecosystem functioning under climate change.}, }
@article {pmid42053608, year = {2026}, author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N}, title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42053608}, issn = {1432-184X}, support = {Project number: 116O328//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; }, abstract = {UNLABELLED: Hazelnut is a major export commodity for Türkiye, the world’s leading producer, yet pest pressure in hazelnut orchards has caused substantial quantitative and qualitative yield losses in recent years. Among emerging pests, the green shield bug (GSB) Palomena prasina (Hemiptera: Pentatomidae) has become a key threat due to direct feeding on developing fruits. Despite its increasing economic relevance, the microbial community associated with P. prasina remains poorly characterized. Here, we present the first comprehensive analysis of the bacterial community associated with P. prasina using 16 S rRNA gene metabarcoding combined with prevalence screening and phylogenetic analyses. A total of 36 bacterial taxa were detected across sampled populations, with Pantoea and Sodalis identified as the dominant genera. Bacterial diversity did not differ significantly between sexes or among geographic locations, indicating a relatively stable microbial community. Prevalence analyses revealed that Pantoea spp. were present in all examined individuals, whereas Sodalis spp. showed variable infection frequencies among populations. Phylogenetic reconstruction indicated contrasting evolutionary patterns between these dominant taxa, with Pantoea lineages displaying a polyphyletic structure suggestive of repeated environmental acquisition, while Sodalis sequences formed a more cohesive, host-associated lineage consistent with a facultative symbiotic lifestyle. Overall, these findings improve our understanding of stink bug-microbe associations and provide an ecological framework for future studies exploring symbiont-based pest management strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02779-2.}, }
@article {pmid42053852, year = {2026}, author = {Peng, Q and Lin, Y}, title = {A case report of infective endocarditis caused by Mycoplasma pneumoniae in a child.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42053852}, issn = {1435-4373}, abstract = {OBJECTIVE: This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by Mycoplasma pneumoniae(M. pneumoniae) in children, in order to enhance understanding of this rare extrapulmonary complication of M. pneumoniae infection and provide clinical insights for its diagnosis and treatment.<br><br>METHODS: We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.<br><br>RESULTS: A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with M. pneumoniae pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. M. pneumoniae was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.<br><br>CONCLUSIONS: M. pneumoniae pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.}, }
@article {pmid42054100, year = {2026}, author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE}, title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.}, journal = {Microbial genomics}, volume = {12}, number = {4}, pages = {}, pmid = {42054100}, issn = {2057-5858}, mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; }, abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.}, }
@article {pmid42054312, year = {2026}, author = {Revel, J and Leroy, J and Delbecq, S and Constant, O and Henry Marty, F and Naili, C and Barthès, A and Nagy, A and Schmidt-Chanasit, J and Cadar, D and Abd Rahaman, NY and Lajoix, AD and Desmetz, C and Simonin, Y}, title = {Differential properties of NS1 glycoproteins in West Nile and Usutu viruses.}, journal = {Emerging microbes &amp; infections}, volume = {15}, number = {1}, pages = {2667565}, pmid = {42054312}, issn = {2222-1751}, mesh = {Animals ; *West Nile virus/genetics/metabolism/chemistry/pathogenicity ; *Viral Nonstructural Proteins/metabolism/genetics/chemistry/blood ; Humans ; *West Nile Fever/virology ; *Flavivirus/genetics/metabolism ; Mice ; Blood-Brain Barrier/virology ; *Flavivirus Infections/virology ; Endothelial Cells/virology ; Mosquito-Borne Diseases ; Female ; Brain/virology ; }, abstract = {West Nile virus (WNV) and Usutu virus (USUV) are neurotropic orthoflaviviruses of the Flaviviridae family, transmitted primarily by Culex mosquitoes and maintained in enzootic cycles involving birds. While WNV is a well-established human pathogen causing hundreds of neuroinvasive cases annually in Europe, USUV has emerged more recently, with fewer documented human infections but increasing evidence of neurovirulence. The viral nonstructural protein 1 (NS1) plays a central role in orthoflavivirus pathogenesis by modulating host immune responses, disrupting endothelial barrier integrity, and facilitating viral dissemination. However, the functional and biochemical properties of NS1 from WNV and USUV remain poorly characterized. We combined in vitro, in vivo, and clinical approaches to compare NS1 secretion, stability, and its impact on blood-brain barrier. Our results show that WNV NS1 is secreted at significantly higher levels, exhibits greater thermal stability, and disrupts brain endothelial barrier integrity in vitro. In contrast, USUV NS1 is secreted less efficiently, is slightly less stable, and does not compromise blood-brain barrier integrity, despite inducing distinct transcriptional responses in brain endothelial cells. In mice, WNV infection led to higher serum NS1 levels and stronger systemic inflammation than USUV. Clinically, WNV NS1 was detected mainly in patients with neurological symptoms, whereas USUV NS1 remained undetectable in all cases. Altogether, these findings reveal differential NS1 properties between these closely related viruses, with key implications for orthoflavivirus diagnosis and neurovirulence mechanisms.}, }
@article {pmid42054365, year = {2026}, author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H}, title = {Resource availability structures microbial competition through genomic niche partitioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {18}, pages = {e2526391123}, pmid = {42054365}, issn = {1091-6490}, support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 22/15842-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 23/02850-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 20/11953-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; }, mesh = {*Metagenome ; Humans ; Phylogeny ; Ecosystem ; *Microbiota/genetics ; Bacteria/genetics/classification ; Biodiversity ; Metagenomics ; Soil Microbiology ; Genomics ; }, abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.}, }
@article {pmid42054706, year = {2026}, author = {Vilaseca, A and Toledano, M and Flanagan, EP}, title = {Complexities in evaluation and management of infectious myelopathies.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {227-239}, doi = {10.1097/QCO.0000000000001204}, pmid = {42054706}, issn = {1473-6527}, mesh = {Humans ; Myelitis/diagnosis/virology ; *COVID-19/complications/epidemiology ; *Spinal Cord Diseases/diagnosis/virology ; SARS-CoV-2 ; Magnetic Resonance Imaging ; Neuromuscular Diseases ; Central Nervous System Viral Diseases ; }, abstract = {PURPOSE OF REVIEW: To review recent advances in infectious myelopathies and integrate them into a practical, syndrome-based approach that supports early recognition, guides testing, and avoids pitfalls.<br><br>RECENT FINDINGS: Advances in MRI pattern recognition and pathogen-specific diagnostics have refined the evaluation of infectious myelopathies, with strategies tailored to geographic epidemiology, host susceptibility, and distinction from immune-mediated causes. During the COVID-19 pandemic, SARS-CoV-2-associated myelopathy emerged as a rare para- or postinfectious cause of myelitis. The pandemic coincided with a decline in enterovirus outbreaks and acute flaccid myelitis, which are now re-emerging, underscoring the importance of epidemiologic surveillance. Metagenomic next-generation sequencing is useful in suspected infectious myelopathy because it can identify unexpected pathogens from cerebrospinal fluid, but its imperfect sensitivity and contamination risk mean it should complement rather than replace conventional testing. Growing recognition of compartmentalized central nervous system inflammation and cerebrospinal fluid viral escape in HIV myelopathy has shifted management toward antiretroviral resistance patterns and treatment optimization. Therapeutic advances remain limited and largely pathogen-specific, although targeted approaches such as mogamulizumab for HTLV-1-associated myelopathy are promising.<br><br>SUMMARY: Recent progress in infectious myelopathies has been driven by improved pathogen detection and more tailored diagnostic strategies, although treatment advances are beginning to emerge.}, }
@article {pmid42055201, year = {2026}, author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M}, title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {306}, number = {}, pages = {110551}, doi = {10.1016/j.cbpc.2026.110551}, pmid = {42055201}, issn = {1532-0456}, mesh = {Animals ; *Fluoxetine/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Zebrafish/physiology ; Female ; *Water Pollutants, Chemical/toxicity ; *Feeding Behavior/drug effects ; *Selective Serotonin Reuptake Inhibitors/toxicity ; Homeostasis/drug effects ; Intestinal Barrier Function/drug effects ; Intestines/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.}, }
@article {pmid42055262, year = {2026}, author = {Trinh, HP and Lee, SH and Park, HD}, title = {Mitigating nitrite stress and restoring functional redundancy in anammox reactor via acetate-driven DNRA-anammox coupling.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134732}, doi = {10.1016/j.biortech.2026.134732}, pmid = {42055262}, issn = {1873-2976}, mesh = {*Bioreactors/microbiology ; *Nitrites/metabolism ; *Acetates/metabolism ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; Nitrogen ; Nitrates/metabolism ; }, abstract = {Frequent fluctuations in nitrite concentrations and unstable control of partial nitritation often lead to excessive NO2[-] accumulation, resulting in performance deterioration in anammox-based systems. To address this challenge, an anammox reactor was operated for 180 days to investigate the inhibitory effects of elevated NO2[-]/NH4[+]ratios on anammox activity and to evaluate the effectiveness of external carbon supplementation in promoting dissimilatory nitrate reduction to ammonium (DNRA)-related pathways that contribute to NO2[-] reduction. Increasing NO2[-]/NH4[+]ratio from 1.3 to 3.0 decreased the nitrogen removal efficiency from 96.7% to 26.6%, reduced the relative abundance of anammox bacteria (Ca. Kuenenia and Ca. Jettenia) from 41.5% to 7.0% and promoted Nitrospira to 7.7%. In contrast, acetate supplementation at a C/N ratio of 0.2 suppressed Nitrospira to 0.2% and enhanced the abundance of anammox and DNRA-performing bacteria (e.g., Fimbriimonadaceae, Mycobacterium, Anaerolineales, Caldilineaceae, and Ignavibacteriaceae) to 31.2% and 15.7%, respectively. Metagenome-assembled genome analysis confirmed the enrichment of functional genes associated with anammox (hzsABC and hdh) and DNRA metabolism (nirBD and nrfAH), corresponding to the recovery of nitrogen removal efficiency to 82.3%. Quantitative microbial network analysis further revealed that functional redundancy index declined from 0.56 to 0.42 under nitrite stress but recovered to 0.53 following acetate supplementation, indicating the restoration of a functionally buffered microbial community. Overall, these results demonstrate that low-level acetate supplementation (C/N = 0.2) effectively stimulated DNRA-mediated NO2[-] reduction to NH4[+] by DNRA-performing bacteria, thereby supporting anammox activity and providing an energy-efficient strategy to mitigate NO2[-] accumulation and stabilize nitrogen removal in anammox-based systems.}, }
@article {pmid42055314, year = {2026}, author = {Zhang, Y and Xia, J and Qiu, Z and Tian, S and Wang, J and Ren, X and Chen, M}, title = {Successful treatment of balamuthia mandrillaris amebic encephalitis diagnosed by MetaCAP in China: A case report and review of 25 survival cases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {168}, number = {}, pages = {108745}, doi = {10.1016/j.ijid.2026.108745}, pmid = {42055314}, issn = {1878-3511}, mesh = {Humans ; Male ; Middle Aged ; *Amebiasis/drug therapy/diagnosis/parasitology ; *Balamuthia mandrillaris/genetics/isolation &amp; purification ; *Central Nervous System Protozoal Infections/drug therapy/diagnosis ; China ; *Encephalitis/drug therapy/parasitology/diagnosis ; *Infectious Encephalitis/drug therapy/diagnosis/parasitology ; Metagenomics/methods ; Sulfasalazine/therapeutic use ; Treatment Outcome ; Case Reports as Topic ; }, abstract = {Balamuthia mandrillaris, a free-living amoeba, can cause Balamuthia amebic encephalitis (BAE), a rare and often fatal cerebral infection. The reported mortality rate is >90%, largely attributable to the absence of specific clinical manifestations, sensitive diagnostic methods, and effective therapeutic interventions. We herein describe a middle-aged, male patient diagnosed with BAE using Metagenomic Capture sequencing (MetaCAP) who achieved full recovery following early medical therapy without neurosurgical treatment. Our findings indicate that MetaCAP serves as a rapid and sensitive diagnostic approach, and sulfasalazine may confer a potential anti-inflammatory benefit in the management of BAE. In addition, we reviewed 25 survival cases of BAE reported in the PubMed database up to now.}, }
@article {pmid42055803, year = {2026}, author = {Auwal, AM and Matthews, R and Cook, C and Sargent, B and Easton, A and Ray, STJ and Ellul, MA and Michael, BD}, title = {Suspected encephalitis in adults.}, journal = {Practical neurology}, volume = {}, number = {}, pages = {}, doi = {10.1136/pn-2024-004299}, pmid = {42055803}, issn = {1474-7766}, abstract = {'Query encephalitis' is one of the most common reasons for inpatient neurology referral in the context of an acutely confused patient. Growing evidence suggests that time to treatment is a key determinant of outcome in both infectious and autoimmune encephalitis; hence, these two causes should be considered simultaneously at presentation. However, under-recognition and the existence of several mimics make a rapid diagnosis of encephalitis challenging. Appreciation of clinical syndromes can guide aetiological investigation and consequent treatment. In this article, we discuss clinical phenotypes associated with both infectious and autoimmune encephalitis, as well as a systematic approach to their investigation and up-to-date treatment strategies. We also highlight ongoing areas of research, such as metagenomics and therapeutic trials.}, }
@article {pmid42056322, year = {2026}, author = {Thakkar, S and Rathour, R and Rana, SS and Samant, S and Kikani, BA and Madamwar, D and Desai, C}, title = {Biochar-augmented microaerophilic fixed-film bioreactor integrated with an aerobic membrane bioreactor effectively reduces persistent, mobile chemicals in the CETP effluent treatment.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {42056322}, issn = {1573-0972}, support = {File No. GSBTM/JD(R&amp;D)/662/2022-23/00292469//Gujarat State Biotechnology Mission (GSBTM), Department of Science and Technology, Government of Gujarat/ ; }, mesh = {*Bioreactors/microbiology ; *Charcoal/chemistry ; Bacteria/classification/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; *Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; *Water Purification/methods ; Membranes, Artificial ; }, abstract = {Different classes of chemical compounds including persistent, mobile chemicals (PMCs) often bypass the conventional treatment processes of common effluent treatment plants (CETPs), resulting in their unmonitored release into aquatic environments. In this study, an integrated treatment system comprising a microaerophilic fixed-film bioreactor (MFB) and an aerobic membrane bioreactor (Ae-MBR) was engineered to treat secondary CETP effluent. Two types of packing materials in the engineered MFBs were evaluated: one with wood charcoal (C-MFB) and another with 30% (w/w) biochar-augmented charcoal (BAC-MFB). The BAC-MFB showed better treatment efficiency, achieving 69.17% colour (Pt-Co units) removal and 93.01% COD removal at an optimal 3d hydraulic retention time (HRT). Integration with Ae-MBR further enhanced the treatment, achieving > 95% COD and > 94% colour removal, with an overall > 85% reduction in total number of parent chemical compounds and a specific > 83% reduction in PMCs from CETP effluent. At 3d HRT, bacterial community analysis revealed dominance of Campylobacterota and Bacillota in BAC-MFB under microaerophilic conditions, whereas Bacillota dominated in the Ae-MBR under aerobic conditions. The predicted metagenome analysis revealed significant enrichment of benzoate and aminobenzoate degradation pathways in the integrated system. While the BAC-MFB treatment alone achieved sufficient COD removal, its integration with Ae-MBR markedly enhanced the reduction in overall chemical complexity including PMCs from the CETP effluent. This study demonstrates that the engineered hybrid BAC-MFB-Ae-MBR system is a sustainable solution for the treatment of industrial CETP effluents.}, }
@article {pmid42056687, year = {2026}, author = {Wedell, E and Shen, C and Warnow, T}, title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2981}, number = {}, pages = {37-52}, pmid = {42056687}, issn = {1940-6029}, mesh = {*Phylogeny ; *Metagenomics/methods ; *Software ; Likelihood Functions ; Algorithms ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; }, abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.}, }
@article {pmid42056742, year = {2026}, author = {Zhang, X and Li, Q and Yang, H and Li, H and Hu, C}, title = {Active responses of cyanobacterial crusts directly exposed to the extreme stratospheric environment.}, journal = {Life sciences in space research}, volume = {50}, number = {}, pages = {133-145}, doi = {10.1016/j.lssr.2026.01.001}, pmid = {42056742}, issn = {2214-5532}, mesh = {*Cyanobacteria/physiology/metabolism ; *Extraterrestrial Environment ; Mars ; Exobiology ; *Extreme Environments ; Indoles ; Phenols ; }, abstract = {The stratosphere's highly hostile environment offers a unique and relatively accessible setting to evaluate extremophilic adaptation for extraterrestrial colonization. The accelerating pace of the Martian project has underscored the need for a better understanding of the synergistic responses of microbial communities in Mars-like habitats. Here, we loaded the cyanobacterial crust, a model system with multiple trophic levels, onto a balloon-borne astrobiology platform for a direct-exposure experiment in the stratosphere, aligned with the ground-control and indoor-simulated groups. After short-term in-situ exposure, we performed multi-omics analyses to delineate alterations in community composition and the community-level metabolic response. We observed a significant shift in the community composition of active members, with the relative abundance of photoautotrophs (except Scytonema) declining while that of chemotrophs increased. However, we demonstrated the unique thriving of the cyanobacterial genus Scytonema, attributed to its synthesis of the anti-ultraviolet compound scytonemin, its diverse material, and its energy acquisition. Meanwhile, the distinct metabolic profiles exhibited by various species and their interspecies metabolic interactions synergistically facilitated the retention of organic carbon and nitrogen, ultimately sustaining the stability of the biocrust community. Our study underscores the adaptive resilience of cyanobacterial crusts under stratospheric stresses. Notably, the robustness of Scytonema, particularly its unique survival capabilities, highlights its potential for extraterrestrial applications.}, }
@article {pmid42056812, year = {2026}, author = {Fu, Y and Zhuang, H and Shi, J}, title = {Reshaping of the electron transport chain and carbon metabolism by low-loading Fe3O4@PU for enhanced phenolic compounds degradation in an algal-bacterial biofilm system.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142207}, doi = {10.1016/j.jhazmat.2026.142207}, pmid = {42056812}, issn = {1873-3336}, mesh = {*Biofilms ; Electron Transport ; *Carbon/metabolism ; Bioreactors ; *Water Pollutants, Chemical/metabolism/chemistry ; *Phenols/metabolism ; Biodegradation, Environmental ; *Polyurethanes/chemistry ; Bacteria/metabolism ; *Ferric Compounds/chemistry ; Wastewater ; Waste Disposal, Fluid/methods ; }, abstract = {While previous algal-bacterial biofilm systems without magnetite have shown limited resilience to high concentration phenolic compounds, this study demonstrates that introducing low loading (5%) nano-Fe3O4 substantially enhances degradation stability by optimizing electron transfer pathways. Four algal-bacterial reactors with varying Fe3O4 loadings (5-50%) were constructed using polyurethane carriers to treat phenolic wastewater under increasing total phenol (TPh) concentrations (50-300 mg/L). The 5% loading reactor (R1) demonstrated outstanding performance, achieving > 80% TPh removal and approximately 76% COD removal even at the highest loading. Compared to without magnetite systems, R1 achieved 13-15% higher TPh degradation at 300 mg/L. R1 also exhibited the highest electron transfer system activity (0.487 μg O2·gVSS[-1]·h[-1]) and cytochrome c content (72.12 mg/g VSS), indicating that Fe3O4 serves as an electron shuttle, compensating for endogenous electron carrier limitations. Metagenomic analysis revealed that the enhanced performance stemmed from robust carbohydrate metabolism, particularly the upregulation of key glycolytic enzymes (pfkA) and glycogen degrading enzymes (GH13), ensuring efficient NADH/ATP production. This metabolic advantage supplied reducing power to the Fe3O4 optimized electron transport chain, synchronizing electron generation with respiratory utilization. These findings demonstrate that low-dose Fe3O4 optimizes natural electron transfer pathways by coupling metabolic flux with respiratory chain activity, offering a cost effective strategy for treating high strength industrial wastewater.}, }
@article {pmid42057016, year = {2026}, author = {Chen, H and Shi, X and Huang, Z and Li, X and Zhou, Y and Tan, D and Xie, Z and Wu, X and Zhou, M and Hong, D}, title = {Co-occurrence of viral encephalitis and autoimmune encephalitis: overlapping peaks encephalitis or coincidence condition?.}, journal = {BMC neurology}, volume = {26}, number = {1}, pages = {}, pmid = {42057016}, issn = {1471-2377}, support = {No.82101419//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Many studies have shown that autoimmune encephalitis (AE) can occur after viral encephalitis. However, no reports have focused on the interval between viral infection peaks and probable AE peaks. OBJECTIVES: To assess the possibility that viral infection and neuronal autoantibodies are concomitantly present within a 72-hour interval in patients diagnosed with encephalitis. METHODS: We retrospectively analyzed encephalitis patients admitted to our institution between 2018 and 2025. The inclusion criteria were as follows: the interval from the initial onset of symptoms to serum and cerebrospinal fluid (CSF) sampling was less than 72 h, with concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies. Viral detection was performed using metagenomic next-generation sequencing (mNGS), whereas neuronal autoantibodies were measured by cytometric bead array (CBA). RESULTS: Among 347 patients with encephalitis, fifteen patients had concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies within 72 h after the initial onset of symptoms.These fifteen patients presented with prominent clinical manifestations including headache, seizures, psychosis and memory disorders. Cerebrospinal fluid (CSF) analysis revealed features consistent with aseptic or viral encephalitis. A variety of neuronal autoantibodies were identified, namely NMDA-R-IgG, CASPR2-IgG, LGI1-IgG, LON5-IgG, GFAP-IgG, GAD65-IgG and mGluR5-IgG.Metagenomic next-generation sequencing (mNGS) assays demonstrated that 5 patients were infected with Human Herpesvirus Type 1 (HSV-1) and 10 patients with Epstein-Barr Virus (EBV). CONCLUSIONS: The concomitant detection of viral infection and neuronal autoantibodies in serum or cerebrospinal fluid (CSF) within a short time window (≤ 72 h) after the initial onset of symptoms was defined in this study as Overlapping Peak Encephalitis (OPE) or coincidence condition, which suggests that it represents a distinct clinical entity. This finding underscores the importance of simultaneously performing both metagenomic next-generation sequencing (mNGS) and neuronal autoantibody assays in patients with suspected viral encephalitis. Early identification of such comorbid conditions is of paramount importance; timely diagnosis combined with antiviral therapy and immunomodulatory intervention may significantly improve clinical outcomes.}, }
@article {pmid42057074, year = {2026}, author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T}, title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {42057074}, issn = {1746-6148}, mesh = {Animals ; *Microbiota ; Swine ; *Mycoplasma hyopneumoniae/immunology ; *Pneumonia of Swine, Mycoplasmal/prevention &amp; control/microbiology ; *Bacterial Vaccines/administration &amp; dosage/immunology ; *Vaccination/veterinary/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Nanotechnology ; Female ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; }, abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.}, }
@article {pmid42057154, year = {2026}, author = {Mahmud, MR and Uddin, MK and Kareljärvi, P and Jalasvuori, M and Peräkylä, J and Eklund, T and Biström, M and Hasan, S and Vatanen, T and Kiljunen, S and Oliviero, C}, title = {Impact of phage therapy in post-weaning piglets challenged with ETEC strain in a controlled minitrial.}, journal = {Porcine health management}, volume = {12}, number = {1}, pages = {}, pmid = {42057154}, issn = {2055-5660}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a pathogen responsible for post-weaning diarrhea (PWD) in piglets, which results in economic losses in pig production. The rise of antibiotic-resistant ETEC strains together with restrictions on addition of zinc oxide in pig feed require alternative management approaches. Our research examines bacteriophage therapy as a solution to control ETEC infections in newly weaned piglets. A cocktail of phages targeting a strain of ETEC F4LT1ST2 was identified and subsequently multiplicated in laboratory. We conducted a trial including nine piglets divided into three groups. The negative control group was exposed to the phage cocktail by administration with the bedding material (saw dust) on the floor of their pen. The treatment group was exposed to the ETEC strain and to the phage cocktail, and the positive control group was exposed to the ETEC strain only. Shotgun metagenomic sequencing was performed on fecal samples to characterize bacterial and phage dynamics. Throughout a 10-day period we monitored daily the rectal temperature and the diarrheal score of piglets. Subsequently we evaluated phage and bacterial counts in fecal samples to determine phage therapy effect on gut microbiota dynamics and piglet health. The PHAGE+ETEC group showed 19.2% lower cumulative diarrhea burden (p = 0.044) and 61.9% higher average daily gain (p = 0.065). Rectal temperature correlated significantly with diarrhea severity (per-piglet Spearman's ρ = 0.727, p = 0.027). Alpha diversity did not differ between treatment groups across timepoints, suggesting that phage administration did not cause major shifts in microbial diversity. Metagenomic analyses showed significant reduction of E. coli abundance in PHAGE+ETEC group compared to PHAGE groups (p = 0.009). Consistent with these observations, plaque assay results confirmed active phage-bacteria interactions: no plaque formation was detected in the feces of the ETEC-only group, whereas the PHAGE+ETEC group showed phage replication, reaching 10[6] PFU/ml. This pilot study highlights the potential of phage therapy as an alternative to antibiotics for ETEC infections in piglets. Additional research with larger pig population and longer duration is required to confirm these findings and develop optimal phage application methods for swine production.}, }
@article {pmid42057164, year = {2026}, author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I}, title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00893-9}, pmid = {42057164}, issn = {2524-6372}, abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.<br><br>RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short&#x2011;term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine&#x2011;scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.<br><br>CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non&#x2011;equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long&#x2011;term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.}, }
@article {pmid42057198, year = {2026}, author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J}, title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42057198}, issn = {1756-994X}, support = {2021-01637//Vetenskapsr&#xe5;det/ ; 967569//V&#xe4;sterbotten L&#xe4;ns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; 09150162410022/ZONMW_/ZonMw/Netherlands ; }, mesh = {Humans ; *COVID-19/epidemiology/microbiology ; *Life Style ; Infant ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; Pandemics ; Feces/microbiology ; Metagenome ; Male ; Female ; Longitudinal Studies ; Hygiene ; }, abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.<br><br>METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.<br><br>RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value&#x2009;=&#x2009;0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.<br><br>CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.}, }
@article {pmid42057295, year = {2026}, author = {Klaps, J and Lemey, P and Bletsa, M and ,  and Kafetzopoulou, LE}, title = {nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {5}, pages = {}, pmid = {42057295}, issn = {1367-4811}, support = {511260616//German Research Foundation [Deutsche Forschungsgemeinschaft/ ; G005323N//Research Foundation-Flanders/ ; G051322N//Research Foundation-Flanders/ ; 1SH2V24N//Research Foundation-Flanders/ ; 12X9222N//Research Foundation-Flanders/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; *Software ; Humans ; High-Throughput Nucleotide Sequencing ; }, abstract = {MOTIVATION: Reconstructing eukaryotic viral genomes from metagenomic data is challenging due to their extensive diversity and potential genome segmentation. Current approaches often rely on labor-intensive manual curation for reference selection and scaffolding, limiting scalability for large studies or rapid outbreak response. We address the critical need for an automated, scalable pipeline for efficient viral metagenomic analysis without manual intervention.<br><br>RESULTS: We present nf-core/viralmetagenome, a comprehensive Nextflow pipeline for the untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation capture enriched samples. The pipeline automates the entire process from read preprocessing to consensus generation, integrating multiple de novo assemblers, automated reference selection, and iterative consensus refinement. It features robust quality control, extensive documentation, and seamless portability via Docker and Singularity. We validated the pipeline on diverse simulated and real datasets, demonstrating its ability to recover high-quality genomes from complex metagenomic samples and resolve co-infections, making it a powerful tool for viral surveillance.<br><br>AVAILABILITY: nf-core/viralmetagenome is freely available at https://github.com/nf-core/viralmetagenome with comprehensive documentation at https://nf-co.re/viralmetagenome. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.17524074.}, }
@article {pmid42057740, year = {2026}, author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM}, title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {18}, pages = {14335-14347}, doi = {10.1021/acs.jafc.5c17636}, pmid = {42057740}, issn = {1520-5118}, mesh = {Rhizosphere ; Soil Microbiology ; Zea mays/growth &amp; development/microbiology/metabolism/drug effects ; *Microbiota/drug effects ; Bacteria/genetics/isolation &amp; purification/drug effects/classification/metabolism ; Soil/chemistry ; *Soil Pollutants/chemistry/pharmacology/toxicity ; *Plastics/chemistry ; }, abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.}, }
@article {pmid42057783, year = {2026}, author = {Harshvardhan,  and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S}, title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799124}, pmid = {42057783}, issn = {1664-302X}, abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.<br><br>METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.<br><br>RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.<br><br>CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.}, }
@article {pmid42057917, year = {2026}, author = {Szentiványi, T and Bruszniczky, B and Biró, Z and Katona, K and Klein, &#xc1; and Bende, A and Bánáti, L and Vass, G and Lehotzky, P and Kovács, D and Földvári, G and Csivincsik, &#xc1; and Nagy, G and Nagy, RR and Miklós, M and Szabadi, KL and Szabó, &#xc9;S and Garamszegi, LZ}, title = {Unwelcome guests: Nematodes of zoonotic and animal health importance in native and invasive carnivores of Hungary.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {9}, number = {}, pages = {100380}, pmid = {42057917}, issn = {2667-114X}, abstract = {Wild carnivores are important reservoirs of parasitic nematodes, several of which have veterinary and zoonotic significance. In Europe, the role of invasive carnivores in parasite circulation remains poorly understood. Here, we screened 371 individuals of six wild carnivore species from Hungary (red foxes, badgers, golden jackals, raccoons, raccoon dogs, and beech martens), using molecular markers (cox1 and S12), and detected five nematode parasites: Dirofilaria immitis, Crenosoma vulpis, Angiostrongylus vasorum, Thelazia callipaeda, and Spirocerca lupi. The highest prevalence was observed in badgers (32.0%) and red foxes (15.7%), while invasive raccoons also showed a relatively high infection rate (13.2%). Dirofilaria immitis was one of the most common nematode species detected: it was found in four host species, including the first confirmed cases in Hungarian badgers and invasive raccoons, extending the known host range of this parasite in central Europe. Importantly, T. callipaeda was recorded in red foxes and an invasive raccoon dog, representing the first invasive host records of this zoonotic eyeworm in Hungary. Crenosoma vulpis was identified in raccoons, suggesting invasive species may act as incidental carriers of endemic parasites. Both C. vulpis and D. immitis showed low host specificity. These findings indicate that invasive carnivores, particularly raccoons, may harbour unexpectedly high prevalence and play a greater role in local parasite networks than previously assumed. Our results highlight the epidemiological significance of both native and invasive carnivores in sustaining nematodes of zoonotic and veterinary importance in central Europe, stressing the need for continued surveillance in wild carnivores.}, }
@article {pmid42058175, year = {2026}, author = {Zhong, H and Sun, C and Lu, Y and Cai, X and Cao, M and Wang, L and Feng, C and Song, M and Sun, W and Shi, M and Tao, Y and Zhou, J and Chen, C and Lu, X and Li, Y and Ni, Y and Cai, Y and Zhong, J and Li, Y and Wu, W and Shi, Y and Wang, M and Su, X}, title = {The clinical value of metagenomic next generation sequencing in the diagnosis of non-neutropenic invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1731736}, pmid = {42058175}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Sputum/microbiology ; Male ; Sensitivity and Specificity ; Middle Aged ; *Aspergillus/genetics/isolation &amp; purification/classification ; Adult ; Galactose/analogs &amp; derivatives ; Aged ; Mannans/analysis/blood ; }, abstract = {BACKGROUND: This study aims to explore the performance of metagenomic next generation sequencing (mNGS) in the diagnosis of non-neutropenic invasive pulmonary aspergillosis (IPA) and its clinical application value.<br><br>METHODS: This multi-center study enrolled 293 suspected IPA patients who conducted mNGS from October 2020 to February 2024. These cases were classified into IPA group and non-IPA group according to IPA diagnostic criteria. We analyzed the diagnostic value of mNGS by comparing with sputum culture, BALF culture, serum and BALF GM test.<br><br>RESULTS: A total of 118 IPA patients (4 proven/113 probable/1 possible diagnosis) were included in our study. The most common Aspergillus species was A. fumigatus (63.4%), followed by A. flavus (23.2%), A. oryzae (7.1%), A. niger (3.6%) and A. terreus (2.7%). The sensitivity of bronchoalveolar lavage fluid (BALF) mNGS was significantly higher than BALF culture (81.9% vs. 27.0%, p<0.001) and BALF galactomannan (GM) (81.9% vs. 55.8% (GM&#x2265;1.0 cutoff value), p<0.001). The specificity of BALF mNGS was 92.2%, which was similar with BALF culture (98.5%) and BALF GM (94.7%). The combination of BALF mNGS and GM could increase the sensitivity to 88.7%, and had great negative predictive value (NPV, 92.3%). The sensitivity of blood mNGS was significantly higher than serum GM (58.8% vs. 16.7%, p<0.001). And the sensitivity of sputum mNGS was 66.7%, which was significantly higher than sputum culture (30.0%, p=0.025).<br><br>CONCLUSION: mNGS demonstrated significant diagnostic value for IPA, exhibiting significantly higher sensitivity compared to current conventional microbiological tests while maintaining equivalent specificity. The combination of BALF mNGS with GM performed great sensitivity and negative predictive value. BALF specimens seemed to be superior to blood and sputum samples. However, for patients unable to undergo bronchoscopy, sputum and blood mNGS were still superior to other methods.}, }
@article {pmid42058649, year = {2026}, author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A}, title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6677609}, pmid = {42058649}, issn = {1687-918X}, abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.}, }
@article {pmid42058681, year = {2026}, author = {Budai, M and Rák, G and Wenner, B and Móré, A and Bancsik, B and Nagy, B and Kovács, G and Szabolcs, M and Ladnyik, Z and Molnár, C and Guller, ZE and Lengyel, A and Vadász, C and Mizsei, E}, title = {The Influence of Plant Species Composition on an Endangered Grassland Specialist Reptile, the Hungarian Meadow Viper.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73579}, pmid = {42058681}, issn = {2045-7758}, abstract = {The Hungarian meadow viper (Vipera ursinii rakosiensis) is one of the most threatened vertebrates in Hungary, whose populations are not growing significantly despite enormous conservation efforts. Previous studies suggested an influence of vertical vegetation structure on habitat use, while the role of horizontal vegetation structure is still poorly understood. In the present study, we used vegetation survey data to investigate the effects of variables related to the horizontal structure and functional composition of vegetation on the occupancy and density of the Hungarian meadow viper. During a spring survey period, we collected viper occurrence data in 59 sampling quadrats alongside plant community samples, then used single-season occupancy models and N-mixture models for analysis. After model selection, the best models included the moisture-related vegetation gradient, species richness, graminoid-forb ratio, and height of plants as explanatory variables for both occupancy and density. Wetter meadows with fewer plant species, a higher graminoid/forb ratio, and habitats with characteristically lower-growing plant species were more probable to be used by the vipers. Our results suggest that the horizontal structure of the vegetation influences the habitat use of vipers and also draw attention to the threats posed by more frequent droughts and heatwaves.}, }
@article {pmid42059272, year = {2026}, author = {Damian, R and Katarzyna, J and Sebastian, W and Piotr, J and Joanna, G and Małgorzata, C and Monika, H and Edyta, K}, title = {Native Aquatic Plastispheres in a River-Wastewater Catchment: Carbapenem-Resistant Bacteria Isolation and Microscopy-Based Structural Analysis.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70312}, doi = {10.1111/1462-2920.70312}, pmid = {42059272}, issn = {1462-2920}, support = {2021/43/B/ST10/01076//Narodowe Centrum Nauki/ ; }, mesh = {*Rivers/microbiology ; *Biofilms/growth &amp; development ; *Wastewater/microbiology ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/isolation &amp; purification/drug effects/genetics/classification ; Drug Resistance, Bacterial ; Plastics ; *Carbapenem-Resistant Enterobacteriaceae/isolation &amp; purification ; }, abstract = {Plastispheres, microbial biofilms formed on plastic surfaces, are increasingly recognised as ecological niches capable of transporting pollutants and antibiotic-resistant microorganisms. However, mechanistic insights into antimicrobial resistance (AMR) dynamics in natural plastispheres remain limited, particularly for priority pathogens such as carbapenem-resistant Enterobacterales (CRE). Here, we evaluated plastispheres as environmental reservoirs and vectors of carbapenem-resistant bacteria, comparing wastewater (secondary settling tanks, representing the final stage before environmental discharge) and riverine environments. Using a combined SEM-CFM approach, we resolved plastic surface topography and the spatial organisation of biofilm-associated bacteria. Although CRE were not detected, carbapenem-resistant bacteria constituted a stable fraction of heterotrophic communities in both environments and were primarily associated with intrinsic resistance mechanisms. Carbapenem-resistant isolates included Aeromonas spp. (blaCphA), Stenotrophomonas maltophilia (blaL1), and Pseudomonas putida (efflux-based resistance). Microscopy revealed dense bacterial clusters on plastic surfaces, suggesting microenvironments that may facilitate cell-cell interactions, including horizontal gene transfer. These findings highlight plastispheres not only as vectors of AMR but also as potential evolutionary hotspots shaping resistance persistence and dissemination in aquatic systems. Future integrating metagenomic and genomic data on resistance gene mobility with spatially resolved microbial community structure will provide critical insights into the mechanisms and risks of AMR dissemination in plastisphere environments.}, }
@article {pmid42059388, year = {2026}, author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA}, title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0360225}, pmid = {42059388}, issn = {2165-0497}, support = {AI157981/NH/NIH HHS/United States ; AI167538/NH/NIH HHS/United States ; DK128053/NH/NIH HHS/United States ; GM136554/NH/NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; //Baylor College of Medicine/ ; }, mesh = {Humans ; Female ; *Arthritis, Rheumatoid/microbiology/immunology ; *Vagina/microbiology/immunology ; Adult ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Cytokines ; *Bacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Young Adult ; Rheumatoid Factor ; C-Reactive Protein/analysis ; Anti-Citrullinated Protein Antibodies/analysis ; }, abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.}, }
@article {pmid42059394, year = {2026}, author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS}, title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0251025}, pmid = {42059394}, issn = {2165-0497}, support = {AP19VSCEAH00C014//U.S. Department of Agriculture/ ; //Texas A&amp;M University/ ; }, mesh = {Animals ; Cattle/microbiology ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Female ; *Gastrointestinal Microbiome/drug effects ; Weaning ; *Drug Resistance, Bacterial ; Texas ; Dairying ; *Microbiota/drug effects ; }, abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.}, }
@article {pmid42059571, year = {2026}, author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF}, title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0164025}, pmid = {42059571}, issn = {2379-5077}, support = {EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft/ ; 237291755//Deutsche Forschungsgemeinschaft/ ; FOR 5042 - 426660215//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; Streptomycin/pharmacology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/genetics/microbiology ; Mice, Knockout ; Male ; Mice, Inbred C57BL ; Metagenomics ; }, abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.<br><br>IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.}, }
@article {pmid42059572, year = {2026}, author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L}, title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0080025}, pmid = {42059572}, issn = {2379-5077}, support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; }, mesh = {*Deep Learning ; *Microbiota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Ecosystem ; }, abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.}, }
@article {pmid42059616, year = {2026}, author = {Moidu Jameela, R and Kedare, MM and Khan, R and Dhankad, N and Sinha, RK and Zade, A and Shah, S and Chatterjee, A}, title = {Whole genome sequence of Tsukamurella tyrosinosolvens extracted from metagenome of human pleural fluid enriched in Mycobacteria Growth Indicator Tube.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0151825}, pmid = {42059616}, issn = {2576-098X}, abstract = {Misdiagnosis of emerging pathogen Tsukamurella tyrosinosolvens is common due to phenotypic similarity with Mycobacterium tuberculosis (MTB). We report a high-quality, near-complete genome of T. tyrosinosolvens from pleural fluid enriched in Mycobacteria Growth Indicator Tube. The genome of this clinically successful strain can be studied to understand pathogenesis and diagnostic challenges.}, }
@article {pmid42059625, year = {2026}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0362625}, pmid = {42059625}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; R01 DE03013, R01 DE022586, 2R01 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Capnocytophaga/genetics/classification/isolation &amp; purification/physiology ; *Mouth/microbiology ; Microbiota ; Phylogeny ; Dental Plaque/microbiology ; Genome, Bacterial ; Metagenomics ; Metagenome ; }, abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.<br><br>IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.}, }
@article {pmid42059663, year = {2026}, author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y}, title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {42059663}, issn = {1477-4054}, support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; }, mesh = {Humans ; *COVID-19/complications/virology/microbiology ; Male ; *SARS-CoV-2 ; Female ; Middle Aged ; Disease Progression ; *Pulmonary Fibrosis/microbiology/etiology/virology/pathology ; *Microbiota ; Aged ; Gastrointestinal Microbiome ; Bronchoalveolar Lavage Fluid/microbiology ; Transcriptome ; Metagenomics ; Multiomics ; }, abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.}, }
@article {pmid42059780, year = {2026}, author = {Wolfe, BE}, title = {Metagenomes enriched with Virgibacillus are associated with a pink paste defect in an unpasteurized blue cheese.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0002726}, pmid = {42059780}, issn = {2576-098X}, abstract = {Shotgun metagenomes were used to identify microbes associated with a pink discoloration of an unpasteurized blue cheese made in the United States. Taxonomic assessments of individual reads and metagenome-assembled genomes revealed that the genus Virgibacillus was present in the pink paste, but not in unaffected paste.}, }
@article {pmid42059891, year = {2026}, author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G}, title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-026-06221-1}, pmid = {42059891}, issn = {1420-9071}, support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; }, abstract = {Pregnancy-induced hypertension (PIH) is a major cause of maternal and perinatal morbidity. However, the longitudinal dynamics of the gut microbiome before clinical onset remain poorly characterized. This nested case-control study within a prospective pregnancy cohort included 75 women who developed PIH and 195 matched controls. Fecal samples collected at early and mid-pregnancy underwent shotgun metagenomic sequencing, integrated with nontargeted plasma metabolomics and clinical data. Compared with healthy pregnancies, women who developed PIH exhibited altered gestational microbiome progression. This was characterized by a persistent enrichment of Bacteroides stercoris and Bacteroides eggerthii. Microbial pathways including amino acid biosynthesis and 2-oxocarboxylic acid metabolism were perturbed before diagnosis, with Bacteroides stercoris as a key contributor. Co-occurrence networks revealed Bacteroides-driven ecological restructuring. Plasma metabolomics identified stage-specific host disturbances. In early pregnancy, glycolytic intermediates were elevated, whereas in mid-pregnancy, bile acid and arachidonic acid metabolism were dysregulated. Notably, these changes included increased cholic acid and decreased pro-resolving mediators such as 15(R)-Lipoxin A4 (15-R-LxA4). These metabolic shifts correlated with microbial features, suggesting microbiota-linked vascular and inflammatory regulation prior to PIH diagnosis. In conclusion, impaired microbiome remodeling and associated metabolic disturbances precede the onset of PIH and may contribute to its development, although causal relationships require further investigation.}, }
@article {pmid42060200, year = {2024}, author = {Demirci, T}, title = {Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing.}, journal = {Food science of animal resources}, volume = {44}, number = {2}, pages = {390-407}, doi = {10.5851/kosfa.2023.e59}, pmid = {42060200}, issn = {2636-0780}, abstract = {Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.}, }
@article {pmid42060748, year = {2026}, author = {Xie, F and Jiang, C and Li, Z and Feng, J and Yan, X and Hu, C and He, J and Chai, X and Huang, Z and Xu, Q and Wang, Y and Xiao, Y and Chen, K and Qin, W and Xiao, Y and Zhang, J and Wang, G and Jin, W and Guo, K and Lin, L and Liu, Y and Gao, X and Zheng, L and Shu, X and Wang, R and Wang, M and Si, H and Du, R and Zhu, W and Guan, LL and Wang, W and Qiu, Q and Mao, S and Xiong, J and Miao, W}, title = {Rumen ciliates modulate methane emissions in ruminants.}, journal = {Science (New York, N.Y.)}, volume = {392}, number = {6797}, pages = {eadv4244}, doi = {10.1126/science.adv4244}, pmid = {42060748}, issn = {1095-9203}, mesh = {Animals ; Cattle/microbiology ; Female ; *Ciliophora/classification/genetics/metabolism ; *Greenhouse Gases/metabolism ; Hydrogen/metabolism ; Hydrogenase/metabolism/genetics ; Metagenome ; *Methane/biosynthesis/metabolism ; Oxygen/metabolism ; *Rumen/microbiology ; *Genome, Microbial ; }, abstract = {Rumen ciliates are major contributors to enteric methane emissions from ruminant animals, yet the underlying mechanisms remain poorly understood. We present a catalog of 450 rumen ciliate genomes, with 87% newly generated. Using this resource, we quantified methane emissions from 100 cows and analyzed 1877 rumen metagenomic and metatranscriptomic datasets, which revealed correlations among ciliate abundance, methanogen abundance, and methane emissions. We further demonstrated that taxon-specific effects of rumen ciliates on methane production arise from a single-membrane, hydrogen-producing organelle called the hydrogenobody (HB), which is distinct from canonical hydrogenosomes in other protists. HBs are positioned near ciliary basal bodies and harbor specific hydrogenases and oxygen reductases. We found that Vestibuliferida ciliates, which have more abundant HBs than do Entodiniomorphida, exhibit enhanced hydrogen production and oxygen-scavenging capacity, thereby strongly promoting methanogenesis.}, }
@article {pmid42060822, year = {2026}, author = {Poretsky, RS and Dhiman, VK and Hendricks, DL and Lin, CY and Sanchez Gonzalez, D and Greenwald, S and Owens, SM and Williams, CH and Leslie, MT and Bemis, K and Frias, M and Kaufman, JT and O'Connor, DH and Johnson, MC}, title = {Detection of a Single Measles Infection Using Untargeted Ultra-Deep Metagenomic Sequencing of Wastewater in Cook County, Illinois.}, journal = {NEJM evidence}, volume = {5}, number = {6}, pages = {EVIDpha2600079}, doi = {10.1056/EVIDpha2600079}, pmid = {42060822}, issn = {2766-5526}, mesh = {Humans ; Illinois ; *Wastewater/virology ; *Measles virus/genetics/isolation &amp; purification ; *Measles/diagnosis ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {AbstractMeasles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic sequencing effort of wastewater in Cook County, Illinois, we detected measles reads from a facility serving more than 1 million people. Out of more than 900 million reads sequenced from wastewater collected on September 14, 2025, 43 matched measles virus genotype B3. Subsequent genomic analysis linked these reads to a confirmed measles infection that was present in the community on that day, demonstrating that untargeted metagenomics appeared to detect a single measles infection in a large municipal wastewater stream.}, }
@article {pmid42060994, year = {2026}, author = {Huang, D and Sun, X and Lin, W and Lan, X and Tan, Z and Ren, Y and Huang, Y and Cao, Y and Sun, W}, title = {Hydrogen oxidation coupled to dissimilatory arsenate reduction: A potentially widespread pathway associated with arsenic mobility in anoxic sediments.}, journal = {Water research}, volume = {301}, number = {}, pages = {125984}, doi = {10.1016/j.watres.2026.125984}, pmid = {42060994}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Hydrogen/metabolism/chemistry ; *Arsenates/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Arsenic/metabolism ; Water Pollutants, Chemical/metabolism ; Anaerobiosis ; Phylogeny ; Bacteria/metabolism/genetics ; }, abstract = {In aquatic environments, the arsenic (As) mobilization from anoxic sediments is an important process affecting water quality and associated health risks, as sediment-bound As can serve as a persistent secondary source to overlying waters and groundwater systems. Dissimilatory arsenate reduction (DAsR) is a key microbial process releasing dissolved As(III), yet the role of inorganic electron donors in this pathway remains poorly constrained. Although hydrogen (H2) is thermodynamically favorable for arsenate respiration, its role in arsenate reduction in natural sediments remains insufficiently resolved. In this study, hydrogen oxidation coupled to arsenate reduction (HOAsR) was investigated using sediments from an As-contaminated, mining-impacted river system. Microcosm incubations showed that H2 amendment stimulated As(V) reduction under anoxic conditions. DNA-stable isotope probing combined with metagenomics identified Sulfuritalea, Dechloromonas, and a Moorellia-related lineage as putative HOAsR-associated populations. Corresponding metagenome-assembled genomes encoded both H2 uptake [NiFe]-hydrogenases and the dissimilatory arsenate reductase gene (arrA). Comparative genome analysis further revealed that ∼75% of arrA-containing genomes harbor H2 uptake [NiFe]-hydrogenases, suggesting that H2 oxidation represents a phylogenetically widespread metabolic trait among DAsR bacteria. Analysis of public riverine metagenomes further indicated that HOAsR-associated genetic configurations are broadly distributed across sediment microbial communities. Together, these results indicated that HOAsR is a biologically plausible and geographically widespread potential pathway contributing to arsenic mobilization in anoxic sediments.}, }
@article {pmid42061080, year = {2026}, author = {Chen, C and Hao, H and Hao, R and Yu, N and Li, X}, title = {Microbial driving mechanisms of sludge reduction in modular wastewater treatment systems under surplus aeration regulation.}, journal = {Journal of environmental management}, volume = {406}, number = {}, pages = {129816}, doi = {10.1016/j.jenvman.2026.129816}, pmid = {42061080}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The treatment and disposal of residual sludge pose a critical bottleneck to the sustainable development of wastewater treatment plants (WWTPs). Modular wastewater treatment systems have garnered significant interest due to their high efficiency and operational flexibility, making them well-suited for small-scale community applications. This study aims to investigate the microbial driving mechanisms underlying sludge reduction in such field-based systems under surplus aeration regulation. By comparing treatment performance, microbial community structure, and metabolic functions between the Surplus Aeration (SA) group and the Conventional (Conv.) group-coupling 16S rRNA high-throughput sequencing and metagenomic analysis -the microbiological basis of sludge reduction was systematically elucidated. Results demonstrated that the SA group achieved a 63.7% reduction in residual sludge while maintaining compliant effluent quality (GB 18918-2002), with COD and NH4[+]-N removal rates both reaching more than 85%. 16S rRNA profiles indicated higher alpha diversity in the SA group and clear community separation from the Conv. group (PERMANOVA, p < 0.001). The SA group was enriched in taxa with documented extracellular polymeric substance (EPS) degradation potential, including Saccharimonadales, Saprospiraceae, and Caldilineaceae, whereas the Conv. group showed relatively higher abundance of taxa often associated with proliferation and EPS production (e.g., OLB17, Acinetobacter). Metagenomic functional annotation suggested higher representation of genes and pathways related to carbohydrate processing and energy metabolism in the SA group. As these omics results primarily reflect functional potential rather than confirmed in situ activity, we present a conceptual mechanism in which surplus aeration improves DO distribution and substrate utilization in the field system, thereby favoring EPS breakdown and energy-use efficiency-consistent with the observed reduction in sludge yield.}, }
@article {pmid42061404, year = {2026}, author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC}, title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117301}, doi = {10.1016/j.celrep.2026.117301}, pmid = {42061404}, issn = {2211-1247}, mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; *Tissue Donors ; Female ; Metagenome ; Male ; }, abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.}, }
@article {pmid42061651, year = {2026}, author = {Neuhaus, S and Tausch, SH and Gulich, K and Körber, N and Grützke, J and Hensel, A and Dahouk, SA and Dieckmann, R}, title = {Kitchen Sponges as Reservoirs of Foodborne Pathogens: Microbial Growth Dynamics, Surface Cross-Contamination, and Hygiene Implications.}, journal = {Journal of food protection}, volume = {89}, number = {6}, pages = {100794}, doi = {10.1016/j.jfp.2026.100794}, pmid = {42061651}, issn = {1944-9097}, mesh = {Staphylococcus aureus/growth &amp; development ; Humans ; Colony Count, Microbial ; Salmonella enteritidis/growth &amp; development ; Escherichia coli/growth &amp; development ; Food Contamination/analysis ; Food Microbiology ; Hygiene ; }, abstract = {Foodborne pathogens pose a persistent risk to public health, with domestic environments representing a major but often underestimated source of contamination. In this study, we investigated the survival, proliferation, and transfer potential of Salmonella Enteritidis, Escherichia coli, and Staphylococcus aureus in kitchen sponges harboring an established core microbiota. Using culture-based, metagenomic, and fluorescence in situ hybridization approaches in combination with confocal laser scanning microscopy, we examined pathogen persistence, desiccation tolerance, cross-contamination potential, and spatial microbial organization over 14 days. All three pathogens persisted within the sponge matrix for at least 2 weeks, even at very low initial populations (approximately 2,5 log10 colony-forming units (CFU) per sponge section). Escherichia coli and Salmonella Enteritidis rapidly established stable populations reaching approximately 9 log CFU per sponge section, whereas S. aureus showed limited growth of approximately 4 log CFU per sponge section, indicating species-specific interactions with the resident microbiota. Notably, pathogen populations remained stable after 3 days of desiccation, confirming the role of sponges as long-term microbial reservoirs. Contact between colonized sponges and surfaces under mild pressure resulted in transfer of up to 5 log CFU to contacted surfaces, highlighting realistic domestic transmission pathways. Sensory changes such as odor or discoloration were not correlated with microbial load, indicating that visual assessment is unreliable for sponge replacement decisions. These results underscore the role of kitchen sponges as critical microbial reservoirs in households and emphasize the need for regular sponge replacement or the use of alternative cleaning utensils. The standardized sponge model developed in this study provides a valuable platform for evaluating sanitation strategies and for understanding microbial interactions relevant to domestic hygiene and public health.}, }
@article {pmid42061790, year = {2026}, author = {Zhang, Y and Zhang, G and Liang, J and Chang, J and Zhang, P and Fang, W and Wang, Q}, title = {Regulation of greenhouse gas emissions and carbon sequestration in wetland by submerged plant mowing time and potential mechanisms.}, journal = {Environmental research}, volume = {302}, number = {}, pages = {124621}, doi = {10.1016/j.envres.2026.124621}, pmid = {42061790}, issn = {1096-0953}, mesh = {*Wetlands ; *Greenhouse Gases/analysis/metabolism ; *Carbon Sequestration ; Methane/metabolism/analysis ; *Magnoliopsida/metabolism/physiology ; Carbon Dioxide/metabolism/analysis ; Nitrous Oxide/metabolism/analysis ; }, abstract = {Mowing is an important submerged plant growth management measure to maintain the balance of inland wetland ecosystems. However, systematic studies on plant mowing time affecting wetland greenhouse gas (GHG) emissions and carbon sequestration remain scarce. In this research a pilot-scale wetland system was established to investigate the effects of submerged plant Ceratophyllum demersum L. mowing time on GHG emissions and carbon sequestration, and metagenomic techniques were employed to explore the functional microorganisms and genes for carbon and nitrogen cycling in wetland. The results showed that C. demersum L. mowing resulted in CO2 flux reduction of 55.76%-79.34%, CH4 flux reduction of 83.54%-99.48%, and N2O flux reduction of 75.80%-82.88%. The optimal plant mowing time was July, achieving abetter trade-off between carbon sequestration and carbon emissions. The C. demersum L. biomass showed obvious temporal dynamics, with the highest biomass for mowing in July, increasing by 12.12% compared with that of control. However, plant mowing slightly reduced the water purification capacity. Microbial analysis revealed that plant mowing downregulated the expression of key functional genes (mcrA, pmoA, norB, nosZ) and decreased the abundance of methanogens and denitrifying bacteria, explaining the reduction in CH4 and N2O fluxes. These findings provide a scientific basis for wetland plant growth management. Future research should explore long-term field validation and effects of environmental variables.}, }
@article {pmid42062403, year = {2026}, author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR}, title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42062403}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.}, }
@article {pmid42062603, year = {2026}, author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N}, title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, pmid = {42062603}, issn = {2662-8457}, support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.}, }
@article {pmid42062664, year = {2026}, author = {Kieliszek, M}, title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.}, journal = {Biological trace element research}, volume = {}, number = {}, pages = {}, pmid = {42062664}, issn = {1559-0720}, abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.}, }
@article {pmid42062918, year = {2026}, author = {Guo, P and Zhang, S and Huang, Z and Zhu, J and Zhang, W}, title = {Potential drug-drug interactions and 30-day mortality in ICU patients with bloodstream infection: a single-center retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13426-z}, pmid = {42062918}, issn = {1471-2334}, abstract = {BACKGROUND: Patients in intensive care units (ICUs) with bloodstream infection (BSI) commonly receive multiple antimicrobials and supportive drugs, which increases the likelihood of potential drug-drug interactions (pDDIs). Evidence focused specifically on ICU patients with BSI remains limited.<br><br>OBJECTIVES: To describe the prevalence and severity of pDDIs in ICU patients with BSI and to examine whether pDDI exposure was associated with 30-day mortality.<br><br>METHODS: We performed a single-center retrospective cohort study of 90 adult ICU patients with an index episode of BSI between January 2019 and December 2024. Time zero was defined as the sampling time of the first qualifying positive blood culture or a clinically accepted positive blood metagenomic next-generation sequencing result for the index episode. Medication administration records, rather than prescription orders alone, were used for pDDI ascertainment. pDDIs were screened with the Micromedex Drug Interactions database (Merative, web-based version updated daily; accessed January 15, 2025). Exposure was defined within a fixed 48-hour window after time zero; a pDDI required actual administration of both interacting agents within the same 24-hour period during this window. Severity was standardized as mild, moderate, or severe. The primary outcome was 30-day all-cause in-hospital mortality. Because only 18 deaths occurred, the primary multivariable model included any pDDI exposure and SOFA score.<br><br>RESULTS: Seventy of 90 patients (77.8%) had at least one pDDI within the fixed exposure window. Based on the highest patient-level severity, 13/70 (18.6%) had mild, 22/70 (31.4%) moderate, and 35/70 (50.0%) severe pDDIs. The most frequent combinations were vancomycin plus amikacin (18/90, 20.0%) and piperacillin/tazobactam plus vancomycin (15/90, 16.7%). The clinical consequences listed for common pairs were reference-predicted interaction consequences rather than adjudicated observed toxicities. In the parsimonious multivariable model, any pDDI exposure was associated with higher observed 30-day mortality (adjusted OR 4.23, 95% CI 1.27-14.09; P&#x2009;=&#x2009;0.02), and each 1-point increase in SOFA score was also associated with mortality (adjusted OR 1.32, 95% CI 1.07-1.64; P&#x2009;=&#x2009;0.01).<br><br>CONCLUSIONS: pDDIs were common in this ICU BSI cohort and were associated with higher observed 30-day mortality. These findings should be interpreted cautiously given the retrospective single-center design, limited event count, residual confounding, and incomplete control of time-dependent exposure. Structured pDDI screening may still support medication safety in critically ill patients.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42063196, year = {2026}, author = {Liu, Z and Meng, C and Shen, J and Wang, H and Guo, J and Zhao, J and Mu, C and Zhu, W}, title = {Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42063196}, issn = {2524-4671}, support = {National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; }, abstract = {Dietary protein plays a crucial role in shaping the gut microbiome and modulating intestinal amino acid metabolism. Gut microbiome is recognized as a reservoir for carrying antimicrobial resistance genes. However, the relationship between amino acids metabolism and antibiotic resistome remains poorly understood. Here, a pig model was used to study this relationship by comparing the impact of dietary casein hydrolysate diet with those of an intact casein diet. Metabolomics analysis revealed that casein hydrolysate supplementation primarily altered amino acid metabolism, characterized by significantly reduced levels of several amino acids, including tyrosine and glutamine, accompanied by increased levels of amino acid–derived metabolites. Metagenomics analyses indicated that these metabolic shifts were closely associated with microbial changes in the gut, particularly the genera Escherichia and Bifidobacterium. Consistently, microbial genes related to amino acid transport and metabolism exhibited higher abundances. Notably, the abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were significantly enriched in response to casein hydrolysate supplementation. Integrated metabolome–resistome correlation analyses revealed significant associations between multiple amino acids, including tyrosine and glutamine, and distinct ARG subtypes, indicating a tight coupling between amino acid metabolism and antibiotic resistance potential. Metagenomics binning and assembly further resolved the taxonomic origins of these functional traits. Specifically, in Escherichia fergusonii and Bifidobacterium thermophilum, genes related to amino acid metabolism, ARGs, and MGEs were co-localized on the same contigs with close genomic proximity. Together, these findings highlight a strong link between microbial amino acid metabolism and the resistome, suggesting that dietary casein hydrolysate reshapes both microbial metabolic functions and antibiotic resistance potential within the intestinal ecosystem.}, }
@article {pmid42063256, year = {2026}, author = {Liu, Y and Wu, J and Yang, Y and He, Y and Zhou, R and Li, Y and Sun, J and Gong, M and Mei, X and Li, Y and Huang, H and Du, F and Deng, W and Ye, C and He, X and Li, L and Hao, J and Yang, M and Zhu, Y and Zhu, S}, title = {Decoupling the "attract-and-kill" strategy: Independent zoospore attraction and ROS-executed killing synergistically drive disease-suppressive intercropping.}, journal = {Plant communications}, volume = {}, number = {}, pages = {101876}, doi = {10.1016/j.xplc.2026.101876}, pmid = {42063256}, issn = {2590-3462}, abstract = {Soilborne Phytophthora diseases pose a major threat to agricultural sustainability. However, how nonhost roots disrupt the transmission of soilborne Phytophthora pathogens without relying solely on classical antimicrobial exudates remains poorly understood. Through a decade-long field study, we demonstrate that strip intercropping can sustainably suppress disease incidence by up to 46.85% by leveraging nonhost roots as ecological barriers that intercept zoospore transmission. Moving beyond the conventional focus on antimicrobial exudates, we resolve the "attract-and-kill" strategy into two discrete functions: a broad-spectrum attraction function widespread among nonhost plants (13 of 15 genera), which alone reduces disease incidence by 9.2%-24.4%, and a specialized killing function restricted to a few species, such as garlic, in which elevated concentrations of sulfur compounds at the root interface induce cystospore rupture and inhibit germination, delivering 42.9%-49.3% field suppression. The synergy between universal attraction and targeted killing enhances disease suppression at the rhizosphere interface. Mechanistically, killing is executed through a conserved reactive oxygen species-programmed cell death (ROS-PCD) pathway, with pathogen sensitivity determined by intrinsic redox-buffering capacity. Metagenomic profiling further revealed that garlic roots and sulfur compounds are associated with the enrichment of genes involved in microbial motility and apoptosis-related pathways, adding a complementary mechanistic layer to the attract-and-kill framework. We thus propose this ecology-based, two-component strategy for sustainable Phytophthora management in diversified cropping systems.}, }
@article {pmid42063433, year = {2026}, author = {Chen, L and Li, J and Liu, X and Chen, X and Li, H and Xie, D and Chen, Y and Yuan, J and Tao, E}, title = {Case Report: Beyond commensal: Staphylococcus epidermidis as a novel cause of NARDS.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1631683}, pmid = {42063433}, issn = {2296-2360}, abstract = {Staphylococcus epidermidis (S. epidermidis), usually a harmless skin bacterium, can become an opportunistic pathogen in newborns, particularly those with risk factors like premature membrane rupture. Although it commonly causes late-onset sepsis, its association with neonatal acute respiratory distress syndrome (NARDS) is rare. This report describes a unique case of NARDS in a full-term newborn caused by S. epidermidis. The infant, born via cesarean at 40 2/7 weeks with a 30.5-hour membrane rupture, developed severe respiratory failure shortly after birth, necessitating mechanical ventilation. Initial treatment with penicillin and cefotaxime was ineffective, and by day 3, the infant's condition worsened, showing respiratory distress, petechial rashes, and high inflammatory markers. Treatment was changed to vancomycin and meropenem, with the addition of intravenous immunoglobulin and two doses of pulmonary surfactant. Metagenomic next-generation sequencing (mNGS) confirmed S. epidermidis in the airway secretions. The patient was discharged after 19 days with a diagnosis of NARDS, intrauterine infectious pneumonia, neonatal air leak syndrome, type II respiratory failure, neonatal sepsis, and congenital heart defects. In conclusion, S. epidermidis is a novel pathogen capable of causing NARDS in high-risk infants with prolonged membrane rupture. The proposed mechanisms-including surfactant dysfunction and biofilm-associated virulence-are supported by experimental literature and are consistent with the clinical phenotype observed in our patient, though direct confirmation requires further study. Notably, skin symptoms like erythematous rash and petechiae may indicate invasive S. epidermidis infection, especially in cases of respiratory distress with skin symptoms following premature rupture of membranes. Moreover, mNGS is vital for pathogen identification when traditional cultures fail.}, }
@article {pmid42063498, year = {2026}, author = {Xiang, L and Wang, X and Wen, M and Wang, X and Zhang, Y and Tian, W and Liu, M and Zhang, W}, title = {Metagenomic insights into the rhizosphere microbiome dysbiosis associated with tobacco bacterial wilt.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809980}, pmid = {42063498}, issn = {1664-302X}, abstract = {Tobacco bacterial wilt, caused by Ralstonia solanacearum, threatens global tobacco production. While the rhizosphere microbiome defends against soil-borne pathogens, mechanisms underlying how bacterial wilt reshapes microbial community structure, function, and ecological interactions remain poorly understood. Here, we employed metagenomic sequencing to investigate taxonomic and functional alterations in the rhizosphere microbiome of symptomatic (S) and asymptomatic (A) tobacco plants across two locations (Fenggang and Bozhou), establishing four groups: FA, FS, BA, and BS. Quality control of sequencing data showed no technical bias between groups (p > 0.05). Contrary to the paradigm that pathogen invasion reduced microbial diversity, alpha diversity analysis revealed higher species richness (Sobs) in symptomatic soils, whereas community evenness (Shannon and Simpson indices) remained unchanged, suggesting selective reshuffling rather than microbiome collapse. Beta-diversity analysis revealed significant compositional shifts associated with disease status (PERMANOVA, R [2] = 0.713, p = 0.001), with symptomatic communities displaying greater heterogeneity. Taxonomic profiling revealed consistent enrichment of the pathogen R. solanacearum and opportunistic bacteria (including Stenotrophomonas and Pseudomonas) in symptomatic rhizospheres, concomitant with depletion of putative beneficial taxa (Candidatus_Solibacter, Luteitalea, and Metarhizium). Functional annotation indicated a metabolic shift from homeostatic maintenance to stress adaptation and pathogenicity. Symptomatic soils exhibited significant enrichment of virulence factors, including motility and secretion system genes, microbial defense mechanism genes (COG), and antibiotic resistance genes (CARD). Additionally, increased abundance of carbohydrate-active enzymes (CAZy)-particularly glycoside hydrolases-suggested intensive nutrient acquisition from decaying tissues. Co-occurrence network analysis revealed that asymptomatic communities formed denser, competition-driven networks characterized by a higher proportion of negative correlations. Disease destabilized these networks by reducing connectivity and, crucially, rewired interactions of R. solanacearum from negative to positive associations with taxa such as Sphingobium, thereby reflecting erosion of competitive constraints and pathogen incorporation into cooperative networks. Our findings revealed that bacterial wilt drove multi-layered dysbiosis, encompassing pathogen-driven taxonomic selection, functional shifts toward stress adaptation and intensified competition, and collapse of stable antagonistic networks associated with plant health. This study provided mechanistic insights into microbiome-mediated disease progression and identified specific microbial taxa and network properties as candidate targets for ecological disease management and early diagnostic indicators.}, }
@article {pmid42063509, year = {2026}, author = {González de Figueras, C and Gómez, S and Lamprecht-Grandío, M and Mirete, S and Díaz-Rullo, J and Martínez-Rodríguez, P and Sánchez-Costa, M and González-Pastor, JE}, title = {Enhancing UV-C and perchlorate resistance in Arabidopsis thaliana through the introduction of microbial genes from hypersaline environment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1789302}, pmid = {42063509}, issn = {1664-302X}, abstract = {Ultraviolet (UV) radiation reaching the Earth's surface affects all living organisms. Recent reports show a trend of increasing exposure levels due to stratospheric ozone depletion and contamination. UV-B radiation (280-315 nm), previously largely absorbed by the ozone layer, now reaches the surface in higher doses, posing a particular threat to plants, which are sessile organisms and cannot escape adverse conditions. The intrinsic protective and repair mechanisms in plants may be insufficient to counteract this increase, potentially impacting crop productivity, distribution, and quality, with serious implications for agriculture and ecological stability. This study aims to enhance plant resistance to UV radiation by introducing genes derived from extremophilic microorganism, which have previously shown to confer UV-protective effects in UV resistance to a radiation-sensitive Escherichia coli strain (recA mutant). Extremophile microorganisms have been discovered in high-irradiation environments, such as hypersaline lakes, where survival relies on unique genetic adaptations. In our laboratory, four genes were selected from metagenomic libraries derived from high-altitude hypersaline lakes in Argentina (Diamante and Ojo Seco, at 4,589 m and 3,200 m respectively) and from the Es Trenc salt flat (Mallorca, Spain). Based on these promising results, the genes were introduced into Arabidopsis thaliana to evaluate their potential to enhance UV-B tolerance in plants. The selected genes included one encoding a TATA-box binding protein, and three hypothetical proteins. Each gene was independently transformed into Arabidopsis thaliana lines and subjected to UV-B and UV-C irradiation (4.5 kJ·m[-2]), with UV-C (100-280 nm) ultimately chosen for its higher damaging potential to test the limits of plant tolerance. Additionally, cross-resistance was evaluated using sodium perchlorate, a common soil contaminant and oxidative stressor. Plants were exposed to concentrations between 3.67 and 7.34 g/L, exceeding those used in previous studies. As a result, the plants obtained were more resistant to UV radiation and were also capable of growing in environments containing higher levels of perchlorate in the growth medium. Thus, the expression of these genes in the plant appears to contribute to enhanced stress resistance.}, }
@article {pmid42063777, year = {2026}, author = {Zhu, M and Sun, C and Zhang, Y and Na, Y and Wang, Y and Zhao, Q and Gu, Y}, title = {Blepharitis driven by microbiome dysbiosis and Demodex infestation: possible pathogenic mechanisms.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1801375}, pmid = {42063777}, issn = {2296-858X}, abstract = {Blepharitis is a chronic inflammation of the eyelid margin that is mediated by the immune system. It is one of the common ocular surface diseases and often leads to serious sequelae that threaten vision, such as dry eye syndrome due to insufficient tear secretion, corneal neovascularization, and stubborn chalazion. Elucidating its precise etiology is therefore imperative. Emerging high-throughput sequencing and metagenomic analyses have unveiled a quantitative and qualitative disruption of the periocular microbiome (dysbiosis), characterized by the expansion of specific bacterial species such as Staphylococcus aureus, coupled with episodic blooms of Demodex. These perturbations are no longer considered epiphenomena. In this review, we reveal the possible mechanisms of the role of blepharitis and microbiota dysbiosis.}, }
@article {pmid42063778, year = {2026}, author = {Wu, S and Wu, M and Li, W and Zhang, C and Bi, Y and Fan, Y and Xu, Y and He, D}, title = {Case Report: Diagnosis of leptospirosis presenting as aseptic meningitis using metagenomics CAPture sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1734396}, pmid = {42063778}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic disease caused by pathogenic Leptospira species. The manifestation of leptospirosis can range widely, from being asymptomatic to causing severe multi-organ failure with a high mortality rate. It is uncommon for leptospirosis to present primarily with neurological complications. In this context, we discuss a notable case of Leptospira borgpetersenii infection manifesting as aseptic meningitis in China.<br><br>CASE PRESENTATION: In this study, we describe a primary case of neuroleptospirosis leading to symptomatic aseptic meningitis following exposure to Leptospira borgpetersenii. Initially managed for viral meningitis, the diagnosis of leptospirosis was subsequently confirmed through cerebrospinal fluid (CSF) analysis using metagenomic next-generation sequencing (mNGS) and Metagenomics CAPture Sequencing (MetaCAP), both of which identified Leptospira borgpetersenii. Following a course of antibiotics and methylprednisolone therapy, the patient fully recovered.<br><br>CONCLUSION: This case underscores the importance of considering leptospirosis in differential diagnoses for aseptic meningitis, especially in individuals with occupational risks related to water or animal exposure. MetaCAP's extensive coverage, sensitivity, and early pathogen detection capabilities can significantly enhance patient outcomes.}, }
@article {pmid42063908, year = {2026}, author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D}, title = {Gut microbial profiles of COVID-19 patients in Uganda.}, journal = {African health sciences}, volume = {26}, number = {1}, pages = {1-15}, pmid = {42063908}, issn = {1729-0503}, mesh = {Humans ; *COVID-19/microbiology/epidemiology ; Uganda/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Bacteria/isolation &amp; purification/genetics ; }, abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.<br><br>METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.<br><br>RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.<br><br>CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42064023, year = {2026}, author = {Liu, Y and Wang, W and Peng, Y and Feng, L and Li, C and Zhang, Z and Zhao, J and Yang, C and Mu, T and Wang, J and Li, C and Yang, C}, title = {Sources of Microbial and Organic Contaminants in the Production of Soybean Whey Protein for Feed and Potential Food Applications.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {5}, pages = {e71709}, pmid = {42064023}, issn = {2048-7177}, abstract = {Soybean whey wastewater (SWW), a rich source of soybean whey protein (SWP), is prone to microbial rancidity, posing environmental and resource challenges. This study explores the causes of rancidity-characterized by a pungent, sour, and putrid odor-in the effluents of sealed buffer tank during SWP recovery via pneumatic flotation. Metagenome, bacterial diversity, and HPLC analyses showed the obligate anaerobe Megasphaera spp. dominated rancid effluents (up to 44% abundance), consumed lactate (decreasing from 10.2 g/L in influent to 2.7 g/L in effluent), and produced malodorous propionate and butyrate (up to 3.6 and 4.3 g/L, respectively). Three mitigation strategies were assessed: (1) full-scale high-throughput aeration-likely effective but energy- and cost-intensive; (2) local aeration-low-cost but weakly inhibitory; and (3) microbial intervention using the probiotic Enterococcus faecium LBSW, which colonizes the buffer tank, with localized aeration used only if microbial control fails. Strategy (3) was adopted for its energy and cost efficiency, successfully reducing pollution and supporting SWP recovery. Although the biosafety of E. faecium LBSW in food applications requires caution, the recovered SWP is primarily intended for animal feed, and subsequent high-temperature drying and sterilization (> 120°C) also offer potential for food-grade use.}, }
@article {pmid42064333, year = {2026}, author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA}, title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112758}, pmid = {42064333}, issn = {2352-3409}, abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.}, }
@article {pmid42064443, year = {2026}, author = {Niyomvong, N and Wongsorn, D and Pitiwittayakul, N}, title = {Metagenomics of a Photo-Fermentative Bacterial Solution and Its Effect on the Growth And Yield of Mini Green Cos Lettuce.}, journal = {Tropical life sciences research}, volume = {37}, number = {1}, pages = {85-108}, pmid = {42064443}, issn = {1985-3718}, abstract = {Photosynthetic bacteria (PSB) are widely utilised in agriculture to enhance plant growth and crop quality by improving nutrient uptake and phytohormone production. This study aimed to analyse the metagenomic composition of a photo-fermentative bacterial solution derived from fermentation and assess its effects on the growth and yield of Mini Green Cos lettuce. Metagenomic analysis revealed that Bacteroidota (38%) was the most abundant phylum, followed by Proteobacteria (23%), Thermotogota (17%) and Firmicutes (15%). Within Proteobacteria, Alphaproteobacteria was dominant followed by Gammaproteobacteria. At the genus level, Petrimonas (22%), uncultured clones belonging to family Petrotogaceae (17%), Rhodopseudomonas (11%), Rubrivivax (6%), and an unidentified genus from Lentimicrobiaceae (4%) were the most prevalent. These findings highlight the microbial diversity of PSB solution, suggesting its potential role in plant growth promotion. A plant growth experiment was conducted using a Completely Randomised Design (CRD) with four treatments: control (T1), chemical fertiliser (T2), undiluted PSB solution (T3) and PSB solution diluted at a 1:1 ratio (T4), with 10 replicates per treatment. Among all treatments, lettuce irrigated with undiluted PSB solution (T3) exhibited the highest growth rate, yield and total chlorophyll content. However, its performance was not significantly different from that of the chemical fertiliser treatment (T2). These results suggest that PSB can effectively promote plant growth and yield, yielding results comparable to chemical fertilisers. Therefore, photo-fermentative bacterial solutions offer a sustainable and eco-friendly alternative to chemical fertilisers, supporting environmentally conscious agricultural practices.}, }
@article {pmid42065019, year = {2026}, author = {Behera, S and Gupta, S and Kale, A and Yadav, A and Rao, GP}, title = {Draft genome of a 'Candidatus Phytoplasma trifolii' -related strain BLL-Delhi associated with brinjal little leaf disease.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {173}, pmid = {42065019}, issn = {2190-572X}, abstract = {The draft genome sequence of the brinjal little leaf (BLL) phytoplasma strain BLL-Delhi, related to 'Candidatus Phytoplasma trifolii' (16SrVI group), was recovered using a metagenome-resolved assembly strategy from Illumina HiSeq data. The genome comprises 476,098 bp assembled into 12 contigs, with a G+C content of 21.86%, encoding 421 predicted protein-coding sequences, 27 tRNAs, one tmRNA and one additional non-coding RNA, and shows 94% completeness. Genome annotation revealed a reduced yet functionally coherent gene repertoire, including putative effector-like proteins and genes associated with mobile genetic elements. This genome provides a resource for high-resolution taxonomic placement, comparative genomics within the 16SrVI phytoplasma group, and genome-based diagnostics for brinjal little leaf disease.}, }
@article {pmid42065375, year = {2026}, author = {Ding, SC and Yu, J and Liao, T and Ahmann, L and Yao, Y and Ho, C and Wang, L and Pinsky, BA and Gu, W}, title = {Adapting clinical chemistry plasma as a source for liquid biopsies.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {42065375}, issn = {2050-084X}, support = {CA230156//NIH Office of the Director/ ; CAMS//Burroughs Wellcome Fund/ ; }, mesh = {Humans ; *Cell-Free Nucleic Acids/blood ; Liquid Biopsy/methods ; *Plasma/chemistry ; *Blood Specimen Collection/methods ; *Specimen Handling/methods ; }, abstract = {Circulating cell-free DNA (cfDNA) is valuable for molecular testing, but typically requires specialized collection tubes or immediate processing. We investigated whether residual plasma from heparin separators, routinely used in clinical chemistry, could serve as an accessible and underused source for cfDNA. We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing comparison across EDTA, Streck, and heparin separator tubes (n=5), and a clinical-handling simulation comparing EDTA and heparin separator tubes under delayed processing at room temperature or 4°C (n=6). We also analyzed matched plasma samples from viral PCR-positive patients in a hospital cohort (n=38). Whole-genome sequencing and enriched methylation sequencing were performed to assess concordance across metagenomics, copy number, methylation, and fragmentomic features. Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Spearman's ρ=0.65-0.70) and fragmentation features. In the Hospital Cohort, heparin separator plasma showed strong concordance with matched EDTA plasma for viral detection (Spearman's ρ=0.95), copy number alteration profiling (Spearman's ρ=0.72-0.96), and methylation patterns (Spearman's ρ=0.50-0.83). These findings support the feasibility of using refrigerated, promptly processed residual plasma from routine clinical chemistry as a supplementary source for cfDNA biobanking and molecular analyses.}, }
@article {pmid42066399, year = {2026}, author = {Yang, X and Chen, M and Song, B and Liu, T and Zhao, YG and He, Q and Chen, Y}, title = {Micro(nano)plastics reshape constructed wetlands: Linking biofilm succession's role to key biogenic substance transformation.}, journal = {Water research}, volume = {301}, number = {}, pages = {126024}, doi = {10.1016/j.watres.2026.126024}, pmid = {42066399}, issn = {1879-2448}, mesh = {*Biofilms ; *Wetlands ; *Plastics ; Microplastics ; }, abstract = {Constructed wetlands (CWs) are increasingly recognized as terminal sinks for micro- and nanoplastics (MNPs), yet how chronic MNPs accumulation reshapes biofilm-mediated biogenic substance transformation remains poorly understood. Here, using a 300-day CW experiment integrating process analysis, biofilm microstructure characterization, and metagenomics, we demonstrate that plastic particle size acts as a decisive ecological switch governing biofilm succession and multi-element cycling. Long-term microplastics (MPs) exposure unexpectedly enhanced denitrification and sulfate reduction, whereas nanoplastics (NPs) persistently suppressed carbon, nitrogen, phosphorus, and sulfur transformations. Mechanistic analyses reveal that these divergent outcomes arise not from direct metabolic toxicity but from size-dependent reorganization of biofilm architecture, regulatory gene networks, and microbial cooperation. MPs promoted extracellular polymeric substance synthesis, reinforced anaerobic redox stratification, and strengthened electron-transfer-driven microbial clustering, while NPs disrupted biofilm integrity, downregulated succession-related genes, and fragmented functional interactions. This study challenges the prevailing assumption that MNPs accumulation uniformly degrades treatment performance and establishes a mechanistic framework linking particle size, biofilm succession, and ecosystem functioning. Our findings provide new insights into the long-term ecological effects of emerging particulate pollutants and offer guidance for designing resilient biofilm-based treatment systems under increasing plastic pressure.}, }
@article {pmid42066496, year = {2026}, author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y}, title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101823}, doi = {10.1016/j.animal.2026.101823}, pmid = {42066496}, issn = {1751-732X}, mesh = {Animals ; Biomarkers/analysis ; *Feces/chemistry/microbiology ; Metabolomics ; *Stress, Psychological/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Swine ; *Metabolome ; Male ; *Sus scrofa/physiology ; }, abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.}, }
@article {pmid42066541, year = {2026}, author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X}, title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117442}, doi = {10.1016/j.diagmicrobio.2026.117442}, pmid = {42066541}, issn = {1879-0070}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Middle Aged ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; Adult ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification/classification ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.<br><br>METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.<br><br>RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.<br><br>CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.}, }
@article {pmid42066584, year = {2026}, author = {Xu, Q and Wang, Q and Hou, D and Zhang, F and Zhang, C and Qi, B and Wei, M and Chen, J and Zha, Q and Qin, H and Song, Y and Wu, X}, title = {Cryptococcal pneumonia susceptibility in immunocompetent patients: Role of pseudomonas aeruginosa via IL-2/IL-12/IL-17 pathways.}, journal = {Journal of infection and public health}, volume = {19}, number = {6}, pages = {103230}, doi = {10.1016/j.jiph.2026.103230}, pmid = {42066584}, issn = {1876-035X}, mesh = {Adult ; Pseudomonas aeruginosa/immunology ; *Pseudomonas Infections/immunology/microbiology ; Cryptococcosis/immunology/microbiology ; *Immunocompetence ; *Immunocompromised Host/immunology ; Interleukin-17/immunology/metabolism ; Bronchoalveolar Lavage Fluid/microbiology ; Interleukin-12/immunology/metabolism ; Interleukin-2/immunology/metabolism ; }, abstract = {BACKGROUND: While pulmonary cryptococcosis affects immunocompromised patients, it also occurs in immunocompetent individuals. However, underlying mechanisms contributing to susceptibility in immunocompetent patients remain poorly understood.<br><br>METHODS: We enrolled 43 patients with pulmonary cryptococcosis, including 19 apparently immunocompetent patients (ICPC) and 24 immunocompromised patients (IMCPC), compared with community-acquired pneumonia (CAP) controls. Bronchoalveolar lavage fluid (BLAF) microbiota composition was analyzed using metagenomic next-generation sequencing. Peripheral blood immune parameters were measured, and correlation analyses were performed to identify potential associations. Publicly available single-cell transcriptomic datasets were analyzed to explore immune pathway alterations associated with chronic Pseudomonas infection.<br><br>RESULTS: ICPC patients were predominantly male, less likely to present with fever, and showed normal inflammatory markers compared to CAP controls. Despite normal reference ranges, ICPC patients demonstrated significantly reduced CD4&#x207a; T lymphocyte percentages&#xff0c;accompanied by elevated IL-2 and reduced IL-12p70 and IL-17A levels. BALF analysis revealed a significant enrichment of nonfermenting gram-negative bacteria: Ralstonia, Sphingomonas, Acinetobacter, Stenotrophomonas, Burkholderi and Pseudomonas, in ICPC patients&#xff0c;whereas no such alterations were observed in the IMCPC group. Correlation analyses demonstrated inverse relationships between the relative abundances of Stenotrophomonas and Pseudomonas abundance and CD4&#x202f;+&#x202f;T lymphocyte percentages and CD4&#x202f;+&#x202f;/CD8&#x202f;+&#x202f;ratios. Furthermore, single-cell transcriptomic analysis of chronic Pseudomonas infection showed enrichment of IL-2 signaling genes and suppression of IL-12 and IL-17A signaling pathways.<br><br>CONCLUSIONS: ICPC patients exhibit decreased peripheral CD4&#x202f;+&#x202f;T lymphocyte percentage with elevated IL-2 and reduced IL-12p70/IL-17A levels. The observed enrichment of specific bacterial taxa, particularly Pseudomonas species, and its inverse correlation with immune parameters suggest potential microbiome-immune interactions that may contribute to cryptococcal susceptibility.}, }
@article {pmid42066983, year = {2026}, author = {Rajabal, V and Ghaly, TM and Colombi, E and Russell, DH and Sia, C and Shah, B and McPherson, VJ and Qi, Q and Coleman, NV and Gillings, MR and Tetu, SG}, title = {Discovery of novel antimicrobial resistance genes: Integrons as a high-throughput gene capture and functional screening platform.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {400}, number = {}, pages = {128228}, doi = {10.1016/j.envpol.2026.128228}, pmid = {42066983}, issn = {1873-6424}, mesh = {*Integrons/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; High-Throughput Screening Assays ; }, abstract = {Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it difficult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed a high-throughput gene cassette capture system that utilises site-specific recombination activity of integrons and a counter selection strategy to capture and express gene cassettes from metagenomes. Coupling this platform with a functional screening approach allowed us to rapidly assay large libraries of environmental gene cassettes. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food and fertiliser. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches.}, }
@article {pmid42067165, year = {2026}, author = {Zong, K and Zhang, T and Li, Y and Ji, M and Lu, J and Guo, Y and Zhao, C and Lv, J and Kong, Q and Wang, Q and Zhang, J}, title = {Mechanism of magnetite coupled microbial enhancement in mariculture wastewater treatment: Dual edged role of magnetite.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134749}, doi = {10.1016/j.biortech.2026.134749}, pmid = {42067165}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; *Ferrosoferric Oxide/chemistry/pharmacology ; Nitrogen/isolation &amp; purification ; Phosphorus/isolation &amp; purification ; Wetlands ; *Aquaculture ; *Water Purification/methods ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; }, abstract = {Marine aquaculture wastewater treatment faces dual challenges of microbial inhibition and greenhouse gas (GHG) emissions under saline stress. This study investigates the synergistic effects of submicron magnetite and intertidal microorganisms on treatment efficiency in constructed wetlands (CWs). Three CWs were designed: "Mag" (magnetite composite microorganisms), "IWS" (microorganisms only) and "CK" (control). Nutrient removal and GHG emissions were evaluated, and microbial mechanisms under saline conditions were explored via metagenomics. Mag achieved the highest removal efficiencies for NH4[+]-N, total nitrogen (TN), COD, and total phosphorus (TP), with TP removal 20.1% and 43.7% higher than in IWS and CK, respectively. Biological iron redox cycling on magnetite surfaces continuously generated reactive sites that enhanced nutrient adsorption and forms conductive pathways that facilitate direct interspecies electron transfer through the upregulation of pilA and cytochrome c, thereby promoting the transformation of aqueous organic pollutants into inorganic gaseous products. IWS promoted sulfur-driven autotrophic denitrification, effectively removing nitrogen and suppressing CH4 through competition between sulfur oxidizers and methanogens. Plant uptake also contributed to high TN and TP removal with low GHG emissions. CK exhibited dominant glycolytic activity with energy directed toward osmotic regulation, resulting in low contaminant removal and high GHG emissions. This study offers practical guidance for balancing nutrient removal efficiency with reduced GHG emissions in the treatment of saline wastewater.}, }
@article {pmid42067590, year = {2026}, author = {Alasadi, GJ and Khakvar, R and Zirak, L}, title = {Metagenomic detection of novel bacterial combinations associated with citrus decline in Iraq.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51185-8}, pmid = {42067590}, issn = {2045-2322}, abstract = {Citrus decline diseases pose significant threats to global fruit production, with complex bacterial pathogen interactions remaining poorly understood. In Iraq's Karbala governorate, severe citrus decline has affected orange orchards for 25 years, causing tree mortality within 3-5 years and substantial economic losses. PCR screening was performed on 75 symptomatic orange trees to detect phloem-limited bacterial pathogens, followed by whole-genome metagenomics on three selected PCR-positive samples to characterize associated microbial communities. Raw NGS reads from these three samples were quality-filtered, then MetaPhlAn2 was used to map reads to a curated marker database and identify bacterial, archaeal, viral, and eukaryotic taxa. The analysis revealed complex mixed infections involving three major plant bacterial pathogens: whereas PCR assays identified Candidatus Phytoplasma citri in 13.3% of the 75 samples, two additional phloem-limited pathogens, Ca. Liberibacter asiaticus and Spiroplasma sp., were exclusively detected via metagenomic sequencing across the three analyzed samples. Trimmed reads were assembled into contigs and analyzed phylogenomically against a global reference dataset. Genome assemblies yielded three for Ca. P. citri (576,881 bp, 424,689 bp, and 72,017 bp) and one each for Ca. L. asiaticus (1,151,288 bp) and Spiroplasma sp. (1,833,004 bp). These findings should be considered exploratory given the limited metagenomic sample size (n = 3); independent validation using targeted molecular approaches is required to confirm the presence of Ca. L. asiaticus and Spiroplasma sp. This is the first report documenting the metagenomic detection and characterization of a mixed infection involving Ca. Phytoplasma citri, Ca. Liberibacter asiaticus, and Spiroplasma sp. associated with citrus decline in Iraq. These findings provide crucial insights into pathogen populations and characterization and inform targeted management strategies for emerging bacterial diseases in Iraqi agricultural systems.}, }
@article {pmid42067625, year = {2026}, author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K}, title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1495-1510}, pmid = {42067625}, issn = {2058-5276}, support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; *Deoxycholic Acid/analogs &amp; derivatives/metabolism/pharmacology/therapeutic use ; Disease Models, Animal ; *Enterococcus/metabolism ; *Gastrointestinal Microbiome ; *Intestinal Barrier Function/drug effects ; Metabolomics ; *Sepsis/microbiology/drug therapy/metabolism ; Case-Control Studies ; }, abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.}, }
@article {pmid42067917, year = {2026}, author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q}, title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42067917}, issn = {2049-2618}, support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Capsaicin/pharmacology ; Fecal Microbiota Transplantation ; *Aminolevulinic Acid/metabolism ; Male ; TRPV Cation Channels/genetics/metabolism ; Bacteria/classification/metabolism/genetics ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Metagenomics ; Metabolomics ; Specific Pathogen-Free Organisms ; }, abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.<br><br>RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.<br><br>CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.}, }
@article {pmid42068031, year = {2026}, author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y}, title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2665870}, pmid = {42068031}, issn = {1949-0984}, mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth &amp; development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth &amp; development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; }, abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.}, }
@article {pmid42068598, year = {2026}, author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J}, title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128530}, doi = {10.1016/j.micres.2026.128530}, pmid = {42068598}, issn = {1618-0623}, mesh = {Animals ; *Anthozoa/microbiology/genetics ; *Vibrio/pathogenicity/genetics ; Metagenomics ; Symbiosis ; *Rhodobacteraceae/genetics/physiology ; Coral Reefs ; Gene Expression Profiling ; Transcriptome ; Virulence/genetics ; Microbiota ; Microalgae/genetics ; Photosynthesis/genetics ; Vibrio Infections ; }, abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.}, }
@article {pmid42068877, year = {2026}, author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G}, title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {156}, number = {}, pages = {158256}, doi = {10.1016/j.phymed.2026.158256}, pmid = {42068877}, issn = {1618-095X}, mesh = {Animals ; *Apoptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Thyroid Gland/drug effects/metabolism ; Male ; Rats ; *Goiter/drug therapy/chemically induced/metabolism ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Propylthiouracil ; Thyroid Hormones/biosynthesis ; Disease Models, Animal ; }, abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.<br><br>METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.<br><br>RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.<br><br>CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.}, }
@article {pmid42069091, year = {2026}, author = {Jin, H and Meng, L and Yulug, B and Altay, O and Li, X and Cankaya, S and Hanoglu, L and Ji, B and Coskun, E and Idil, E and Nogaylar, R and Oktem, EO and Sayman, D and Karaca, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Borén, J and Zhang, C and Uhlén, M and Mardinoglu, A}, title = {Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.}, journal = {Neurobiology of disease}, volume = {225}, number = {}, pages = {107424}, doi = {10.1016/j.nbd.2026.107424}, pmid = {42069091}, issn = {1095-953X}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Biomarkers/metabolism/blood ; *Machine Learning ; Metabolomics/methods ; Multiomics ; *Parkinson Disease/metabolism/diagnosis/genetics ; *Predictive Learning Models ; Proteomics ; Severity of Illness Index ; }, abstract = {While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.}, }
@article {pmid42069117, year = {2026}, author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA}, title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {402}, number = {}, pages = {128242}, doi = {10.1016/j.envpol.2026.128242}, pmid = {42069117}, issn = {1873-6424}, mesh = {Arctic Regions ; Humans ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Virulence/genetics ; *Environmental Monitoring ; Estuaries ; Sewage/microbiology ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Microbiota ; Metagenome ; Stress, Physiological/genetics ; Genes, Bacterial ; }, abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detected high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.}, }
@article {pmid42069315, year = {2026}, author = {Wu, G and Du, J and Li, H and Dong, Y and Wang, Q and Hu, F and Ji, J}, title = {Synergistic integration of sustainable wastewater treatment and agricultural waste valorization: Rapid in-situ enrichment of anammox bacteria via corncob biocarriers.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134769}, doi = {10.1016/j.biortech.2026.134769}, pmid = {42069315}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; Biofilms ; Nitrogen/isolation &amp; purification/metabolism ; *Bacteria/metabolism ; *Agriculture ; *Water Purification/methods ; Oxidation-Reduction ; }, abstract = {The slow proliferation of anammox bacteria (AnAOB) limits the large-scale application of anammox technology in mainstream wastewater treatment. Here, an innovative strategy was proposed in which agricultural waste corncob was utilized as biocarriers for the rapid enrichment of AnAOB. This study systematically validated the feasibility of using corncob as biocarriers to enhance the self-enrichment of AnAOB. Results showed that corncob addition shortened the anammox startup time by approximately 64.0% and increased total inorganic nitrogen (TIN) removal efficiency by 28.4%. The anammox activity of the corncob biofilm and flocs was 3.2- and 1.1-fold higher, respectively, than that of the control. The microbial community analysis indicated that corncob biofilm harbored the highest relative abundance of AnAOB (23.9%). Within the corncob biofilm, lignocellulolytic microbes degraded macromolecular organics to provide electron donors for denitrifiers, which facilitated nitrogen metabolic couplingbetween denitrifiers and AnAOB, therebyestablishing favorable microenvironment for the enrichment of AnAOB. Furthermore, metagenomic revealed NO cross-feeding between AnAOB and their symbionts further offered an ideal niche for AnAOB. Concurrently, the upregulation of key carbon metabolism genes indicated heightened microbial activity within the biofilm, while quorum sensing (QS) mechanisms also played a significant role in maintaining the dynamic stability of microbial community. This work established a natural and highly efficient pathway for the self-enrichment of AnAOB, simultaneously providing a synergistic solution for agricultural wastes (AWs) valorization, advanced wastewater nitrogen removal, and carbon neutrality, demonstrating broad application prospects and significant ecological value.}, }
@article {pmid42069316, year = {2026}, author = {Zhao, X and Tian, X and Zhang, H and Dang, Y and Ma, J}, title = {Metagenomic understanding of the performance enhancement in anaerobic digestion by granular activated carbon coupled with riboflavin under high organic loading.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134752}, doi = {10.1016/j.biortech.2026.134752}, pmid = {42069316}, issn = {1873-2976}, mesh = {Anaerobiosis/drug effects ; *Riboflavin/pharmacology ; *Metagenomics/methods ; Bioreactors/microbiology ; Methane/metabolism ; Fatty Acids, Volatile/metabolism ; *Charcoal/chemistry ; Biological Oxygen Demand Analysis ; *Metagenome ; }, abstract = {Anaerobic digestion (AD) often suffers operation failure from ammonia inhibition and volatile fatty acids (VFAs) accumulation under high organic loading rates (OLRs). To overcome these limitations, this study employed granular activated carbon coupled with riboflavin (RFGAC) by stimulating direct interspecies electron transfer (DIET). A semi-continuous AD experiment was conducted for 145 days with OLRs ranging from 2.25 to 11.25 kg COD/(m[3]·d). The results showed that the RFGAC group achieved the highest methane content of 78%, and maintained a COD removal rate above 95%, outperforming the GAC group and the control. At an OLR of 6.75 kg COD/(m[3]·d), the control collapsed due to severe acidification when the pH dropped lower than 6.5, while the RFGAC group stably operated with effluent COD of 2200-5300 mg/L and seldom VFAs accumulation. Microbial community analysis revealed that RFGAC selectively shifted microbial community composition especially at high OLR, promoting Methanosarcina to form a synergistic consortium. The Pearson correlation analysis of digestion performance and metagenome revealed that Methanosarcina had a stronger correlation with methanogenesis than Methanothrix, which was enriched in the presence of GAC alone. Metabolic pathway analysis confirmed key DIET-related functional genes, hdrA2 and methyl transfer-associated mtrH, were respectively upregulated by 7-fold and 5-fold. This study offers a viable strategy to improve chicken manure AD, and provides deep mechanistic insights on RFGAC modulation of microbial community succession and functional gene expression.}, }
@article {pmid42069539, year = {2026}, author = {Hagenbeek, A and Masukagami, Y and Palanichamy, P and Husnik, F}, title = {Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12881-x}, pmid = {42069539}, issn = {1471-2164}, support = {RGEC29/2024;DOI:https://doi.org/10.52044/HFSP.RGEC292024.pc.gr.194160//Human Frontier Science Program/ ; }, abstract = {The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.}, }
@article {pmid42069617, year = {2026}, author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG}, title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.}, journal = {Parasites &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42069617}, issn = {1756-3305}, support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Animals ; *Toxoplasma/isolation &amp; purification/pathogenicity/genetics ; *Arachidonic Acid/metabolism/pharmacology ; *Toxoplasmosis, Animal/parasitology/pathology ; Mice, Inbred C57BL ; Mice ; Gastrointestinal Microbiome ; *Intestines/pathology/parasitology ; Female ; Virulence ; Animals, Wild/parasitology ; }, abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.<br><br>METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.<br><br>RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.<br><br>CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.}, }
@article {pmid42069941, year = {2026}, author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I}, title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42069941}, issn = {1432-0991}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; }, abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.}, }
@article {pmid42070641, year = {2026}, author = {Wu, M and Liao, H and Luo, Y and Yao, Y and Yang, D and Hu, Z and Gao, L and Xia, X}, title = {Moisture transfer-driven quality enhancement in solid-state fermented Daqu: Synergistic effects of microbial community adaptation and functional enzyme metabolism.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134771}, doi = {10.1016/j.biortech.2026.134771}, pmid = {42070641}, issn = {1873-2976}, mesh = {*Fermentation ; *Water/metabolism ; *Microbiota ; alpha-Amylases/metabolism ; }, abstract = {Solid-state fermented Daqu exhibits a typical heterogeneous structure, where moisture regulates the microbial activity by driving gas diffusion in the pores and nutrient enrichment, playing a crucial role in the quality of the final product. However, there is a lack of clarity regarding how moisture transfer affects Daqu microbial assembly and metabolic flux. This study pioneered a real-time controllable fermentation platform, employing stoichiometry, nuclear magnetic resonance, and metagenomics to investigate microbial saccharifying metabolic functions under moisture transfer regulation. Comparing representative low (LM: 34%, 36%) and high (HM: 38%, 40%) moisture groups, we found that porosity exhibited a strong positive correlation with water activity (coefficient > 0.9, p < 0.01), serving as the primary physicochemical contributor governing moisture transfer priority. Furthermore, steady-state mass transfer in the HM group (≥ 38%) enhanced the transfer rate from free water (T23) to capillary water (T22: 10-100 ms), shaping a saccharifying functional microbial community dominated by Rhizopus and Bacillus. Weighted network and functional gene predictions indicated that this process strengthened the substrate preference of core microorganisms toward starch, significantly reinforcing the metabolic synergy between glucoamylase and α-amylase. Conversely, transient mass transfer in the LM group (< 38%) triggered microbial functional differentiation, promoting the redistribution of non-starch polysaccharide hydrolases. Our research revealed the effects of moisture transfer on nutrient availability, microbial adaptation, and metabolic functions in stack-fermented Daqu. This work ensures Daqu stability and presents novel strategies to optimize solid-state fermentation efficiency through moisture-driven microbial metabolic trade-offs.}, }
@article {pmid42070688, year = {2026}, author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L}, title = {Unveiling the plant growth-promoting and antifungal potential of Melissa officinalis endophytes: The integrative culture-dependent and metagenomic approaches.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {369}, number = {}, pages = {113182}, doi = {10.1016/j.plantsci.2026.113182}, pmid = {42070688}, issn = {1873-2259}, mesh = {*Endophytes/physiology/genetics ; *Melissa/microbiology/growth &amp; development ; *Antifungal Agents/metabolism ; Metagenomics ; *Plant Growth Regulators/metabolism ; Fusarium ; Bacteria/genetics ; Microbiota ; }, abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113 and 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.}, }
@article {pmid42070841, year = {2026}, author = {Li, S and Yan, X and Ndayishimiye, JC and Smirnov, A and Tsyganov, AN and Nassonova, E and Mazei, NG and Mazei, YA and Yang, J}, title = {Urban park metagenomics highlights sediments as a potential hotspot for CH4 and N2O emission across diverse habitats.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {481-491}, doi = {10.1016/j.jes.2025.07.053}, pmid = {42070841}, issn = {1001-0742}, mesh = {*Methane/analysis ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; *Nitrous Oxide/analysis ; Ecosystem ; *Environmental Monitoring ; *Air Pollutants/analysis ; Greenhouse Gases/analysis ; Microbiota ; }, abstract = {Urban areas contribute the vast majority of greenhouse gas (GHG) emissions, and urban greenspaces, including urban parks, are being established to promote environmental health by mitigating GHG emissions. However, the diversity of CH4 and N2O cycling genes and microbiomes in urban park ecosystems remains poorly understood. Here, we sampled five types of habitats in subtropical urban parks, including moss, sediment, soil, tree hole, and water, to explore the microbial communities and microbially mediated CH4 and N2O cycling processes using metagenomic sequencing. We found strongly positive biodiversity-ecosystem-functioning (BEF) relationships in nitrogen cycling functions, as well as in CH4 cycling, except in sediment, indicating the microbial community in the sediment had reached function saturation for CH4 cycling. CH4 cycling was driven by a few specific microbial genera, whereas many microorganisms participated in the denitrification process. Microbes in sediment exhibited the highest CH4 and N2O metabolic potential among the five habitats, especially for methanogenesis and N2O production processes. Significant positive correlations were observed between the mcrA and N2O cycling genes, suggesting methanogenesis could be coupled with denitrification. Environmental factors, such as dissolved oxygen, total nitrogen, and total carbon greatly affected microbial community composition and functional gene families. These results highlight that pond sediments are an overlooked potential source of CH4 and N2O emissions, which may undermine the role of urban greenspace in reducing GHG emissions. Reducing nitrogen pollution and eutrophication is recommended to mitigate CH4 and N2O emissions from pond sediments in urban environments.}, }
@article {pmid42070844, year = {2026}, author = {Wu, C and Wu, Y and Pan, J and Lv, Y and Li, W and Hu, M and Wang, J and Su, S and Zou, Q and Xue, S}, title = {Evolution and role of manganese-transforming bacterial microorganisms during natural manganese-tailing succession.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {516-525}, doi = {10.1016/j.jes.2026.01.018}, pmid = {42070844}, issn = {1001-0742}, mesh = {*Manganese/metabolism ; *Bacteria/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Mining ; }, abstract = {The natural succession of tailings is critical for reducing their adverse environmental impacts. However, the current knowledge of the Mn-transforming microorganisms involved in the natural vegetation succession of Mn tailings is very limited. This study reveals for the first time the evolution of Mn-transforming microorganisms during vegetation succession in Mn tailing. The results revealed that the amount of reducible Mn increased during the succession process (divided into nake-land, bryophyte, herb and woody-plant stages), which is the most important geochemical property driving bacterial community diversity. Metagenomic functional profile analysis revealed that the abundance of genes involved in nutrient uptake, metal tolerance, and metal detoxification increased during succession. A total of 51 metagenome-assembled genomes (MAGs) were reconstructed, in which 6 encoding multicopper oxidase (cotA)-containing MAGs were identified. The relative abundance of these cotA-containing MAGs first increased but then decreased during succession. Notably, genes associated with carbon fixation and denitrification were also identified in these cotA-containing MAGs, indicating their roles in coupling the cycling of manganese, carbon and nitrogen. These results suggest that Mn(II)- oxidizing bacteria could be crucial for lowering Mn toxicity, obtaining nutrients, and potentially contributing to the ecological succession of Mn tailings. The investigation of Mn-transforming microorganisms (cotA-MAGs) has also contributed to understanding the succession mechanisms and restoration of Mn tailing ecosystems.}, }
@article {pmid42070845, year = {2026}, author = {Yan, S and Li, R and Shen, X and Zhu, Y and Li, Y and Xu, M and Xie, S}, title = {Unveiling the role of bacterial communities in carbon fixation of mangrove wetlands: Insights into the redox potential and biogeochemical interactions.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {526-537}, doi = {10.1016/j.jes.2025.08.024}, pmid = {42070845}, issn = {1001-0742}, mesh = {*Wetlands ; *Carbon Cycle ; Oxidation-Reduction ; *Soil Microbiology ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mangrove wetlands are crucial for carbon sequestration, however, the contributions of bacterial carbon fixation in these ecosystems are often overlooked, and the predominant pathways remains unknown. This gap seriously hinders the understanding and precise assessment of carbon sequestration. This study systematically investigates the pathways, rates, and influential factors of bacterial carbon fixation in mangrove wetlands, utilizing soils from various tidal zones and depths. Through an integrated approach that combines in situ metagenome sequencing, [13]CO2 tagging experiment, functional gene abundance measurement, and 16S rRNA sequencing, we provide the first evidence that the reverse tricarboxylic acid cycle is the predominant pathway for carbon (C) fixation in mangrove soils. The mangrove ecosystem was identified as a significant hotspot for bacterial carbon fixation, with rates in topsoil ranging from 15 to 63 mmol C/(m[2]·day), significantly influenced by environmental variables such as oxidation-reduction potential, and ammonium and nitrate concentrations. In deep soils, high carbon fixation rates were detected in low tidal zones but not in middle and high tidal zones, which did not align with the abundance of carbon fixation functional genes. Notably, we found a strong correlation between carbon fixation rates and nitrogen metabolism processes, underscoring the ecological interactions between these biogeochemical cycles. These findings greatly enhance our understanding of microbial contributions to carbon cycling in mangrove ecosystems and offer novel insights into blue carbon sequestration and the management of coastal wetlands under varying environmental conditions.}, }
@article {pmid42070879, year = {2026}, author = {Xin, Y and Liu, L and Chen, SH and Zhao, QB and Zheng, YM}, title = {Enhancing urban river self-purification through riverbed substrates configuration: A nature-based solution for nutrient removal and restoration planning.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {95-108}, doi = {10.1016/j.jes.2026.01.038}, pmid = {42070879}, issn = {1001-0742}, mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; Nitrogen/analysis ; *Environmental Restoration and Remediation/methods ; Nutrients ; Phosphorus/analysis ; }, abstract = {Appropriate riverbed substrates, as nature-based engineering components, are critical for enhancing nutrient mitigation and ecosystem sustainability in urban rivers. However, their role in regulating hydrologically mediated nutrient fluxes and biofilm functions remains unclear, limiting substrate-optimized design for urban river restoration. This study integrated machine learning modeling, scenario simulations, and metagenomic analysis to quantify substrate-driven interfacial nutrient removal efficiencies and uncover microbial regulation mechanisms. A back propagation neural network could accurately predict interfacial ammonium and total organic carbon removal efficiencies (RMSE: 0.59-6.92 mg/(L·h·m[2]), R[2]: 0.66-0.97), with retention time, temperature, dissolved oxygen, and nutrient load identified as key predictors. Building upon the model-predicted scenario results, analysis of similarity tests confirmed that substrate type significantly influenced interfacial nutrient removal efficiencies (R > 0.05, P < 0.001). Scoring metrics demonstrated fine sand (1295) and gravel (1281) gained higher total scores than other substrates (1110-1182), indicating higher interfacial nutrient removal capacities. Metagenomic analyses revealed that these differences were driven by divergence in microbial functional potential. Substrate type selectively enriched functional genes related to nitrogen and carbon cycling (R > 0.18, P < 0.05), with gravel microcosms showing significantly higher gene abundance (8.00 × 10[-4]-2.08 × 10[-3]), despite similar community compositions governed by stochastic assembly (R[2] > 0.84). Topological analysis revealed that redundancy of functional gene network significantly influenced ammonium removal efficiency (P < 0.05), with fine sand and gravel enhancing ammonium removal, while lower clustering coefficients in artificial filler and gravel microcosms significantly promoted total organic carbon removal. This study suggested that fine sand and gravel should be more effective riverbed substrates for enhancing interfacial nutrient removal in urban river restoration.}, }
@article {pmid42071059, year = {2026}, author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D}, title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50831-5}, pmid = {42071059}, issn = {2045-2322}, support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; }, abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.}, }
@article {pmid42071227, year = {2026}, author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z}, title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.}, journal = {Clinical and translational medicine}, volume = {16}, number = {5}, pages = {e70667}, pmid = {42071227}, issn = {2001-1326}, support = {2022YFA1304000//National Key R&amp;D Program of China/ ; 2024B1111150001//Guangdong S&amp;T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; }, abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.}, }
@article {pmid42071909, year = {2026}, author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R}, title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {8}, pages = {}, pmid = {42071909}, issn = {2076-2615}, support = {NA//Alltech (Ireland)/ ; }, abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.}, }
@article {pmid42072313, year = {2026}, author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S}, title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.}, journal = {Biomedicines}, volume = {14}, number = {4}, pages = {}, pmid = {42072313}, issn = {2227-9059}, support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research &amp; Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; }, abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.}, }
@article {pmid42073328, year = {2026}, author = {Indio, V and Mekonnen, YT and Oliveri, C and Rubboli, S and Candela, M and Seguino, A and Serraino, A and De Cesare, A}, title = {Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, pmid = {42073328}, issn = {2304-8158}, support = {Horizon 2020 "Controlling Microbiomes Circulations for Better Food Systems" (CIRCLES) no. 818290.//European Union/ ; }, abstract = {The aim of this study was to assess how raising chickens without the use of antimicrobials affects the microbiome of poultry carcasses. A total of 151 caeca and neck skin samples from chickens raised without antimicrobials were collected in the same slaughterhouse and submitted to shotgun metagenomic sequencing. Caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota. The caeca microbiome was enriched in genes related to a proliferating and metabolically active microbial community. Carcass-associated microbiomes were enriched in functional genes linked to adaptation to nutritionally limited and oxidative environments. A significantly higher cumulative antimicrobial resistance gene abundance was detected in carcasses compared to caeca. Specifically, carcasses exhibited approximately 1.5 times more AMR genes, reflecting an increase of nearly 49%. While caeca showed enrichment of resistance determinants associated with Gram-positive anaerobic gut commensals, carcasses were characterized by a predominance of multidrug efflux systems and clinically relevant β-lactam resistance genes, commonly associated with environmental and opportunistic Gram-negative bacteria. In carcasses, carbapenem-associated genes, such as OXA-58-like and CphA, were detected. However, these genes have not been associated with carbapenemase-producing Enterobacterales. Overall, the findings of this study indicate that reducing antimicrobial resistance in food animal production systems extends beyond farm-level intervention. At present, the benefits of the interventions aimed at reducing antimicrobial resistance at farm level seem to be compromised during the post-harvest stages.}, }
@article {pmid42073366, year = {2026}, author = {Brasileiro, CG and Moreno, MTDC and Santos, EO and Saranraj, P and Cardoso, AM and Vieira, JMBD}, title = {Assessing Food Safety Risks in Homemade Fermented Beverages: A Case Study with Quinoa Rejuvelac.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {42073366}, issn = {2075-1729}, support = {E2023//FAPERJ, CNPq, and CAPES/ ; }, abstract = {Spontaneous fermentation processes can promote uncontrolled microbial growth and increase the risk of foodborne contamination, making the characterization of artisanal beverages essential for consumer safety. This study investigated the microbial composition of quinoa-based rejuvelac, a homemade fermented drink often perceived as a functional food, with the objective of identifying potential microbiological hazards associated with its preparation. High-throughput sequencing of the 16S rRNA V3-V4 region was combined with shotgun metagenomics to profile bacterial communities and recover metagenome-assembled genomes. The analysis revealed a strong dominance of Pseudomonadales, mainly Pseudomonas, Acinetobacter, Enterobacter and Burkholderiales, while lactic acid bacteria typically responsible for stable and safe fermentations were not detected. Shotgun metagenomics recovered medium- to high-quality genomes from Burkholderiaceae and Clostridiales, supporting the overrepresentation of non-beneficial taxa and indicating deviations from expected fermentation microbiota. These results show that the spontaneous preparation of rejuvelac may favor bacterial groups associated with environmental contamination rather than fermentative pathways, underscoring the importance of hygiene practices, controlled starter cultures and monitoring strategies to mitigate microbiological risk. The study highlights the need for improved safety standards in artisanal fermented foods to prevent unintended microbial contamination and protect consumers.}, }
@article {pmid42073451, year = {2026}, author = {Cerreto, M and Maestri, M and Pallozzi, M and Cerrito, L and Stella, L and Ianiro, G and Gasbarrini, A and Ponziani, FR}, title = {Gut Microbiota Biomarkers in Patients with Hepatocellular Carcinoma in the Era of Immune Checkpoint Inhibitors.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {42073451}, issn = {2075-1729}, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape for hepatocellular carcinoma (HCC); however, a considerable proportion of patients do not achieve durable clinical benefits. This highlights the need for reliable predictive biomarkers, which are currently lacking. The accumulated evidence supports a relevant role of the gut-liver axis in modulating immunotherapy outcomes, and several studies have identified distinct microbial features associated with either responders or non-responders. Responders to immunotherapy frequently present with higher microbial diversity and enrichment of beneficial taxa, whereas the expansion of pro-inflammatory and pathogenic bacteria has been associated with primary resistance and increased treatment-related toxicity in non-responders. However, the available findings remain heterogeneous across cohorts, likely owing to differences in geography, diet, liver disease etiology, treatment regimens, and microbiome analytical methods. Machine-learning models integrating metagenomic and metabolomic data have shown encouraging results in defining microbial signatures associated with treatment outcomes, although variability among cohorts currently limits their clinical applicability and generalizability. Beyond microbial taxonomic composition, microbiota-derived metabolites-such as short-chain fatty acids, bile acids, inosine, and tryptophan catabolites-appear to play a crucial role in shaping the tumor microenvironment and host immune responses, thus representing additional candidate biomarkers, also due to the relative ease of their measurement. Finally, microbiota-targeted interventions are emerging as potential strategies to enhance immunotherapy efficacy. Overall, the gut microbiome and its metabolic activity represent promising tools, albeit still under investigation, for patient stratification and personalized management in HCC treated with ICIs. Therefore, this review aims to summarize and critically discuss the current evidence on gut microbiota-derived biomarkers of response and resistance to ICIs in HCC, with particular focus on microbial composition, microbiota-related metabolites, and emerging microbiome-based therapeutic strategies. This narrative review provides an updated overview of the role of gut microbiota as both a biomarker and a therapeutic target in patients with hepatocellular carcinoma (HCC) receiving immune checkpoint inhibitor (ICI) therapy.}, }
@article {pmid42073497, year = {2026}, author = {Carraturo, F and Salamone, M and Annunziata, M and Di Brizzi, EV and Giorgio, CM and Petrillo, A and Fedi, L and Maione, A and Guida, M and Galdiero, E}, title = {Preliminary Characterization of Skin Microbiota and Mycobiota in Atopic Dermatitis by Metagenomic and Culture-Based Analyse