@article {pmid42484632,
year = {2026},
author = {Vernon, JJ and Lynch, J and Yu, X and Do, T},
title = {Clostridioides difficile in the oral microbiome: an in silico analysis.},
journal = {Journal of medical microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002188},
pmid = {42484632},
issn = {1473-5644},
mesh = {Humans ; *Clostridioides difficile/genetics/isolation & purification/classification ; Saliva/microbiology ; *Dental Plaque/microbiology ; *Microbiota ; *Clostridium Infections/microbiology/epidemiology ; Periodontitis/microbiology ; *Mouth/microbiology ; Computer Simulation ; Computational Biology ; Metagenomics ; Female ; Male ; },
abstract = {Introduction. High rates of recurrent Clostridioides difficile infection (CDI) and environmental contamination are attributed to its ability to form spores. Periodontal diseases are characterized by gingival inflammation, caused by dental plaque accumulation.Hypothesis. Periodontal plaque could harbour C. difficile spores, acting as a reservoir for reinfection.Aim. Compare the prevalence and abundance of C. difficile in metagenomic sequences of saliva and dental plaque from healthy and periodontal disease patients.Methodology. Publicly available metagenomic reads from oral samples of healthy (n=80) and periodontitis (n=204) patients were analysed for C. difficile presence through an in-house bioinformatic pipeline. Briefly, reads underwent quality control (cutadapt/fastQC) prior to subsampling of 3 million reads (seqtk). Reads and MEGAHIT-assembled contigs were aligned to a C. difficile reference genome (ASM1888508v1) or a full non-redundant protein DIAMOND database. Outputs were filtered, annotated (Entrez Direct) and top hits identified via National Center for Biotechnology Information blast. Abundance and prevalence were compared between cohorts.Results. Low levels of C. difficile sequences were observed, with significantly higher prevalence in periodontitis (7.4%, n=15/204) vs. healthy cohorts (5.0%, n=4/80) (P=0.0087) with reference genome alignment. Using the full non-redundant database, prevalence was also higher in periodontitis (14.2% vs. 3.8%; P=0.012), along with significantly greater average C. difficile sequence counts (0.608 vs. 0.075; P=0.018) and relative abundance (0.00029% vs. 0.0000003%; P=0.009).Conclusion. Sequences pertaining to C. difficile were detected in oral samples, with significantly more observed in periodontal disease compared to healthy cohorts. This highlights the possibility for dental plaque to act as a reservoir, potentially contributing to reinfection in CDI patients.},
}

Humans
*Clostridioides difficile/genetics/isolation & purification/classification
Saliva/microbiology
*Dental Plaque/microbiology
*Microbiota
*Clostridium Infections/microbiology/epidemiology
Periodontitis/microbiology
*Mouth/microbiology
Computer Simulation
Computational Biology
Metagenomics
Female
Male

@article {pmid42484695,
year = {2026},
author = {Vieira, CS and Lemos, LN and Morais, DK and Rosado, AS and Pylro, VS},
title = {Uneven global coverage of halophilic metagenomes limits comparative analyses of microbial adaptation to saline environments.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42484695},
issn = {1678-4405},
mesh = {Metagenomics ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Ecosystem ; Salinity ; *Adaptation, Physiological ; Biodiversity ; },
abstract = {Halophilic microorganisms are central to biotechnology, bioremediation, and astrobiology because they persist under extreme and polyextreme conditions analogous to extraterrestrial environments. Although metagenomics has transformed the study of halophilic biodiversity, available datasets remain fragmented and unevenly documented. To assess how halophilic metagenomic research reflects the global exploration of hypersaline environments, we analyzed PubMed-indexed studies and associated sequencing metadata deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using a curation workflow. Our quantitative analysis reveals a severe geographic bias linked to uneven global research investment (Gini coefficient = 0.736), with a small number of countries contributing to many publicly available datasets. In contrast, the environmental distribution of these samples showed moderate ecological uniformity (Pielou's Evenness = 0.818), though we identified pervasive gaps in metadata completeness that hinder dataset interoperability. Our curated dataset highlights a strong research focus on polyextremophilic habitats, positioning these ecosystems as prime targets for biotechnological and astrobiological bioprospecting. Additionally, the geographical bias highlights the need for interoperable global data frameworks and more equitable investment in data generation and analysis, especially in underrepresented regions of the Global South.},
}

Metagenomics
*Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
Ecosystem
Salinity
*Adaptation, Physiological
Biodiversity

@article {pmid42485280,
year = {2026},
author = {K V, S and Thaha, N and Dehury, B},
title = {In silico identification and biophysical characterization of candidate antimicrobial peptides from the Indian marine microbiome targeting multidrug-resistant ESKAPE pathogens.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353985},
pmid = {42485280},
issn = {1932-6203},
mesh = {*Antimicrobial Peptides/pharmacology/chemistry ; Molecular Dynamics Simulation ; *Microbiota ; *Drug Resistance, Multiple, Bacterial/drug effects ; Acinetobacter baumannii/drug effects ; India ; Computer Simulation ; *Anti-Bacterial Agents/pharmacology/chemistry ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Machine Learning ; },
abstract = {The global health crisis of antimicrobial resistance necessitates the discovery of new antibacterial agents. Underexplored marine microbiomes, particularly from the biodiverse Indian coast, represent a rich potential source of antimicrobial peptides (AMPs). Targeting the urgent threat of multidrug-resistant ESKAPE pathogens, the present study aimed to computationally identify novel, membrane-active AMPs from these unique metagenomic datasets, with a focus on inhibiting Gram-negative bacteria. In this study, we computationally mined Indian marine high-resolution shotgun metagenomic datasets through quality filtering, de novo assembly, and small open reading frame prediction. An ensemble of six machine learning-based AMP prediction tools identified over 51,000 high-confidence candidate AMPs. Subsequent filtering based on physicochemical properties and AlphaFold3-predicted structures prioritized ten peptides with favourable membrane-active characteristics. Two lead candidates, c_AMP_1 and c_AMP_2, were subjected to all-atom molecular dynamics simulations within Gram-negative membrane mimetic models of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Our simulations indicated distinct membrane interaction modes: c_AMP_1 adopted a stable, surface-associated α-helical orientation, while c_AMP_2 displayed a more flexible, membrane-inserting orientation in the simulations. Analysis of the MD simulations revealed distinct predicted peptide-membrane interaction profiles, characterized by specific hydrogen bonding patterns, peptide tilt angles, and membrane thinning, which collectively suggest differing biophysical interaction modes. Taken together, our work suggests the Indian marine microbiome as a promising reservoir for novel AMP candidates and suggests that an integrated computational pipeline - combining machine learning, structural biology, and biophysical simulation - may help prioritize candidate peptides for future experimental validation against critical pathogens.},
}

*Antimicrobial Peptides/pharmacology/chemistry
Molecular Dynamics Simulation
*Microbiota
*Drug Resistance, Multiple, Bacterial/drug effects
Acinetobacter baumannii/drug effects
India
Computer Simulation
*Anti-Bacterial Agents/pharmacology/chemistry
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Machine Learning

@article {pmid42485562,
year = {2026},
author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K},
title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70185},
pmid = {42485562},
issn = {1521-4028},
support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; },
abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.},
}

RNA, Ribosomal, 16S/genetics
*Eichhornia/microbiology
Metagenomics
Biomass
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Animals
*Soil Microbiology
Archaea/classification/genetics/isolation & purification/metabolism
Composting
Agriculture
Fungi/classification/genetics/isolation & purification/metabolism
Shotgun Sequencing
Phylogeny

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

@article {pmid42486223,
year = {2026},
author = {Leena, DA and Chaudhary, S and Mehdi, MM},
title = {Pesticide-driven microbial resistance: Ecological impact and mitigation strategies development of multiple drug resistance due to pesticide exposure.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110630},
doi = {10.1016/j.cbpc.2026.110630},
pmid = {42486223},
issn = {1532-0456},
abstract = {The persistent use of agricultural pesticides is increasingly recognized as an important driver of antimicrobial resistance (AMR) and multidrug resistance (MDR) in environmental microorganisms. This review synthesizes current knowledge on the molecular mechanisms underlying pesticide-induced MDR, its ecological and evolutionary consequences, advances in resistance surveillance, and emerging mitigation strategies. Chronic pesticide exposure promotes MDR through interconnected genetic mechanisms (mutations and horizontal gene transfer), biochemical mechanisms (detoxification enzymes), physiological adaptations (stress responses and biofilm-associated tolerance), and molecular regulatory processes (efflux pump activation and altered gene expression), resulting in cross-resistance to clinically relevant antimicrobial agents. These mechanisms alter microbial community structure, facilitate the dissemination of antibiotic resistance genes, and impair essential ecosystem functions. Recent advances in PCR, whole-genome sequencing, metagenomics, and other omics technologies have improved resistance detection, although important knowledge gaps remain regarding the long-term effects of sub-lethal pesticide exposure and resistance dynamics in environmental microbiomes. By integrating mechanistic, ecological, evolutionary, and surveillance perspectives within a One Health framework, this review provides a comprehensive synthesis of pesticide-induced MDR and identifies key research priorities for developing sustainable resistance mitigation strategies.},
}

@article {pmid42486447,
year = {2026},
author = {Lv, Z and You, H and Leng, H and Sheng, H and Li, W and Liu, F and Li, Z and Zhu, J and Zhang, G},
title = {Recycling sludge carbon sources via different iron-based activated PDS into denitrification systems for nitrogen removal: focusing on efficacy, community structure and molecular mechanism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135481},
doi = {10.1016/j.biortech.2026.135481},
pmid = {42486447},
issn = {1873-2976},
abstract = {Advanced oxidation processes (AOPs) effectively solubilized organic matter from sludge, generating a liquid phase with substantial recovery potential. Because organic composition and concentration were governed by oxidation intensity, elucidating this relationship was essential for optimizing downstream resource recovery. This study systematically compared the cracking solution generated from sewage sludge utilizing different AOPs (US/Fe(II)/PDS vs US/Fe1/PDS vs US/Fe-C/PDS). The SCOD were 673 mg/L, 556.8 mg/L, and 676 mg/L in US/Fe(II)/PDS, US/Fe1/PDS and US/Fe-C/PDS systems, respectively, including high concentrations of short-chain volatile fatty acid, proteins and polysaccharides (PS). Correspondingly, there demonstrated superior NO3[-]-N, NH4[+]-N and total nitrogen removal efficiencies of 13.6%, 50%, and 50%, respectively, primarily attributed to the optimal oxidation capacity and abundant organic carbon in US/Fe-C/PDS system. Additionally, no significant difference was observed between US/Fe-C/PDS system and control group (CH3COONa) during denitrification, suggesting cracking solution in sludge had strong application potential as a carbon source. Sequencing results revealed stable bacterial communities across all systems, implying that the cracking solution had negligible influence on the structure of core denitrifying taxa. A robust nitrogen-cycling function was maintained, accompanied by up-regulate of genes (napAB, nirS/K, norBC and nosZ) associated with PS-sustained-release carbon source metabolism and denitrification in US/Fe-C/PDS system. These results suggested that PS-sustained-release carbon source driving efficient nitrogen removal and promoting sludge resource recycling in US/Fe-C/PDS system.},
}

@article {pmid42486450,
year = {2026},
author = {Wu, Y and Sun, Y and Yu, R and Cui, Y and Yang, F and Li, J and Zhang, Z},
title = {In situ sludge reduction induced by graphene oxide: Mechanistic insights into metabolic uncoupling, maintenance energy and cryptic growth.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135479},
doi = {10.1016/j.biortech.2026.135479},
pmid = {42486450},
issn = {1873-2976},
abstract = {Nanomaterials are increasingly recognized as stressors in biological wastewater treatment systems, yet the effects on biomass yield remain poorly understood. This study systematically evaluated the effects of low-dose graphene oxide (GO; 0.1 and 1 mg/L) on pollutant removal and sludge yield in activated sludge systems. At day 40, sludge yields were 0.356, 0.298, and 0.237 g VSS/g COD in the Control, 0.1 and 1 mg/L GO systems, respectively, corresponding to reductions of 16.29% (p = 0.055) and 33.43% (p < 0.05) without compromising nitrogen removal. GO exposure also loosened floc structure and increased mean intrafloc dissolved oxygen concentrations by 23.88% and 32.84%, respectively (both p < 0.01). Activities of isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and the electron transport system increased, indicating intensified endogenous oxidative metabolism. Despite enhanced respiration, ATP production decreased by 19.48% (p < 0.05) and 27.95% (p < 0.01), suggesting uncoupling between oxidation and phosphorylation. Intracellular reactive oxygen species increased by 65.46% and 145.60% (both p < 0.01), respectively. The resulting oxidative stress increased maintenance energy demand and promoted cell death and cryptic growth. Metagenomic analysis further revealed enrichment of genes related to oxidative stress responses, macromolecular repair, and extracellular polymeric substance secretion, together with decrease of genes involved in cell replication and division. Collectively, enhanced intrafloc oxygen transfer and endogenous respiration, oxidation-phosphorylation uncoupling, increased maintenance energy demand, and cryptic growth jointly drove GO-induced sludge reduction.},
}

@article {pmid42486470,
year = {2026},
author = {Delebecque, CJ and La Monica, MB and Keller, D and Shannon, W and Ziegenfuss, TN and Zimmerman, NP},
title = {The effects of a postbiotic supplement on biomarkers of microbiome, gastrointestinal, cardiometabolic, and immunometabolic health.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00129},
pmid = {42486470},
issn = {1876-2891},
abstract = {The gut microbiome is increasingly recognised as a modifiable contributor to metabolic, immune, and stress-related physiology, yet many nutritional interventions produce broad microbial shifts that may be poorly tolerated. We investigated the effects of a fermented and pasteurised oat-based preparation (Keystone) on microbiome composition and selected biomarkers in a 4-week randomised, double-blind, placebo-controlled trial in generally healthy adults. Seventy-six participants completed the intervention (38 placebo, 38 Keystone). Stool samples collected at baseline and week 4 underwent shotgun metagenomic sequencing, and serum butyrate, IL-8, morning cortisol, albumin/globulin ratio, routine clinical chemistries, DASS-21, and SF-36 were assessed. The intervention did not affect alpha or beta diversity. In contrast, species-level analysis showed a distinct compositional signature, with enrichment of taxa including Akkermansia spp., Bacteroides intestinalis, Bifidobacterium pseudocatenulatum, and Anaerostipes caccae in the Keystone group, alongside lower abundance of several Haemophilus, Megasphaera, and Prevotella taxa relative to placebo (FDR < 0.001). Nominally significant baseline-by-treatment interactions were observed for morning cortisol (P = 0.03), IL-8 (P = 0.04), and albumin/globulin ratio (P = 0.03), while serum butyrate showed a near-significant trend (P = 0.053). SF-36 emotional well-being improved within the Keystone group. No adverse events were reported. These results indicate that Keystone was safe and well tolerated and selectively modulates the gut microbiome, with exploratory associations for host stress and inflammatory markers that offer key insights for future follow-up studies. Trial registration: The trial was IRB approved and registered with ClinicalTrials.gov NCT07527286.},
}

@article {pmid42486576,
year = {2026},
author = {Venugopal, DC and Srinivas, KS},
title = {Challenges and future directions in head and neck microbiome research.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {189-227},
doi = {10.1016/bs.ai.2026.03.010},
pmid = {42486576},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; },
abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.},
}

Humans
*Head and Neck Neoplasms/microbiology/therapy/immunology
*Microbiota/immunology
Animals
*Dysbiosis/microbiology/immunology/therapy
Fecal Microbiota Transplantation
Metabolomics
Metagenomics
Probiotics/therapeutic use

@article {pmid42486580,
year = {2026},
author = {Perera, ML and Perera, IR},
title = {Microbiome based diagnostic approaches.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {93-125},
doi = {10.1016/bs.ai.2026.03.004},
pmid = {42486580},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; },
abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.},
}

Humans
*Microbiota/immunology
*Head and Neck Neoplasms/diagnosis/microbiology
Dysbiosis
Animals
Early Detection of Cancer

@article {pmid42487113,
year = {2026},
author = {Ma, Y and Sun, J and Guo, C and Cao, J and Zhang, L and Zhu, F and Yu, X and Yang, L and Fang, J},
title = {Exploring brain-gut interaction mechanisms in Transcutaneous auricular Vagus Nerve stimulation for Major Depressive Disorder.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42487113},
issn = {1471-244X},
support = {82474663//National Natural Science Foundation of China/ ; HLCMHPP2023072//High Level Chinese Medical Hospital Promotion Projec/ ; },
mesh = {Humans ; Magnetic Resonance Imaging ; *Major Depressive Disorder/therapy/physiopathology/diagnostic imaging ; Female ; *Vagus Nerve Stimulation/methods ; Male ; Adult ; *Transcutaneous Electric Nerve Stimulation/methods ; *Brain/physiopathology/diagnostic imaging ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Brain-Gut Axis/physiology ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiota is intricately implicated in the pathogenesis of Major Depressive Disorder (MDD), with the vagus nerve serving as a key regulatory bridge. Transcutaneous Auricular Vagus Nerve Stimulation (taVNS) has emerged as a promising non-invasive therapeutic strategy for MDD by modulating the gut-brain axis, yet the precise brain-gut interaction mechanisms underlying its antidepressant effects remain poorly characterized. This study is a registered clinical trial (ChiCTR2200059591; Registered 4 May 2022; https://www.chictr.org.cn).

OBJECTIVE/HYPOTHESIS: This study aimed to verify the clinical efficacy of taVNS for MDD and elucidate the underlying brain-gut crosstalk mechanisms, by integrating comprehensive clinical assessments, resting-state functional magnetic resonance imaging (rs-fMRI) neuroimaging data and gut metagenomic profiling.

METHODS: Ninety-five patients diagnosed with MDD were randomly allocated at a 1:1 ratio to either the active taVNS group (auricular concha stimulation) or the sham taVNS group (superior concha of mid-helix stimulation). Eighty patients (40 per group) completed the entire intervention course and were included in the final statistical analysis. All participants underwent 30-minute stimulation twice daily (4/20 Hz, 3-8 mA) for 8 consecutive weeks (5 days per week). Standardized clinical assessments were administered at baseline and post-intervention, including the 17-item Hamilton Depression Rating Scale (HAMD-17), 14-item Hamilton Anxiety Rating Scale (HAMA-14), and Gastrointestinal Symptom Rating Scale (GSRS). Rs-fMRI was performed to quantify core neural activity metrics, including amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo), and degree centrality (DC); fecal samples were collected for high-throughput metagenomic analysis. Spearman correlation analysis and mediation analysis were further conducted to dissect the interactive relationships between brain neural activity and gut microbiota.

RESULTS: The active taVNS group achieved significantly superior clinical efficacy relative to the sham group, with a HAMD-17 response rate of 62.50% and remission rate of 35.00%, versus 30.00% and 2.50% in the sham group (all P < 0.05). Rs-fMRI analyses revealed significant group×time interaction effects on neural activity: decreased ALFF in the right calcarine sulcus; altered fALFF in the right inferior temporal gyrus, left cuneus, right superior frontal gyrus (SFG) and right angular gyrus; reduced ReHo in the right calcarine sulcus and bilateral insula; and increased DC in the right caudate nucleus and left anterior cingulate gyrus. Gut microbiota profiling identified anaerobic butyrate-producing bacteria and Faecalibacterium prausnitzii as potential biomarkers linked to taVNS therapeutic effects. HAMD-17 scores were negatively correlated with Faecalibacterium prausnitzii abundance (r=-0.566, P < 0.01) and positively correlated with anaerobic butyrate-producing bacteria abundance (r = 0.406, P < 0.01). Mediation analysis suggested that fALFF values in the right SFG may indirectly modulate depressive symptoms via regulating Faecalibacterium prausnitzii abundance (indirect effect 95% CI: 0.3039-2.4466), with a significant partial mediation effect observed, though future studies controlling for dietary and other confounding variables are needed to confirm this relationship.

CONCLUSION: taVNS effectively alleviates depressive symptoms in MDD patients via dual complementary pathways: directly modulating neural activity in the right SFG to regulate depression-related brain function, and indirectly maintaining gut microbiota homeostasis by enriching beneficial taxa such as Faecalibacterium prausnitzii. These findings provide novel mechanistic insights into the brain-gut interaction underlying the antidepressant effects of taVNS, laying a theoretical foundation for its clinical application in MDD management.},
}

Humans
Magnetic Resonance Imaging
*Major Depressive Disorder/therapy/physiopathology/diagnostic imaging
Female
*Vagus Nerve Stimulation/methods
Male
Adult
*Transcutaneous Electric Nerve Stimulation/methods
*Brain/physiopathology/diagnostic imaging
*Gastrointestinal Microbiome/physiology
Middle Aged
*Brain-Gut Axis/physiology
Treatment Outcome

@article {pmid42487141,
year = {2026},
author = {Kedia, S and Rani, PS and Nyambero, M and Bandsode, V and Peddireddy, V and Ahmed, N},
title = {Comparative genomics of Bifidobacterium crudilactis NASR_001 - unveiling the tapestry of a putative probiotic.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42487141},
issn = {1757-4749},
abstract = {BACKGROUND: Bifidobacteria are the initial colonizers of the human gastrointestinal tract. Due to an obligate anaerobic character, the isolation and culture of Bifidobacterium spp. is challenging. This bottleneck has led to studies being focused on metagenomic analysis rather than genome sequencing of Bifidobacterium spp. from pure cultures. Our metadata analysis revealed paucity of Bifidobacterium genomes reported from the Indian subcontinent. In this report, we describe the selective isolation and whole genome sequencing (WGS) of Bifidobacterium crudilactis from a pure culture of dairy origin from India.

RESULTS: The WGS by Oxford Nanopore long-read sequencing of genomic DNA of B. crudilactis isolate NASR_001 revealed a single circular chromosome of 2,347,652 bp with a GC content of 57.5%. Genome annotation predicted 1923 coding sequences, 6 rRNAs, 46 tRNAs with no CRISPR arrays. Moreover, average nucleotide identity (ANI) analysis with B. crudilactis LMG 23 609 (RefSeq accession GCF_000738005.1) and B. crudilactis MAG UW_FK_BIF1_1 (RefSeq accession GCF_047836735.1) showed 98.8% and 97.3% similarity, respectively, revealing thereby a closest identity and functional similarity to B. crudilactis. The presence of genetic attributes for carbohydrate metabolism, stress response genes and absence of antimicrobial resistance (AMR) encoding genes, as well as paucity of virulence genes signify B. crudilactis NASR_001 to be a putative probiotic organism.

CONCLUSION: The genome sequence of B. crudilactis NASR_001 represents a high-quality genome, representative of the species. It offers valuable insights for further exploration of its promising probiotic potential and functional characteristics.},
}

@article {pmid42487569,
year = {2026},
author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV},
title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70485},
pmid = {42487569},
issn = {1365-294X},
support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; },
mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; },
abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.},
}

*Triticum/microbiology/genetics
*Ascomycota/pathogenicity/genetics
*Plant Diseases/microbiology/genetics
*Mycobiome/genetics
Host-Pathogen Interactions/genetics
North Carolina
Plant Leaves/microbiology
Metagenomics

@article {pmid42487618,
year = {2026},
author = {Atara, S and Antaliya, K and Vaghamshi, N and Vansia, A and Ghelani, A and Patel, R and Dudhagara, P},
title = {Environmental emergence and dissemination of clinically relevant multidrug-resistant bacteria and resistance genes in sewage and aquatic ecosystems.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2026.0186},
pmid = {42487618},
issn = {2210-9099},
abstract = {OBJECTIVES: This study characterized multidrug-resistant (MDR) bacteria in sewage, river, and marine ecosystems in South Gujarat, India.

METHODS: Water samples were collected from 25 hospital drainage, sewage treatment/pumping, Tapi River, and coastal marine sites at multiple time points. From 270 screened colonies, 166 morphologically and biochemically distinct nonduplicate isolates were retained. Antimicrobial susceptibility was assessed, and isolates were classified as MDR, extensively drug-resistant (XDR), or pan-drug-resistant (PDR). Biofilm formation, metabolic activity, extracellular polymeric substance protein, heavy metal tolerance, extended-spectrum β-lactamase production, carbapenemase production, and metallo-β-lactamase activity were assessed phenotypically. Tapi River estuary water was used for taxonomic profiling and antibiotic resistance gene (ARG) detection.

RESULTS: The 166 isolates comprised 45 bacterial species, with clinically significant Gram-negative pathogens predominating, including Pseudomonas aeruginosa (n=24, 14.5%), Ochrobactrum intermedium (n=16, 9.6%), Stenotrophomonas maltophilia (n=15, 9.0%), and Escherichia coli (n=12, 7.2%). MDR phenotypes were detected in 80.1% of isolates; 18.1% were XDR, and 1.8% were PDR, with PDR isolates confined to river water samples. Biofilm formation was observed in 86.1% (n=143) of isolates, including 28.3% (n=47) strong, 24.7% (n=41) moderate, and 32.5% (n=54) weak producers. Extended-spectrum β-lactamase production was confirmed in 13.4% of Gram-negative isolates, and carbapenemase activity was detected in 11 isolates. Zinc and copper tolerance were significantly higher in XDR than in MDR isolates (p<0.05). Metagenomics identified efflux pumps as the dominant ARG class (36.2%), followed by target-site mutations (21.3%) and β-lactamases (14.9%), and detected blaCTX-M-15, blaTEM-207, gyrA, and parC.

CONCLUSION: These interconnected aquatic systems represent important reservoirs for community-level antimicrobial resistance transmission.},
}

@article {pmid42487706,
year = {2026},
author = {He, Z and Hua, R and Wu, T and Qu, H and Yang, G and Wang, S and Gao, F and Jing, Y},
title = {Microbial functional gene assembly is associated with soil carbon and nitrogen dynamics during grassland degradation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1878594},
pmid = {42487706},
issn = {1664-302X},
abstract = {INTRODUCTION: Grassland degradation is often accompanied by changes in the structure and function of soil microbial communities. However, the mechanisms by which the assembly of microbial functional communities is associated with alterations in soil carbon and nitrogen pools remain unclear.

METHODS: This study was conducted along a degradation gradient in a typical steppe of Inner Mongolia. Metagenomics, community null models, and structural equation modeling were used to examine microbial functional gene assembly, carbon and nitrogen cycling genes, and their associations with soil carbon and nitrogen pools.

RESULTS: The assembly of microbial functions shifted from being predominantly influenced by stochastic processes to deterministic processes, with the strongest deterministic filtering observed during the moderate degradation stage. The abundance of the aerobic oxidation gene porA decreased with increasing degradation, whereas fermentation genes, including ldh and atoB, increased significantly during moderate degradation. Denitrification genes, including narG, nirK, norB, and nosZ, reached their highest abundance during the heavy degradation stage. Mineral-associated organic carbon exhibited a nonlinear pattern characterized by an initial increase followed by a decrease. Structural equation modeling revealed that microbial biomass carbon was the central variable linking microbial functional differentiation with changes in soil carbon and nitrogen pools. During the heavy degradation stage, soil ammonium nitrogen showed a numerical increase, suggesting that nitrogen released from mineral-associated organic carbon decomposition may be predominantly converted into inorganic forms.

DISCUSSION: These findings indicate that the threshold-like decline of microbial biomass carbon, rather than specific restructuring of functional gene profiles, was closely associated with the collapse of stable carbon-nitrogen pool stability during grassland degradation. Changes in functional genes may therefore represent responsive signals accompanying microbial biomass carbon attenuation. The continuous decrease in microbial biomass carbon and associated shifts in functional gene ratios may serve as potential indicators of declining carbon-nitrogen stability in grassland soils.},
}

@article {pmid42487710,
year = {2026},
author = {Zhili, G and Jie, L and Yuyue, X and Fang, Y and Dianqun, R and Qin, Z and Xiaojun, L},
title = {Fecal metagenomic profiling in patients with colorectal adenomas to characterize gut microbial composition and functional potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842365},
pmid = {42487710},
issn = {1664-302X},
abstract = {OBJECTIVE: To investigate differences in gut microbiota between patients with colorectal adenoma (CRA) and healthy individuals using metagenomic sequencing, and to analyze the correlation between microbial abundance and polyp diameter and number.

METHODS: Metagenomic sequencing was performed on fecal samples from 60 patients with CRA and 30 healthy controls. Species-level and functional analyses of the gut microbiome were conducted.

RESULTS: Metagenomic profiling revealed a distinct microbial signature in CRA. Statistical analysis identified significant differences in taxonomic composition between the two groups. Overall, 487 genes showed significant abundance differences. Among these, approximately 55.37% were significantly enriched in the adenoma group, suggesting specificity for CRA, while 175 genes were significantly reduced. Alpha diversity analysis indicated similar microbial richness and evenness between the groups, whereas beta diversity confirmed significant structural differences in the microbial community. KEGG enrichment analysis of the top 20 differentially abundant species showed that these microbes were primarily associated with metabolic pathways. The greater number of increased versus decreased genes implied a more pronounced expansion of pathogenic bacteria relative to the loss of beneficial bacteria. Linear discriminant analysis effect size (LEfSe) analysis indicated that Fusobacterium nucleatum, Alistipes, and Bacteroides fragilis could serve as diagnostic microbial biomarkers for CRA. LEfSe further identified 38 differentially abundant bacterial clades, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides enriched in patients. Finally, correlation analysis linked the abundance of specific microbial taxa with polyp number and diameter.

CONCLUSION: This study confirms distinct gut microbiota profiles in patients with CRA compared with healthy individuals, highlights significant microbiome alterations associated with CRA, and reveals novel correlations between specific microorganisms and polyp characteristics, suggesting that microbial changes may contribute to adenoma development.},
}

@article {pmid42487713,
year = {2026},
author = {Chen, M and Zhang, S and Lu, M and Zhu, D and Xiao, M and Liao, Y and Li, Y and Zhou, T and Wang, M and Song, Q},
title = {Age-associated gut microbiome succession, colonization resistance, and relative resistome patterns in an antibiotic-restricted infant cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862116},
pmid = {42487713},
issn = {1664-302X},
abstract = {BACKGROUND: Early infancy is critical for gut microbiome assembly and the establishment of colonization resistance against pathobionts. Whether age-associated microbiome maturation is accompanied by changes in colonization-resistance proxies and relative antimicrobial resistance gene profiles under low infant antibiotic exposure remains unclear.

METHODS: We analyzed shotgun metagenomes from 82 fecal samples collected from 54 healthy infants (54 at 1 month and 28 at 6 months). Taxonomic and functional profiles were generated using MetaPhlAn 4 and HUMAnN3, and AMR genes were annotated using RGI/CARD. Age-associated taxa were screened by LEfSe and tested using MaAsLin2 with adjustment for key perinatal covariates.

RESULTS: Age group was associated with modest but statistically significant differences in community structure (Bray-Curtis PERMANOVA R [2] = 0.03, p = 0.005) and higher species richness at 6 months (p < 0.001), with no statistically significant difference in Shannon or Simpson indices. In adjusted models, skin-associated pioneer taxa, including Staphylococcus epidermidis, were lower at 6 months, whereas several anaerobic or oral-associated taxa were higher, including Flavonifractor plautii. Enterobacteriaceae relative abundance was lower at 6 months than at 1 month (median 16.64 vs. 1.86%, p < 0.001), and Bifidobacterium-Enterobacteriaceae antagonism indices were higher. However, Escherichia coli and Klebsiella spp. did not show significant genus-level reductions. Copies per million (CPM)-normalized β-lactamase (bla) relative abundance showed no statistically significant timepoint difference and was positively correlated with selected Bifidobacterium species.

CONCLUSIONS: In this infant antibiotic-restricted cohort, microbiome profiles at 6 months were associated with lower relative abundance of potential pathobionts and higher colonization-resistance proxy indices. CPM-normalized bla relative abundance showed no statistically significant timepoint difference. These observational findings do not establish the genomic host or mobility of bla genes. Quantitative and host-resolved studies are needed to distinguish compositional shifts from absolute resistome trajectories.},
}

@article {pmid42487715,
year = {2026},
author = {Zlatnar, M and Alves, RP and Toledo, GV and Wicaksono, WA and Berg, G},
title = {Metagenomic analysis reveals functional potential and storage-driven dynamics of the Kalamata olive microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1890405},
pmid = {42487715},
issn = {1664-302X},
abstract = {BACKGROUND: Fermented olives are a staple of the Mediterranean diet due to their nutritional value. Despite advances in olive microbiome research, published research on the functional contributions of fermented food-associated microbiota and the impact of storage on these microbial communities remains limited.

METHODS: We studied the bacterial communities of ready-to-eat Kalamata olives, stored in glass jars or vacuum-sealed bags at various temperatures (4°C, 8°C and 15°C) for 55-day period. The bacterial abundance, taxonomical composition and functional potential were analyzed by quantitative PCR and amplicon sequencing of 16 rRNA gene, and metagenome sequencing.

RESULTS: The microbiota was dominated by Lactobacillaceae (94.6%), a family of lactic acid bacteria (LAB), with dominant genera such as Pediococcus, Lactiplantibacillus and Secundilactobacillus. At the functional level, bacterial genes involved in the biosynthesis of vitamins B1, B2, B5, B7, B9, B12, and vitamin K, as well as short-chain fatty acid metabolism, were observed. Importantly, those functions were not restricted to LAB, underscoring the potential functional contribution of non-LAB taxa to the olive microbiome. Despite conservation, post-fermentation storage, especially the incubation time, temperature, and packaging, influenced the bacterial communities. Lactic acid bacteria were enriched in olives stored at 15°C, whereas non-LAB taxa proliferated more at lower temperatures.

CONCLUSION: Our study showed that Kalamata olives contain a highly abundant and diverse microbiota that responds to storage practices and carries genes encoding functions that may contribute to the characteristics and quality of the fermented product.},
}

@article {pmid42487717,
year = {2026},
author = {Li, X and Ke, L and Wang, T and Lei, Z and Tian, F and Zhang, Y and Liu, X},
title = {Shared and condition-associated gut microbiota alterations in older adults with depression and constipation: evidence from the American Gut Project.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1891231},
pmid = {42487717},
issn = {1664-302X},
abstract = {BACKGROUND: Constipation and depression frequently co-occur in older adults, and growing evidence suggests that gut microbiota dysbiosis may be a shared feature of both conditions. The microbiota has well-established roles in gastrointestinal motility and gut-brain axis signaling, and compositional alterations have been independently reported in each condition. However, whether older adults with constipation and those with depression share common microbiota characteristics have not been systematically investigated.

AIM: This study aimed to characterize gut microbiota alterations in older adults with depression or constipation using 16S rRNA amplicon sequencing data from the American Gut Project, focusing on microbial features shared by, or specific to, the two conditions.

METHODS: We retrieved fecal 16S rRNA sequencing data from 513 older adults in the publicly available American Gut Project database, including HC (n = 277), DP (n = 78), and CP (n = 158). We compared alpha and beta diversity, taxonomic composition, and genus-level differential abundance among groups, used random forest models to explore features contributing to group discrimination, and performed covariate-adjusted and sensitivity analyses to assess robustness.

RESULTS: Alpha diversity was comparable among groups, whereas beta diversity revealed detectable differences in community composition. After adjustment for age, sex, and BMI, Bray-Curtis-based differences remained evident, with the most consistent pairwise difference between CP and HC. At the genus level, CP showed depletion of health-associated butyrate-producing taxa and enrichment of selected mucin- or inflammation-associated taxa, whereas DP was characterized by enrichment of Erysipelatoclostridium and [Ruminococcus]_gnavus_group and depletion of UCG-002 and selected health-associated genera. Random forest analyses further identified key microbial contributors to group discrimination.

CONCLUSION: We identified subtle and partially overlapping genus-level microbiota alterations in older adults with constipation and depression, with constipation showing the most consistent differences from healthy controls. These findings provide exploratory evidence that selected microbiota alterations may be relevant to the clinical overlap between the two conditions, although their functional roles require validation in longitudinal studies integrating metagenomic and metabolomic profiling.},
}

@article {pmid42487961,
year = {2026},
author = {Li, X and Wang, J and Wang, J and Yang, J and Li, Y and Li, Y and Liu, B},
title = {Pulmonary function impairment patterns and their clinical correlates in patients with pulmonary tuberculosis complicated by pulmonary infection: a single-center retrospective cross-sectional study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1870280},
pmid = {42487961},
issn = {2296-858X},
abstract = {BACKGROUND AND OBJECTIVE: Pulmonary tuberculosis is a major cause of respiratory morbidity worldwide, and pulmonary function impairment is increasingly recognized as an important consequence of the disease. However, the functional patterns of pulmonary impairment in patients with pulmonary tuberculosis complicated by pulmonary infection, especially in hospitalized populations, remain insufficiently characterized. This study aimed to describe pulmonary function impairment patterns in such patients and to explore their clinical correlates.

METHODS: This single-center retrospective cross-sectional study included hospitalized patients with pulmonary tuberculosis complicated by pulmonary infection who were admitted between November 2024 and October 2025, underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing, and had interpretable pulmonary function results. The analysis was retrospective because all study variables were extracted from pre-existing hospitalization records and database entries rather than being prospectively collected for the present pulmonary function study. Although the parent project is an ongoing prospective study with follow-up, no longitudinal follow-up data were used in the present analysis. Clinical, laboratory, immunologic, gas-exchange, microbiological, and pulmonary function data were extracted from the institutional database and electronic medical records.

RESULTS: A total of 72 patients were included. Pulmonary function abnormalities were common. Diffusion impairment was the most frequent phenotype, occurring in 37 patients (51.4%), followed by reduced respiratory reserve in 36 (50.0%) and obstructive ventilatory impairment in 30 (41.7%). Restrictive ventilatory impairment, mixed ventilatory impairment, and small airway dysfunction were less common. Patients with diffusion impairment were more likely to be male than those without diffusion impairment (73.0% vs. 42.9%, P = 0.019), and smoking history showed a borderline between-group difference. Patients with reduced respiratory reserve had significantly higher IL-6 levels than those without reduced respiratory reserve [13.18 (5.52-38.00) vs. 4.53 (1.94-12.28) pg/ml, P = 0.005]. In exploratory multivariable analysis, no variable was independently associated with diffusion impairment or reduced respiratory reserve after adjustment, although lymphocyte count showed a non-significant positive trend for diffusion impairment.

CONCLUSION: Pulmonary function impairment was highly prevalent in patients with pulmonary tuberculosis complicated by pulmonary infection, with diffusion impairment and reduced respiratory reserve as the predominant phenotypes. These findings suggest that pulmonary dysfunction in this population extends beyond conventional ventilatory defects and may involve substantial abnormalities in gas transfer and respiratory capacity. Comprehensive pulmonary function assessment may provide clinically relevant information for functional evaluation and individualized management in this patient group.},
}

@article {pmid42488200,
year = {2026},
author = {Nayak, SK and Bhattacharyya, P and Pradhan, C and Tripathy, PS and Padhy, SR and Parida, SP and Moharana, A and Rath, M and Nayak, A and Dash, SS and Das, SK and Priya, H},
title = {Identification of key carbon-fixation pathways and underlying genes for higher CO2 fixation of mangrove-associated microalgae.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {350},
pmid = {42488200},
issn = {2190-572X},
abstract = {UNLABELLED: Mangrove systems are major blue-carbon reservoirs, storing 4.4 to 11.7 petagrams of organic carbon globally and supporting diverse microalgal communities that drive primary productivity and coastal carbon cycling. The Sundarban, one of the world's largest (3,629.57 km[2]) mangrove-dominated coastal systems, holds a substantial carbon stock (26.62 Tg). Rising salinity and anthropogenic pressure are altering the diversity of microalgal communities, highlighting the importance of identifying resilient taxa capable of sustaining carbon fixation. To address this need, we conducted whole-genome metagenomic profiling of degraded mangrove soils. The data revealed six dominant microalgal taxa adapted to prevailing salinity and nutrient stress. These six taxa were subsequently isolated from the same habitats, and a 16-day ambient CO2 (420 ppm) screening was undertaken to evaluate the specific growth rate and biomass gain of the algae. Among them, three physiologically resilient strains Chlorella sp., Limnospira platensis, and Leptolyngbya boryana were selected for controlled CO2-enrichment concentrations (0.04%, 0.05%, 0.20%, 10%) to mimic future climate change scenarios. Among those microalgae, the Leptolyngbya boryana showed the highest biomass yield (1.31 g L[-1]), carbon content (0.52 g C g[-1] dry weight), and CO2-fixation rate (up to 149 mg CO2 L[-1] d[-1]). Metagenomic analysis further identified that L. boryana possessed the strongest representation of carbon-fixation pathways like Calvin-Benson-Bassham (CBB) cycle and the reductive TCA (rTCA) cycle, regulated by enriched key genes such as cbbL, cbbS, gap2, zwf, and accC. Therefore, this result positions L. boryana as a promising microalgal candidate for carbon sequestration in future CO2-rich environments under saline coastal ecology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04986-7.},
}

@article {pmid42488424,
year = {2026},
author = {Ni, Y and Wu, W and Liu, J and Feng, C and Jin, B and Zhao, T and Gu, Y and Su, X and Li, C and Yuan, X},
title = {Clinical diagnostic value of targeted next generation sequencing for lower respiratory tract infection: a retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1713445},
pmid = {42488424},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Aged ; Metagenomics/methods ; Sensitivity and Specificity ; Fungi/genetics/classification/isolation & purification ; Viruses/classification/genetics/isolation & purification ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) progress swiftly and require timely, accurate pathogen detection to enhance patient outcomes. This study aims to utilize the targeted metagenomic next-generation sequencing (tNGS) technology as a novel approach to investigate the types of pathogens involved in infections following different structural lung diseases.

METHODS: This retrospective cohort study enrolled 329 patients with suspected LRTIs admitted to three medical centers from June 2023 and June 2024. The study analyzed the pathogenic spectrum of lung infections and compared the diagnostic outcomes of tNGS with those of conventional microbiological techniques (CMTs).

RESULTS: tNGS demonstrated significantly higher sensitivity (97.8% vs. 28.9%, p<0.05) and accuracy (96.6% vs. 30.3%, p<0.05) than CMTs, along with a high concordance rate (87.8%) with clinically confirmed pathogens. Pathogen profiling revealed that Mycoplasma pneumoniae (21.88%), Aspergillus fumigatus (5.17%), and influenza A virus subtype H3N2 (13.07%) were the predominant bacterial, fungal, and viral pathogens, respectively. Several key pathogens, including Pseudomonas aeruginosa, Haemophilus influenzae, Nocardia abscessus, Aspergillus fumigatus, Influenza A virus H3N2, and Influenza B virus, were detected more frequently in the SLD group than in the non-SLD group. Among 193 patients whose treatment was adjusted based on tNGS results, 35.2% initiated new treatment regimens, 25.4% continued their original treatment, and 7.3% required treatment escalation, with 90.2% of these patients showing clinical improvement.

CONCLUSION: These findings showed that tNGS demonstrates significant promise for the etiological diagnosis and tailored management of LRTIs.},
}

Humans
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Respiratory Tract Infections/diagnosis/microbiology/virology
Female
Male
Bacteria/genetics/classification/isolation & purification
Middle Aged
Aged
Metagenomics/methods
Sensitivity and Specificity
Fungi/genetics/classification/isolation & purification
Viruses/classification/genetics/isolation & purification

@article {pmid42488460,
year = {2026},
author = {Gangwar, P and Xu, Q and Seangmany, J and Katte, P and Turakhia, Y},
title = {metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag080},
pmid = {42488460},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Phylogeny ; *Haplotypes ; Humans ; *Software ; Biological Specimen Banks ; },
abstract = {Metagenomic sequencing is transforming diverse areas of health and biological sciences, including pathogen surveillance, clinical diagnostics, and microbiome research. However, the inherent complexity of metagenomic data limits most computational tools to species-level classification and abundance estimation, overlooking within-species genetic diversity that drives key phenotypes. We present metaWEPP, a novel computational pipeline that achieves near-haplotype resolution in metagenomic analysis for species with adequate representation in reference genome biobanks and having sufficient sequencing depth and genome coverage. Specifically, metaWEPP assigns sequencing reads to species using standard taxonomic classifiers, phylogenetically places them onto species-specific mutation-annotated trees of publicly available sequences, and selects the haplotypes that best explain the sample. It also reports unaccounted alleles indicative of novel variants and provides an interactive dashboard for read-level visualization. Applied to diverse metagenomic and mixed-genome samples from prior studies, metaWEPP produced concordant species-level results, while revealing finer lineage- and haplotype-level insights not captured by existing tools. On various clinical samples, metaWEPP identified infecting pathogens and additionally provided credible lineage- and haplotype-level information that can support clinical decision-making. On wastewater samples, metaWEPP uncovered previously undetected haplotype clusters of epidemiological relevance. These findings demonstrate metaWEPP's ability to advance various clinical, epidemiological, and research applications with deeper, actionable insights.},
}

*Metagenomics/methods
*Phylogeny
*Haplotypes
Humans
*Software
Biological Specimen Banks

@article {pmid42488632,
year = {2026},
author = {Long, T and Song, J and Li, SG},
title = {Case Report: Hemophagocytic lymphohistiocytosis after SARS-CoV-2 infection revealing clinically diagnosed stage IVB diffuse large B-cell lymphoma in quiescent adult-onset Still's disease.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1879628},
pmid = {42488632},
issn = {1664-3224},
mesh = {Humans ; Male ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/drug therapy ; Aged ; *COVID-19/complications ; SARS-CoV-2 ; *Lymphoma, Large B-Cell, Diffuse/diagnosis/drug therapy/complications/pathology ; *Still's Disease, Adult-Onset/complications/drug therapy/diagnosis ; Rituximab/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; },
abstract = {BACKGROUND: Adult hemophagocytic lymphohistiocytosis (HLH) may be triggered by infection, malignancy, or systemic inflammatory disease. Attribution is challenging when recent SARS-CoV-2 infection, quiescent adult-onset Still's disease (AOSD), and an occult B-cell clonal disorder coexist.

CASE REPORT: A 71-year-old man with AOSD controlled for 14 years on low-dose methotrexate developed persistent fever and fatigue after mild SARS-CoV-2 infection. He subsequently developed cytopenias, hyperferritinemia, markedly elevated lactate dehydrogenase, diffuse FDG-avid lymphadenopathy, hepatosplenomegaly, elevated soluble interleukin-2 receptor, reduced natural killer-cell activity, and bone marrow hemophagocytosis, fulfilling HLH criteria. Broad pathogen evaluation, including blood and bone marrow metagenomic next-generation sequencing, did not identify an alternative infectious trigger. Bone marrow histopathology did not show definite tumor cells; however, flow cytometry identified monoclonal mature B cells, and peripheral-blood smear high-throughput sequencing detected lymphoma-associated mutations including MYD88, CD79B, IGLL5, PRDM1, DTX1, DUSP2, and BTG1. Multidisciplinary consultation favored probable lymphoma-associated HLH with clinically diagnosed stage IVB diffuse large B-cell lymphoma. HLH-directed therapy followed by rituximab-based lymphoma-directed chemotherapy led to transient clinical improvement, but the patient later died from infectious complications.

CONCLUSION: Mild SARS-CoV-2 infection may act as a co-trigger or unmasking event rather than the sole cause of HLH. Persistent high lactate dehydrogenase and soluble interleukin-2 receptor, diffuse lymphadenopathy, clonal mature B cells, lymphoma-associated mutations, and negative broad pathogen testing should prompt evaluation for occult lymphoma-associated HLH.},
}

Humans
Male
*Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/drug therapy
Aged
*COVID-19/complications
SARS-CoV-2
*Lymphoma, Large B-Cell, Diffuse/diagnosis/drug therapy/complications/pathology
*Still's Disease, Adult-Onset/complications/drug therapy/diagnosis
Rituximab/therapeutic use
Antineoplastic Combined Chemotherapy Protocols/therapeutic use

@article {pmid42488664,
year = {2026},
author = {Chen, M and Zhou, H and Zhou, Z and He, Y and Jiang, Y},
title = {Clinical features of Q fever confirmed by plasma metagenomic next-generation sequencing.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847365},
pmid = {42488664},
issn = {1664-3224},
mesh = {Humans ; *Q Fever/immunology/blood/diagnosis/microbiology/genetics ; Male ; Middle Aged ; Female ; Retrospective Studies ; *Coxiella burnetii/immunology ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Adult ; Autoantibodies/blood/immunology ; Fever ; Aged ; Antibodies, Antiphospholipid/blood ; },
abstract = {BACKGROUND: The clinical features of acute Q fever and their link to transient autoantibodies remain poorly defined. We characterized 44 plasma mNGS-confirmed cases and identified predictors of prolonged fever.

METHODS: Retrospective study (2021-2026) of 44 patients with confirmed Q fever (mNGS + clinical + exposure criteria). Patients were grouped by post-treatment fever duration (>7 days vs. ≤7 days).

RESULTS: Cohort was predominantly middle-aged (median 52.5 years) and male (95.5%). Common presentations: fever (95.5%), headache (45.5%), pulmonary involvement (51.2%). Elevated CRP (97.7%) and ESR (90.9%) were universal. Transient antiphospholipid antibodies (78.9%, all negative at 12 weeks) and ANA (23.5%) were frequent. Prolonged fever (>7 days) was associated with higher WBC, CRP, ESR, lower CD8+ and B cells, and aPL positivity (all p<0.05).

CONCLUSIONS: Acute Q fever frequently induces transient autoantibodies. Prolonged fever correlates with an inflammatory and lymphopenic phenotype, underscoring immune dysregulation in recovery.},
}

Humans
*Q Fever/immunology/blood/diagnosis/microbiology/genetics
Male
Middle Aged
Female
Retrospective Studies
*Coxiella burnetii/immunology
*Metagenomics/methods
High-Throughput Nucleotide Sequencing
Adult
Autoantibodies/blood/immunology
Fever
Aged
Antibodies, Antiphospholipid/blood

@article {pmid42488891,
year = {2026},
author = {Slullitel, PA and Lohmann, FA and Albani-Forneris, AF and Buljubasich, M and García-Mansilla, AM and Salagoity, F and Lucero, CM and Comba, F and Zanotti, G and Piñero, TA and Buttaro, MA},
title = {The Gut-Joint Axis in Hip Osteoarthritis: Distinct Articular Microbial Profiles and Metabolic Potential Compared With Nonarthritic Controls.},
journal = {JB & JS open access},
volume = {11},
number = {3},
pages = {},
pmid = {42488891},
issn = {2472-7245},
abstract = {BACKGROUND: Intestinal dysbiosis and systemic microbial translocation potentially contribute to chronic joint inflammation. However, the role of the gut-joint axis in the genesis of osteoarthritis still needs to be elucidated. This investigation characterized taxonomic signatures and proinflammatory metabolic pathways within the hip joint to define their contribution to the pathophysiology of osteoarthritis relative to nonarthritic controls.

METHODS: A prospective cohort of 48 patients undergoing hip arthroplasty was enrolled. Specimens including synovial fluid, articular cartilage, and acetabular fossa tissue were collected from patients with primary hip osteoarthritis (n = 20) and femoral neck fracture (n = 20). Metagenomic profiling was performed using 16S-rRNA gene sequencing (V3-V4 region). Alpha and beta diversity, taxonomic composition, and predicted functional pathways (PICRUSt2) were compared based on diagnosis (arthritis vs. fracture) and sample location.

RESULTS: Osteoarthritic samples demonstrated reduced alpha diversity evenness compared with fracture controls (p = 0.031). While beta diversity was primarily driven by specimen type rather than diagnosis, significant taxonomic differences were observed at the genus level. Pseudomonas, Atopostipes, and Staphylococcus showed significant differential abundance between groups, both by specimen location and diagnosis. Functional predictive analysis revealed a marked enrichment of the KDO2-lipid A biosynthesis pathway in osteoarthritic specimens, specifically within the genus Pseudomonas. Key genes involved in lipopolysaccharide biosynthesis and export, including lpxB, lpxL, and lpxM, exhibited significantly higher median abundances in osteoarthritic joints compared with controls (p < 0.00000001).

CONCLUSIONS: Patients with hip osteoarthritis exhibited specific taxonomic and predicted lipopolysaccharide-related pathways differences compared with nonarthritic controls, consistent with microbial molecular signatures in a noninfectious inflammatory joint environment, despite the absence of major diagnosis-driven community-level differences.

LEVEL OF EVIDENCE: Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.},
}

@article {pmid42488935,
year = {2026},
author = {Whelan, FJ},
title = {How the social lives of bacteria affect their pangenome.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250039},
pmid = {42488935},
issn = {1744-1358},
support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; },
abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.},
}

@article {pmid42488938,
year = {2026},
author = {Kraft, TS and Venkataraman, VV and Gurven, M and Suratman, MN and Goldberg, TL},
title = {Ethno-etiology meets virology: land leeches (family: Haemadipsidae) as potential disease vectors.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/trag077},
pmid = {42488938},
issn = {1878-3503},
support = {//American Association of Biological Anthropologists/ ; //University of Wisconsin-Madison/ ; //John D. MacArthur Professorship Chair/ ; },
abstract = {OBJECTIVES: Hematophagous terrestrial leeches are common in rainforest habitats and widely regarded as pests. Despite limited research, circumstantial evidence raises the possibility that, beyond being an annoyance, terrestrial leeches could potentially transmit diseases.

METHODS: We explored this possibility using multiple approaches. First, we reviewed published literature to synthesize knowledge related to disease transmission by leeches. Second, we collected terrestrial leeches (genus Haemadipsa) from human-occupied rainforests in Peninsular Malaysia and applied metagenomic methods for virus discovery to their anterior segments. Finally, we conducted interviews to probe local knowledge and behavior related to leeches, testing whether cultures may encode information that recognizes and helps to prevent vector-borne disease transmission.

RESULTS: Results indicate that terrestrial leeches are potential disease vectors, particularly via mechanical vector-borne transmission stimulated by human removal techniques. Supporting this, we identified four novel viruses within leeches, three of which are distantly related to medically important animal and human viruses which could potentially be transmitted among animal species, including humans. However, ethno-etiological evidence suggests that local Indigenous cultures do not recognize land leeches as disease vectors or promote behaviors likely to reduce transmission, suggesting knowledge may not encompass difficult-to-observe vectors.

CONCLUSION: We conclude that disease transmission by terrestrial leeches is plausible and merits experimental study. Accession numbers: PX094876, PX118495, PX118496, PX118497, PX118498, PX118499.},
}

@article {pmid42489029,
year = {2026},
author = {Ma, R and Guo, G and Liu, C and Deng, P and Dong, X and Mu, L and Qu, Q and Hu, X},
title = {Microplastic Pollution Is Associated with Fragmentation and Environmental Sensitivity of Marine Planktonic Microbial Communities.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c06158},
pmid = {42489029},
issn = {1520-5851},
abstract = {The effects of increasing marine microplastic (MP) pollution on the microbial community structure and function remain uncertain, particularly under natural conditions. Specifically, our study focuses on free-living marine microbial communities (0.8-5 μm) rather than plastisphere biofilms. Here, we systematically evaluated differences in microbial community responses to environmental gradients across MP concentration regimes on the basis of a response modulation analysis framework (RMAF). In this framework, co-occurrence network analysis, random forest modeling, and SHapley Additive exPlanations (SHAP) and partial dependence-based interpretation methods are integrated to quantify changes in microbial sensitivity and ecological interactions. Through the use of Tara Oceans metagenomic data, we analyzed seven functional gene categories and species diversity across MP concentration gradients. High-MP environments (with concentrations exceeding 5,500 items·km[-2]) were characterized by a notable decrease in nondominant taxa (from 17-21% to 6.53-9.45%) alongside increased dominance of abundant species. The functional profiles showed higher abundance levels of genes involved in carbon, nitrogen, and sulfur cycling. The results of network analysis indicated reduced connectivity and increased fragmentation, suggesting weakened ecological interactions and decreased system stability. Microbial communities in high-MP environments exhibited increased sensitivity to environmental drivers, characterized by response centralization and niche compression, suggesting a narrower range of environmental responses. MPs were associated with high microbial functional activity and potential indications of low ecosystem resilience.},
}

@article {pmid42489451,
year = {2026},
author = {Roques, S and Tournayre, J and Dou, PS and Yanibada, B and Boudra, H and Popova, M and Morgavi, DP},
title = {Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026926},
doi = {10.1128/spectrum.00269-26},
pmid = {42489451},
issn = {2165-0497},
abstract = {Enteric methane emission from dairy cattle is an environmental challenge. The most efficient mitigation strategies nowadays include the use of methanogenesis inhibitors that specifically target the rumen methanogens. Specific inhibitors, such as 3-nitrooxypropanol (3-NOP), reduce methane emissions without negative effects on the products of fermentation that serve as energy metabolites for the host. However, the concomitant effects of methanogenesis inhibition on rumen microbiota and host metabolism are poorly characterized. Thus, the objective of this study was to explore the association between rumen microbiota and host metabolism when methanogenesis is inhibited. Thirteen dairy cows were used as controls, and 12 were supplemented with 3-NOP for 6 weeks. Rumen microbiota composition and activity were characterized using metagenomics and metatranscriptomics. The host metabolism was assessed in a previous publication by a metabolomic analysis of the plasma. Microbiota data were used as explanatory variables of the metabolome data in a multiblock sparse partial least squares analysis. Overall, the association between rumen microbiota and host metabolism was moderate. Notwithstanding this, a few downregulated transcripts related to glycolysis, hydrogen transfer, and protein synthesis, together with a decrease in the proportion of taxa of the Oscillospirales order, showed a correlation with host one-carbon metabolites (|r| > 0.6). These associations raised novel hypotheses that remain to be elucidated, especially with regard to the effects of dihydrogen on the accumulation of microbial glycolysis and methanogenesis metabolite intermediates.IMPORTANCEDairy cattle produce a substantial amount of methane, a potent greenhouse gas. Several strategies have been designed to reduce methane production by targeting the rumen microbiota. One such strategy specifically inhibits methanogens with a molecule called 3-nitrooxypropanol. This study uses an integrative data analysis approach, combining rumen microbiota and host metabolome information, to explore the consequences of inhibiting methanogenesis on the holobiont. This provides additional holistic insight into the effect of methane mitigation strategies on dairy cattle.},
}

@article {pmid42489455,
year = {2026},
author = {Aguilar-Rangel, EJ and Lüneberg, K and Medina, DA and Siebe, C and Alcántara-Hernández, RJ and Servín-Garcidueñas, LE},
title = {Metagenomes from untreated wastewater and the soil irrigated with it for 50 years in the Mezquital Valley, Mexico.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129925},
doi = {10.1128/mra.01299-25},
pmid = {42489455},
issn = {2576-098X},
abstract = {The Mezquital Valley is a unique site for studying the gradual effects of wastewater irrigation on agricultural soils. We report metagenomes from soils irrigated for 50 years and their corresponding irrigation water. Potentially pathogenic bacteria dominated the wastewater, while the soil harbored a diverse community mainly involved in biogeochemical cycling.},
}

@article {pmid42489464,
year = {2026},
author = {Mori, K and Nishimura, Y and Ijichi, M and Iwahashi, Y and Sudo, S and Yoshizawa, S},
title = {Metagenome-assembled genomes from time-series samples of artificial seawater aquarium water.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0069526},
doi = {10.1128/mra.00695-26},
pmid = {42489464},
issn = {2576-098X},
abstract = {We report 804 metagenome-assembled genomes (MAGs) reconstructed from a water conditioning tank during the establishment of an artificial seawater aquarium at SEA LIFE Nagoya. These MAGs were assigned to 27 phyla (26 bacterial phyla and 1 archaeal phylum), providing a genome-resolved resource for investigating the microbial diversity of artificially managed marine environments.},
}

@article {pmid42489979,
year = {2026},
author = {Zhao, Z and Zhao, Y and Sun, Y and Bao, Y and Feng, J and Jiang, T and Lin, A},
title = {Metagenomic screening of antimicrobial peptide candidates and isolation of two active peptides from bat gut bacteria.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42489979},
issn = {1573-0972},
support = {32430066, 32271558, 32571749//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Antimicrobial Peptides/pharmacology/isolation & purification/genetics/chemistry ; Microbial Sensitivity Tests ; Metagenomics/methods ; *Chiroptera/microbiology ; Anti-Bacterial Agents/pharmacology/isolation & purification ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Bacteriocins/pharmacology/isolation & purification/genetics ; Amino Acid Sequence ; Tandem Mass Spectrometry ; Metagenome ; },
abstract = {Bacterial antibiotic resistance has intensified the need to identify new antimicrobial molecules from underexplored microbial systems. Wild mammalian gut microbiota may harbor antimicrobial peptide (AMP) candidates and candidate bacteriocins, but these systems remain poorly investigated as sources for antimicrobial discovery. Here, we used parallel metagenomic and culture-dependent approaches to explore candidate AMP sequences and candidate bacteriocins from the gut bacteria of the Asian particolored bat Vespertilio sinensis. Machine-learning screening of 553,401 short non-redundant ORF protein sequences identified 12,907 candidate AMP sequences. Of these, 31 were prioritized after in silico safety and structural filtering. In parallel, culture-dependent screening yielded two antagonistic bacterial isolates, CQJ and LYS. Activity-guided purification followed by LC-MS/MS identified two active peptides, CQJ01 and LYS01, with no exact matches in public databases. Both peptides exhibited broad in vitro antibacterial activity against 16 pathogenic strains, with minimum inhibitory concentration (MIC) values as low as 8 µg/mL against selected Gram-positive and Gram-negative bacteria. CQJ01 retained activity across pH 2-9 and after heat treatment up to 80 °C, whereas LYS01 retained activity from - 20 °C to 100 °C. Both peptides remained active after catalase, trypsin, papain, and proteinase K treatments but were sensitive to pepsin. They showed low hemolytic activity and limited cytotoxicity in preliminary assays. These findings support bat gut bacteria as an underexplored source of AMP candidates and candidate bacteriocins.},
}

Animals
*Antimicrobial Peptides/pharmacology/isolation & purification/genetics/chemistry
Microbial Sensitivity Tests
Metagenomics/methods
*Chiroptera/microbiology
Anti-Bacterial Agents/pharmacology/isolation & purification
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/drug effects
Bacteriocins/pharmacology/isolation & purification/genetics
Amino Acid Sequence
Tandem Mass Spectrometry
Metagenome

@article {pmid42490446,
year = {2026},
author = {Löwe, J and von Kügelgen, A and Planelles-Herrero, VJ and McAndrew, MBL and Oliva, MA and Vosseberg, J and Köstlbacher, S and Dharamshi, JE and Appler, KE and MacLeod, FI and Nobs, SJ and Jørgensen, SL and Burns, BP and Baker, BJ and Bharat, TAM and Derivery, E and Tamarit, D and Ettema, TJG},
title = {Eukaryotic-like microtubules and dynamic instability of Asgard archaeal tubulins.},
journal = {Science advances},
volume = {12},
number = {30},
pages = {eaeh1082},
doi = {10.1126/sciadv.aeh1082},
pmid = {42490446},
issn = {2375-2548},
mesh = {*Tubulin/metabolism/chemistry/genetics ; *Microtubules/metabolism/chemistry ; *Archaea/metabolism/genetics ; Phylogeny ; *Archaeal Proteins/chemistry/metabolism/genetics ; Models, Molecular ; Eukaryota/metabolism ; },
abstract = {Eukaryotic cells change their shapes, actively segregate their DNA, and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins because actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our previously unidentified heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.},
}

*Tubulin/metabolism/chemistry/genetics
*Microtubules/metabolism/chemistry
*Archaea/metabolism/genetics
Phylogeny
*Archaeal Proteins/chemistry/metabolism/genetics
Models, Molecular
Eukaryota/metabolism

@article {pmid42490589,
year = {2026},
author = {Torgerson, EG and Adams, M and Lock, LR and Simonis, MC and Dyer, KE and Vicente-Santos, A and Fenton, MB and Simmons, NB and Becker, DJ and Achee, NL},
title = {Neotropical bats as sentinels for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {7},
pages = {e0013851},
pmid = {42490589},
issn = {1935-2735},
mesh = {Animals ; *Chiroptera/parasitology ; High-Throughput Nucleotide Sequencing ; *Trypanosoma cruzi/isolation & purification/genetics ; Metagenomics ; *Zoonoses/parasitology/epidemiology ; Belize/epidemiology ; *Chagas Disease/veterinary/epidemiology/parasitology ; *Communicable Diseases, Emerging/epidemiology/parasitology/veterinary ; Disease Reservoirs/parasitology ; Humans ; },
abstract = {Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as sentinels that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we conducted an exploratory study surveying the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi, which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis. qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as sentinels.},
}

Animals
*Chiroptera/parasitology
High-Throughput Nucleotide Sequencing
*Trypanosoma cruzi/isolation & purification/genetics
Metagenomics
*Zoonoses/parasitology/epidemiology
Belize/epidemiology
*Chagas Disease/veterinary/epidemiology/parasitology
*Communicable Diseases, Emerging/epidemiology/parasitology/veterinary
Disease Reservoirs/parasitology
Humans

@article {pmid42490944,
year = {2026},
author = {Song, Y and Wang, H and Lin, L and Cheng, Y and Shen, Y},
title = {Clinical characteristics and outcomes of severe Legionella pneumophila pneumonia diagnosed by metagenomic next-generation sequencing in children: a case series of 8 patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1865333},
doi = {10.3389/fcimb.2026.1865333},
pmid = {42490944},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; *Legionella pneumophila/genetics/isolation & purification ; *Legionnaires' Disease/diagnosis/drug therapy/microbiology ; Infant ; Child, Preschool ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Infant, Newborn ; Anti-Bacterial Agents/therapeutic use ; Child ; Community-Acquired Pneumonia ; Treatment Outcome ; China ; },
abstract = {INTRODUCTION: Severe Legionella pneumophila (LP) pneumonia is exceedingly rare in children, and clinical data remain scarce.

METHODS: We retrospectively analyzed the clinical data of 8 children with severe LP pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) at Henan Children's Hospital between January 2020 and January 2026.

RESULTS: The cohort comprised 3 males and 5 females with a median age of 74 days (range, 8 days to 9 years); neonates accounted for 50.0% (4/8), and 75.0% (6/8) had no underlying diseases. Six cases were community-acquired and 2 were hospital-acquired. The predominant manifestations were tachypnea/dyspnea (100.0%) and fever (87.5%); neonates presented with lethargy and poor feeding. Complications included respiratory failure (87.5%), multiple organ dysfunction (62.5%), and septic shock (37.5%). Procalcitonin, interleukin-6, and LDH were elevated in all cases, while ALB was uniformly decreased. Bilateral pulmonary involvement was seen in 87.5% on chest imaging. mNGS detected LP in all 8 cases (100%), whereas conventional sputum and blood cultures failed to identify LP in any case; LP was isolated from a surgical pus specimen in only 1 case. Co-infections were identified in 50.0%. All initial empirical regimens failed to cover LP. After mNGS-guided targeted therapy, the fluoroquinolone-rifampin combination (2 cases) achieved complete recovery, while macrolide-based regimens yielded variable outcomes. Overall, 50.0% were cured or improved, while 50.0% died or had treatment withdrawn. LP bacteremia and septic shock were uniformly associated with poor outcomes.

DISCUSSION: Severe LP pneumonia in children predominantly affects neonates and can occur without recognized immunodeficiency. mNGS detected LP in all cases where conventional culture failed. In this small cohort, fluoroquinolone-containing combination regimens were associated with favorable outcomes.},
}

Humans
Male
Female
*Legionella pneumophila/genetics/isolation & purification
*Legionnaires' Disease/diagnosis/drug therapy/microbiology
Infant
Child, Preschool
Retrospective Studies
*High-Throughput Nucleotide Sequencing
*Metagenomics
Infant, Newborn
Anti-Bacterial Agents/therapeutic use
Child
Community-Acquired Pneumonia
Treatment Outcome
China

@article {pmid42490978,
year = {2026},
author = {Balkrishna, A and Chaudhary, P and Singh, S and Saini, A and Kumari, A and Mahato, KI and Arya, V},
title = {Artificial intelligence in soil microbiome-driven agriculture: from practical limits to a translational roadmap.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1860559},
doi = {10.3389/frmbi.2026.1860559},
pmid = {42490978},
issn = {2813-4338},
abstract = {BACKGROUND: Soil microbiome research has been revolutionized by advances in high-throughput sequencing and multi-omics technologies, generating massive datasets that capture the taxonomic, functional, and metabolic diversity of microbial communities in agricultural soils; however, interpreting these complex datasets and translating them into practical agronomic insights remains challenging.

OBJECTIVES: To critically assess the role of artificial intelligence (AI) in soil microbiome-driven agriculture, focusing on methodological developments, prediction performance, existing limitations, and translational opportunities.

METHODS: A narrative review was conducted to evaluate commonly used AI approaches, including random forest, gradient boosting, support vector machines, and deep learning architectures, alongside key microbiome data types such as amplicon sequencing, metagenomics, and functional gene profiling, with integration of environmental, agronomic, and meteorological datasets.

RESULTS: The prediction of crop productivity, disease risk, nutrient cycling dynamics, and soil health indicators may be enhanced by AI-assisted integration of microbiome, soil physicochemical, and meteorological data, according to several studies. However, broad generalizations about predictive robustness and generalizability are limited by significant diversity in datasets, validation methods, and model architectures.

DISCUSSION: To address these limitations, a five-phase implementation framework integrating centralized data systems, AI-driven analytics, multi-omics profiling, standardized soil sampling, and feedback-based model retraining within precision agriculture systems is proposed, providing a pathway for translating microbiome insights into field-scale decision support.

CONCLUSION: AI-enabled soil microbiome applications hold significant potential for sustainable agriculture, but future advancements will require large, multisite datasets, improved validation strategies, interpretable modeling approaches, and integration with digital agriculture technologies, highlighting both opportunities and practical constraints.},
}

@article {pmid42491000,
year = {2026},
author = {Duman, M and Armwood, A and Ajmi, N and Taşçı, G and Speare, D and Yavaş, Ö and Saticioglu, IB},
title = {Capsulated Lactococcus garvieae caused devastating mortality in Atlantic bluefin tuna, Thunnus thynnus: genomic and histopathologic characterization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1831351},
doi = {10.3389/fcimb.2026.1831351},
pmid = {42491000},
issn = {2235-2988},
mesh = {Animals ; *Tuna/microbiology ; *Lactococcus/genetics/isolation & purification/classification/pathogenicity ; *Gram-Positive Bacterial Infections/veterinary/microbiology/mortality/pathology ; *Fish Diseases/microbiology/mortality/pathology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics ; Microscopy, Electron, Transmission ; },
abstract = {Atlantic bluefin tuna (ABFT; Thunnus thynnus) is among the most valuable commodities in Mediterranean mariculture, and recent increases in seawater temperatures have coincided with the re-emergence of bacterial diseases causing catastrophic losses. During the summer 2025 mortality event, we investigated stranded and moribund ABFT using bacteriological isolation and identification, high-throughput 16S amplicon profiling of tissue-associated bacterial communities, whole-genome sequencing to resolve a complete genome of the etiologic agent, transmission electron microscopy, and gross and histopathological examinations. Across multiple organs, the metagenomic profiles were overwhelmingly dominated by Lactococcus garvieae, supporting a primary systemic bacterial etiology. The isolate displayed a capsulated phenotype, and genome analysis identified a capsule-associated gene cluster consistent with a capsulated lineage. Capsule expression was further confirmed ultrastructurally by transmission electron microscopy. Pathology indicated fulminant septicemia with prominent hemorrhagic lesions and severe cardioperitoneal involvement, including fibrinous epicarditis with abundant Gram-positive cocci, alongside marked hepatic and splenic pathology. Collectively, these data document, for the first time in two decades, the detection of a capsulated L. garvieae serotype or lineage associated with ABFT mass mortality. Rapid etiologic confirmation, mitigation of temperature-related and husbandry-associated stress, and targeted prevention strategies (including vaccination and biosecurity) are recommended to reduce recurrence in warming coastal waters.},
}

Animals
*Tuna/microbiology
*Lactococcus/genetics/isolation & purification/classification/pathogenicity
*Gram-Positive Bacterial Infections/veterinary/microbiology/mortality/pathology
*Fish Diseases/microbiology/mortality/pathology
RNA, Ribosomal, 16S/genetics
Phylogeny
Genome, Bacterial
Whole Genome Sequencing
Genomics
Microscopy, Electron, Transmission

@article {pmid42491023,
year = {2026},
author = {Xu, Z and Xu, L and Liu, J and Pang, L and Xia, L},
title = {Clinical characteristics of lung abscess by red complex bacteria infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1861751},
doi = {10.3389/fmed.2026.1861751},
pmid = {42491023},
issn = {2296-858X},
abstract = {BACKGROUND: Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are common oral pathogens collectively referred to as the "red complex bacteria", serve as crucial periodontopathic agents. Owing to the challenges associated with anaerobic culture, their contribution to lower respiratory tract infections, especially lung abscess, is often undervalued. Metagenomic next-generation sequencing (mNGS) has evolved as a potent instrument for the identification of fastidious organisms.

CASE PRESENTATION: A 63-year-old male with chronic cough and hemoptysis was admitted to our hospital. Chest computed tomography showed an indeterminate space-occupying lesion in the right upper lobe, and repeated sputum cultures were negative. Lung cancer was the primary consideration, so a CT-guided percutaneous core needle biopsy of the lung lesion was performed. Nevertheless, the pathology favored inflammation over lung cancer, leading us to continue investigating the causative pathogen. Following mNGS analysis of the puncture biopsy tissue, Treponema denticola and Porphyromonas gingivalis were detected. Both organisms belong to the red complex bacteria, closely associated with periodontitis that the patient had. Intravenous piperacillin-tazobactam followed by oral amoxicillin-clavulanate was prescribed. The patient recovered and subsequent chest computed tomography confirmed the improvement.

CONCLUSIONS: This case highlights the role of oral red complex bacteria in culture-negative chronic lung abscesses. mNGS is a crucial diagnostic tool for identifying these fastidious anaerobes, enabling targeted therapy and improving clinical outcomes.},
}

@article {pmid42491029,
year = {2026},
author = {DeSalle, AJ and Agbajelola, VI and Ericsson, AC and Shyu, CR and Palaniappan, K and Shacham, E and Raghavan, RK},
title = {Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1863755},
doi = {10.3389/fmicb.2026.1863755},
pmid = {42491029},
issn = {1664-302X},
abstract = {BACKGROUND: Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.

METHODS: Questing ticks were collected during early and late seasonal periods at a livestock-associated site in central Missouri. To minimize confounding by developmental stage, microbiome analyses were restricted to nymphal ticks. Bacterial communities were characterized using 16S rRNA gene sequencing. Alpha diversity (richness, Shannon, and Simpson indices), beta diversity (Jaccard and Bray-Curtis dissimilarities), and differential abundance analyses were performed. Community differences were evaluated using permutational multivariate analysis of variance (PERMANOVA).

RESULTS: Sequencing generated 984-101,293 reads per sample. Sequencing depth was strongly correlated with observed richness (R [2] = 0.808, p = 2 × 10[-7]). Comparisons of non-rarefied and rarefied datasets revealed no significant differences between early- and late-season nymphal ticks in observed richness, Shannon diversity, or Simpson diversity (all p > 0.05). In contrast, beta-diversity analyses identified significant differences in bacterial community membership between seasonal groups based on Jaccard dissimilarity (PERMANOVA: F = 1.5, R [2] = 0.066, p = 0.0102), whereas Bray-Curtis dissimilarity showed a non-significant trend toward seasonal separation (F = 2.2, R [2] = 0.090, p = 0.0834). Differential abundance analysis identified 18 amplicon sequence variants (ASVs) with raw p-values < 0.05, of which one Rickettsia-associated ASV remained significant following false discovery rate correction.

CONCLUSION: Seasonal differences in bacterial community composition were detected among nymphal ticks despite similar levels of microbial richness and alpha diversity. The enrichment of a Rickettsia-associated ASV in early-season ticks suggests that season may influence the occurrence of specific bacterial taxa within tick microbiomes. Further studies using higher-resolution sequencing and pathogen-specific approaches are needed to clarify the ecological significance of these seasonal patterns.},
}

@article {pmid42491347,
year = {2026},
author = {Jin, Y and Clasen, F and Garcia-Guevara, F and Arif, S and Schierwagen, R and Bidkhori, G and Praktiknjo, M and Brol, MJ and Uschner, FE and Castelli, FA and Pons, N and Quinquis, B and Galleron, N and Da Silva, K and Junot, C and Shawcross, DL and Moyes, DL and Jalan, R and Ehrlich, SD and Patel, VC and Trebicka, J and Shoaie, S},
title = {Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70131},
doi = {10.1002/imt2.70131},
pmid = {42491347},
issn = {2770-596X},
abstract = {Liver cirrhosis is associated with profound disruption of host-microbiome metabolic interactions. Using paired oral and fecal metagenomics combined with genome-scale metabolic modeling, we investigated how microbial translocation along the oral-gut axis influences microbial metabolism at different cirrhosis severities. Reactobiome-based functional profiling revealed progressive metabolic convergence between oral and gut microbiomes, quantified by a decrease in oral-gut metabolic distance. Translocation-associated microbial species enriched in patients with cirrhosis were predicted to have elevated capacities for ammonia and acetate production. Microbial-community and host metabolic modeling further suggested that these microbial metabolic shifts may influence host energy metabolism and redox balance across the liver, brain, and skeletal muscle. Together, these findings suggest a potential acetate-ammonia metabolic axis linking oral-gut microbial translocation with systemic metabolic stress in advanced cirrhosis.},
}

@article {pmid42491466,
year = {2026},
author = {Zhang, J and Lu, T and Tang, Q and Chen, SC and Garza, DR and Liu, B and Cui, Y and Wei, Y and Richnow, HH},
title = {Antiviral defense systems drive persistence of antimicrobial-resistant bacteria but limit the transfer of antimicrobial resistance genes in anaerobic digestion.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70145},
doi = {10.1002/imt2.70145},
pmid = {42491466},
issn = {2770-596X},
abstract = {Phage-host interactions critically shape environmental antimicrobial resistance (AMR). Using swine manure anaerobic digestion and multi-omics (metagenomics, meta-transcriptomics, and Hi-C), we mapped the phage-bacteria arms race and its impact on AMR dynamics. We revealed that phage-mediated lysis overwhelmingly dominates transduction, while phages rarely carry antimicrobial resistance genes (ARGs), and phage-borne ARGs showed no expression, challenging the paradigm of phages as primary vectors of ARGs. Crucially, the intense on-going phage-host arms race drives the widespread presence and expression of antiviral defense systems (ADSs) in antimicrobial-resistant bacteria (ARB). These ADSs exhibit a vital ecological dual role: they protect ARBs from phage lysis promoting persistence while simultaneously suppressing horizontal gene transfer (HGT, e.g., conjugation), as validated by in vitro conjugation assays. Our findings elucidate this duality, offering a novel framework to harness phage lytic pressure and ADS-mediated HGT suppression for environmental AMR mitigation.},
}

@article {pmid42491572,
year = {2026},
author = {Tian, L and Qin, J and Deng, Y and Liu, L and Wang, S and Zhang, M and Guan, T and Xu, Y},
title = {Ecological and functional succession of the microbial community during pit mud maturation in Nongxiangxing Baijiu.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100640},
doi = {10.1016/j.crmicr.2026.100640},
pmid = {42491572},
issn = {2666-5174},
abstract = {Pit mud (PM) microbiota play a vital role in Baijiu flavor formation, yet its ecological and functional succession during maturation remains incompletely elucidated. Here, physicochemical profiling, amplicon sequencing, and metagenomics were integrated to investigate 5-, 15-, and 30-year PM of Sichuan Tang Dynasty Laojiao cellars. Bacteria dominated the community (82.59%), followed by Archaea (16.99%), with Lactobacillus acetotolerans, Ruminococcaceae CPB6, and Methanobacterium paludis as major species. Discrepancies between sequencing methods were reflected in fungal taxa which had low-abundance. The 15-year PM exhibited distinct community and functional features, indicating a critical transitional stage. Functional analysis revealed that fermentation-relevant functions were mainly contributed by 7 key genera and 5 species. Physicochemical properties changed with pit age, characterized by increased moisture as well as decreased acidity and humic substance levels. Moisture, ammonium nitrogen (NH4[+]-N), available phosphorus, and age were identified as key drivers shaping microbial composition and function. Moisture was identified as the most central mediator, establishing a three-tier cascade causal chain from microorganisms to nutrient accumulation. Functionally, 5-year PM sustained a simple, Lactobacillus-dominated, growth-oriented community; 15-year PM shifted toward aromatic compound degradation, nitrogen utilization, flavor-precursor synthesis; and 30-year PM developed into a stable, flavor-optimized ecosystem enriched in caproic-acid-producing Ruminococcaceae CPB6. Overall, PM maturation is driven by microbiome functional evolution, and the 15-year represented a pivotal period. This study provides a theoretical foundation for scientific PM management and targeted microbial regulation in Baijiu production.},
}

@article {pmid42491666,
year = {2026},
author = {Liu, C and Li, X and Mansoldo, FRP and Chen, T and Meng, F and Tang, R and Zhou, S and Yang, Q and Shao, R and Yao, M},
title = {microeco 2: A comprehensive R package for downstream analysis of microbiome omics data.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70132},
doi = {10.1002/imt2.70132},
pmid = {42491666},
issn = {2770-596X},
abstract = {Efficient downstream analysis of microbiome data remains a major challenge for researchers. Since its initial release in late 2020, the R microeco package has been widely used for downstream statistical analysis and visualization of omics data, such as amplicon sequencing. Compared with its initial release, the current second version of the microeco package has undergone extensive updates and enhancements. The key upgrades include: (1) The addition of classes for data normalization and machine learning, respectively; (2) The incorporation of additional analytical methods and the addition of functions across various classes; (3) Optimization of the parameter system to expand the applicable scenarios of relevant methods; (4) Code restructuring to enhance the connectivity between statistical analysis and visualization within each class; (5) Extension of certain functions to enable the analysis of abundance data in complex formats generated from bioinformatic analyses of metagenomic/metatranscriptomic data; (6) Incorporation of several analytical methods commonly used in transcriptomic and metabolomic data analyses. Overall, the microeco package 2.0 offers broader method coverage and a wider range of application scenarios compared to the previous version and other existing R packages. The steady growth in user downloads demonstrates that the microeco package, which is built on R6 (a class-based object-oriented programming system for R), has established a broad and active user base. The second version of the microeco R package is open-source and available on the Comprehensive R Archive Network and GitHub (https://github.com/ChiLiubio/microeco).},
}

@article {pmid42491728,
year = {2026},
author = {Suzuki, D and Yang, J and Obana, N and Yachida, S and Shiba, S and Mizutani, S and Takamaru, H and Saito, Y and Fukuda, S and Yamada, T},
title = {Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21488},
doi = {10.7717/peerj.21488},
pmid = {42491728},
issn = {2167-8359},
mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Animals ; Mice ; *Carcinogenesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenome ; Male ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is prevalent worldwide and is associated with gut commensals. Recent studies have highlighted the effects of gut microbes on CRC development driven by their strain diversity. Nevertheless, the impact of the gut microbial community on tumorigenesis in early-stage (ES) CRC remains unexplored.

METHODS: To assess the potential gut microbial community, which is critical to tumorigenesis in early-stage CRC, we collected publicly available shotgun metagenomes from CRC patient faecal samples from a Japanese population. Correlation analysis of the microbial profiles derived from the metagenomes revealed an ES CRC-associated community. To elucidate the strain diversity of the targeted community, we isolated strains from ES CRC patient faecal samples and employed comparative genomics. To evaluate the strain-specific effects of the community on tumorigenesis, we introduced an isolated strain cocktail into a CRC mouse model.

RESULTS: Among the most significant ES CRC-associated species, we identified Lancefieldella parvula (Lp), as reported in a previous study. The 20 species were identified as positively correlated with Lp. Seven of the 20 species were associated with ES CRC, including Actinomyces and Solobacterium. Schaalia odontolytica (So) (formerly known as Actinomyces odontolyticus) and Solobacterium moorei (Sm) were previously reported as potential species that promote CRC. Thus, we isolated clinical strains of Lp, So, and Sm from faecal samples as potential members of the ES CRC-associated community. Comparative genomics revealed that iron-related genes were shared among clinical strains. In the oral challenge with clinical strains, namely, Lp, So, and Sm, the mice exhibited shorter survival and significantly increased tumorigenesis, suggesting that the cocktail of clinical strains is more pathogenic to the CRC mouse model than the type strain is. In summary, we inferred that the ES CRC-associated community could promote CRC, and the effects depend on the strains involved.},
}

*Colorectal Neoplasms/microbiology/pathology
Humans
Animals
Mice
*Carcinogenesis
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Female
Metagenome
Male

@article {pmid42491748,
year = {2026},
author = {Taurino, G and Mancabelli, L and Milani, C and Longhi, G and Lugli, GA and Ughini, C and Bianchi, MG and Chiu, M and Kayali, S and Gaiani, F and Aloe, R and Turroni, F and Bussolati, O and Ventura, M},
title = {Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy.},
journal = {iScience},
volume = {29},
number = {7},
pages = {116578},
doi = {10.1016/j.isci.2026.116578},
pmid = {42491748},
issn = {2589-0042},
abstract = {Fecal calprotectin is a biomarker for intestinal inflammatory conditions, while specific taxa of gut microbiota are proposed as biomarkers for inflammatory bowel disease. However, the relationship between microbiota and calprotectin levels is still largely unexplored. Using shallow shotgun metagenomics, we investigate microbial taxonomic and functional patterns correlated with calprotectin levels in fecal samples of 515 adult individuals without known intestinal pathologies, enrolled within the Parma Microbiota Project. The median value of calprotectin was 23.6 μg/g, but levels higher than the normal threshold of 50 μg/g were measured in 20% of participants. While no changes were detected in alpha- and beta-diversities, calprotectin levels were negatively associated with butyrate-producing bacteria, while positively correlated with several opportunistic pathogens. Functional analysis showed significant correlations between calprotectin levels and the predicted microbial enzymatic functions. If confirmed in longitudinal studies, these findings could indicate early microbial biomarkers of gut inflammatory conditions.},
}

@article {pmid42492212,
year = {2026},
author = {Kong, Y and Jimenez, K and Osborn, K and Zhang, Y and Low, S and Sytko, C and Tran, T and Choi, YSA and Ho, SJ and Nguyen, J and Astilla, T and Aziz, S and Low, O and Chowdhry, R and Henning, L and Dickerson, C and Jones, A and Mahendra, S and Jay, JA},
title = {Integrating multi-method approach reveals extensive antibiotic resistance dissemination from concentrated animal feeding operations to surface waters.},
journal = {Water research},
volume = {305},
number = {},
pages = {126548},
doi = {10.1016/j.watres.2026.126548},
pmid = {42492212},
issn = {1879-2448},
abstract = {Concentrated animal feeding operations (CAFOs) are important sources of antimicrobial resistance (AMR), but how mixed livestock inputs and seasonality shape antibiotic resistance profiles in receiving surface waters remains uncertain. We integrated culture-based screening, qPCR, and shotgun metagenomics to assess AMR in surface waters influenced by dairy and mixed swine and dairy operations across seasonal campaigns. CAFO-impacted sites, which were shown to have much greater levels of multidrug resistance among purified Escherichia coli isolates in our previous study, had higher culturable E. coli than reference sites, and extended-spectrum beta-lactamase (ESBL)-producing E. coli were detected only at CAFO sites during spring. qPCR analysis showed significantly higher relative abundances of tetracycline (tetW) and macrolide (ermF) resistance genes at CAFO-impacted sites, with strong co-occurrence between the cattle fecal marker CowM3 and these antibiotic resistance genes (ARGs) (adjusted p < 0.05). Metagenomic profiling identified 619 unique ARG subtypes. CAFO-impacted sites contributed substantially greater resistance diversity, with 198 unique subtypes detected compared to 15 unique subtypes at reference sites. Seasonal shifts in metagenomic data were pronounced at dairy sites, including spring increases in tetracycline-, rifamycin-, and florfenicol-associated resistance. ESKAPE pathogens were detected only at CAFO-impacted sites, while Pseudomonas aeruginosa and Klebsiella pneumoniae were identified as putative ARG hosts. Across methods, culture and molecular approaches provided complementary information, with ESBL total coliforms correlating better with qPCR and metagenomic results (p < 0.005) then ESBL E. coli. By integrating phenotypic and molecular evidence, this study highlights seasonal windows of enhanced detectability and supports integrated One Health surveillance of AMR at agricultural-environment interfaces.},
}

@article {pmid42492447,
year = {2026},
author = {Li, L and Gad, M and Adyari, B and Hou, L and Wang, Y and Rizk, NM and Marouf, MA and Claude, NJ and Al-Herrawy, AZ and Abdelfadiel, A and Hu, A},
title = {Cross-regional metagenomic insights into clinical and stable resistomes in urban wastewater systems.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143012},
doi = {10.1016/j.jhazmat.2026.143012},
pmid = {42492447},
issn = {1873-3336},
abstract = {Antimicrobial resistance (AMR) is a growing global threat, with elevating risks in low- and middle-income countries due to inadequate infrastructure and limited regulation. However, comprehensive analyses on AMR profiles in these regions remain scarce. We compared AMR risks across full-scale wastewater treatment plants (WWTPs) in Egypt (Cairo) and China (Xiamen), utilizing shotgun metagenomic sequencing, bioinformatics, and multivariate analysis. Our results indicated that while influent samples exhibited comparable AMR risk levels, the activated sludge and effluent from Egyptian WWTPs showed significantly higher risks, characterized by greater clinical ARG abundance, enhanced mobility potential, and more diverse pathogenic hosts. We identified 51 stable ARGs that persisted across WWTPs, seasons and treatment units. These stable ARGs showed strong association with pathogen community and were detected across a broader range of pathogenic hosts, and were predominantly plasmids-borne. Plasmids were the primary vectors of horizontal gene transfer (HGT) of clinical ARGs, whereas viruses showed selective associations with stable ARGs. Key pathogens facilitating HGT of both clinical and stable ARGs included Alcaligenes faecalis and Shigella spp., with cross-domain putative HGT events also being detected. These findings address a critical knowledge gap in underrepresented regions and provide risk-based strategies to mitigate ARG dissemination in urban wastewater systems.},
}

@article {pmid42492757,
year = {2026},
author = {Demirci, M},
title = {Metabolic Reprogramming and Taxonomic Drivers in Bacterial Vaginosis: A Large-Scale Metagenomic Meta-Analysis.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103067},
doi = {10.1016/j.anaerobe.2026.103067},
pmid = {42492757},
issn = {1095-8274},
abstract = {OBJECTIVE: Bacterial vaginosis (BV) represents a profound ecological shift from a Lactobacillus-dominated microbiota to a diverse polymicrobial biofilm associated with adverse outcomes. While taxonomic signatures are well-documented, the functional mechanisms driving this transition remain obscured. This study elucidates the genomic potential for metabolic reprogramming and the putative "functional handover" underpinning the stability of the dysbiotic state.

METHODS: A computational meta-analysis of 3,557 vaginal microbiomes from diverse global cohorts was performed using the standardized MGnify pipeline. A high-resolution subset of 187 whole-genome shotgun (WGS) metagenomes was stratified to compare functional potential across demographic groups. Taxon-function interaction networks were constructed, utilizing a dual-filter statistical approach (p < 0.05 and effect size ranking), to map the shift from homeostatic maintenance to dysbiotic metabolic potential.

RESULTS: BV was characterized by a fundamental shift from "maintenance" pathways to high-turnover "growth-oriented" genomic repertoires. While ABC transporter-like domains were present in healthy communities, dysbiosis was marked by a quantitative expansion and diversification of these systems alongside P-loop NTPases. Network analysis revealed a putative "functional handover": while Gardnerella serves as the adherent structural scaffold, the metabolic burden appears to be associated with secondary anaerobes, specifically BVAB1 and Sneathia, which exhibit strong genomic correlations with nutrient transport and stress response pathways. Crucially, microbiomes from women of African ancestry (Black cohort) exhibited a distinct functional profile with genomic signatures consistent with functions previously associated with resistome expansion (e.g., tetracycline/macrolide resistance), contrasting with Asian cohorts.

CONCLUSION: BV is a state of metabolic reprogramming where genomic functional dominance is transferred from Lactobacillus to a cooperative network of anaerobic opportunists. Identifying BVAB1 and Sneathia as candidate metabolic engines, supported by a Gardnerella scaffold, challenges current therapeutic paradigms and highlights the potential for precision medicine targeting specific functional drivers and resistome profiles across diverse populations.},
}

@article {pmid42479457,
year = {2026},
author = {You, J and Khan, RM and Reji, N},
title = {Gut microbiome profiles as predictors of response to chemoradiotherapy in locally advanced rectal cancer.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02874},
pmid = {42479457},
issn = {1588-2640},
abstract = {This prospective cohort study investigates the predictive role of gut microbiota composition in determining the therapeutic response to neoadjuvant chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (LARC) at Qiqihar Jianhua Hospital. A total of 178 patients underwent standardized CRT protocols and were stratified into responders and non-responders based on pathological tumor regression grades. Gut microbiome profiling was conducted via 16S rRNA amplicon sequencing and shotgun metagenomics at three treatment stages (pre-, mid-, and post-CRT). Responders exhibited significantly higher alpha diversity (Shannon, Chao1) at baseline and maintained greater microbial richness throughout treatment. Taxonomic analysis identified Faecalibacterium, Akkermansia, and Bifidobacterium as enriched in responders, while non-responders showed elevated Clostridium, Escherichia, and Streptococcus. Multivariate regression confirmed Faecalibacterium (OR = 1.16, P = 0.0002) and Akkermansia (OR = 1.27, P = 0.0146) as independent predictors of CRT response. Functional profiling revealed enrichment of anti-inflammatory pathways (butyrate synthesis, tryptophan metabolism) in responders and pro-inflammatory, stress-related functions (lipopolysaccharide biosynthesis, oxidative stress) in non-responders. Exploratory microbiome modulation using probiotics or fecal microbiota transplantation (FMT) targeting Faecalibacterium and Akkermansia demonstrated increased responder rates by 12.5 and 18.2%, respectively. These findings highlight the potential of gut microbiome signatures as non-invasive biomarkers for CRT response prediction and as targets for adjunctive therapeutic strategies. Personalized microbiome-informed treatment may enhance CRT efficacy and reduce unnecessary exposure in non-responders, paving the way for precision oncology in rectal cancer.},
}

@article {pmid42479737,
year = {2026},
author = {Wang, H and Zhang, Q and Sun, B and Shen, D and Lu, L and Li, H and Fang, K and Li, H and Yan, H and Chen, F and Zhao, T and Chen, L and Rong, M and Liu, W and Hu, Z and Ai, J and Zhang, W},
title = {Artificial intelligence risk prediction model for common respiratory pathogens in China based on heterogeneous multi-source clinical and geographic data: A modeling study.},
journal = {PLOS digital health},
volume = {5},
number = {7},
pages = {e0001553},
pmid = {42479737},
issn = {2767-3170},
abstract = {Most respiratory pathogens exhibit distinct seasonal and periodic outbreak patterns driven by climatic factors. However, predictive models that jointly consider climate, air quality index (AQI), and socioeconomic variables are lacking. We retrospectively analyzed targeted or metagenomic next-generation sequencing data from 153,544 respiratory samples collected from 1,880 centers across 30 provinces in China between September 2022 and September 2024. Monthly positivity rates were matched with geographic, climatic, AQI, and GDP data. CO(0.098 ± 0.016), HCHO(0.096 ± 0.021), O3(0.102 ± 0.019), sunshine hours(0.103 ± 0.028), wind speed(0.114 ± 0.024), and GDP(0.095 ± 0.019). were identified as the key geographical factors for the positivity across most respiratory pathogens via mean Gini index reduction, and a gradient boosting decision tree(GBDT) model was trained and benchmarked against other AI methods using the DISO metric. This model accurately simulated the epidemiological trends from September 2022 to September 2024 and outperformed alternative models with the lowest DISO metric of 0.12 in influenza A, 0.21 in SARS-CoV-2, 0.25 in RSV. The GBDT model was used to predict the short-term epidemic of 10 respiratory pathogens between October and December 2024. The predictions showed consistent trends with the external validation cohort for RNA viruses including SARS-CoV-2 and influenza A virus, but differed for bacterial pathogens. Integrating air quality, climatic, and socioeconomic data yields robust predictions of respiratory infection dynamics in the short-term by the GBDT model, bolstering public health surveillance and offering a framework potentially applicable to other infectious diseases.},
}

@article {pmid42479812,
year = {2026},
author = {Jia, Y and Yan, Y and Chen, B and Shu, WS and Lu, H},
title = {Revealing Dual Synergistic Strategies in Sulfate-Reducing Microbiomes for Sulfamethoxazole Biodegradation via DNA-SIP and Metagenomics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05921},
pmid = {42479812},
issn = {1520-5851},
abstract = {Sulfate-reducing microbiomes (SRMs) have shown strong potential for antibiotic remediation, yet the active microorganisms and community-level strategies associated with sulfamethoxazole (SMX) biotransformation remain poorly understood. In this study, long-term bioreactor operation (269 days; 500-1500 μg/L SMX), DNA-stable isotope probing (DNA-SIP), and metagenomic analyses were integrated to investigate the microbial contributors and functional organization underlying SRM-driven SMX biotransformation. Desulfobacterium, a key SRM member, was co-enriched with Geobacter and Leptolinea in the [13]C-labeled heavy fraction, suggesting potential metabolic complementarity during community-level SMX biotransformation. Genome-resolved analyses further revealed structured patterns of inferred horizontal gene transfer (HGT) and predicted metabolite exchange among keystone taxa. The transferred genes were mainly associated with energy conservation, transport, sulfur-associated metabolism, and stress-response functions, whereas the predicted exchanged metabolites included carbon metabolites, amino acid-related sulfur compounds, purine-related intermediates, and cofactor-associated metabolites. Together, these findings suggest that HGT-associated functional redistribution and metabolic complementarity may contribute to the persistence and coordinated activity of sulfate-reducing microbiomes under high SMX stress. This study links SIP-identified active populations with genome-inferred interaction patterns in a sulfate-reducing system and provides new insight into microbiome-based anaerobic strategies for antibiotic-containing wastewater treatment.},
}

@article {pmid42480186,
year = {2026},
author = {Xiang, Y and Cui, K and Zhou, H and Tian, Y and Liu, X and Yao, H and Li, X},
title = {Perfluorooctane sulfonate drives the synergistic dissemination of antimicrobial resistance and pathogenicity during sludge anaerobic digestion.},
journal = {Water research},
volume = {305},
number = {},
pages = {126541},
doi = {10.1016/j.watres.2026.126541},
pmid = {42480186},
issn = {1879-2448},
abstract = {Per- and polyfluoroalkyl substances, one of the most prevalent and persistent emerging contaminants in sludge, may drive the dissemination of antimicrobial resistance and pathogenicity during sludge treatment. However, the mechanisms underlying perfluorooctane sulfonate (PFOS)-mediated propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) remain poorly understood. This study investigated the effects of PFOS (1 and 10 μg/g-dw) on ARGs dynamics and virulence risks. Quantitative PCR and metagenomic analysis revealed that PFOS stress led to the widespread enrichment of ARGs, the total abundance of mobile genetic elements (MGEs) and VFs also increased by 33.22-37.62% and 6.71-8.41%, respectively. Metagenomic binning results demonstrated that most metagenome-assembled genomes carrying ARGs or VFs simultaneously harbored MGEs. Mechanistically, excessive reactive oxygen species production and enhanced substrate-level phosphorylation for ATP generation may contribute to the increased horizontal transfer potential of ARGs under PFOS stress, which further facilitated the convergence of antimicrobial resistance and virulence traits within pathogens. Furthermore, PFOS may have hindered the negative regulation of the RhlI/RhlR quorum sensing system on the Type III secretion system, stimulating the secretion of VFs. This study elucidates the mechanisms by which PFOS promotes the dissemination of ARGs and pathogenicity during anaerobic digestion, highlighting the potentially overlooked environmental health risks of PFOS during sludge disposal.},
}

@article {pmid42480452,
year = {2026},
author = {Shan, X and Shi, L and Zhu, T and Liang, X and Yang, J and Zhou, G and He, L and Mei, B and Wang, S and Li, F},
title = {Microbial tryptophan-IPA axis mediates 6:2 chlorinated polyfluorinated ether sulfonate (6:2Cl-PFESA)-induced gut-brain dysfunction and neurobehavioral impairments.},
journal = {Environment international},
volume = {214},
number = {},
pages = {110422},
doi = {10.1016/j.envint.2026.110422},
pmid = {42480452},
issn = {1873-6750},
abstract = {Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are widely used substitutes for perfluorooctane sulfonate (PFOS) and are increasingly detected in environmental and human matrices, yet their neurobehavioral risks during early life remain poorly defined. Here, male C57BL/6J mice were orally exposed to F-53B (6:2Cl-PFESA; 0.1 or 1 mg/kg/day) during juvenility for four weeks. F-53B selectively impaired recognition memory and social novelty preference, whereas locomotor activity, anxiety-like behavior, and Y-maze working memory were largely preserved. Mechanistically, F-53B compromised intestinal barrier integrity, as evidenced by reduced occludin expression and disrupted ZO-1 continuity, accompanied by elevated circulating lipopolysaccharide (LPS) and a systemic pro-inflammatory cytokine shift. In parallel, the hippocampus exhibited microglial activation, enhanced inflammatory signaling, and reduced PSD95 expression, consistent with neuroinflammatory stress and synaptic vulnerability. Shotgun metagenomics revealed pronounced microbiome restructuring and network rewiring, while widely targeted metabolomics converged on a marked disruption of tryptophan metabolism, characterized by depletion of microbiota-derived indole metabolites, including indole-3-propionic acid (IPA), together with altered serotonin-related signatures. Notably, oral IPA supplementation rescued behavioral deficits and attenuated gut-brain inflammatory alterations, restoring intestinal aryl hydrocarbon receptor (AhR) nuclear translocation, reducing LPS and cytokine levels, and ameliorating hippocampal inflammatory phenotypes. Collectively, these findings provide mechanistic evidence that a microbiota-tryptophan metabolite-gut barrier-inflammation axis links exposure to substitute PFAS with selective neurobehavioral dysfunction, highlighting microbiota-derived metabolites as potential modulators of PFAS-associated neurotoxicity.},
}

@article {pmid42480622,
year = {2026},
author = {Ren, X and Ma, J and Zhao, Y and Yang, M and Li, Y and Song, W and Wang, N},
title = {Microbiome Remodeling During Aging: Integrative Multi-Omics and Spatiotemporal Perspectives on Immune and Metabolic Regulation.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103269},
doi = {10.1016/j.arr.2026.103269},
pmid = {42480622},
issn = {1872-9649},
abstract = {Changes in the gut microbiota occur throughout the human lifespan, and maintaining microbial homeostasis plays a critical role in promoting healthy aging. In recent years, substantial progress has been made in elucidating the mechanistic links between aging and microbiota remodeling, highlighting the central role of microbiota-host interactions in regulating immune responses and maintaining metabolic homeostasis. These findings provide new potential targets for the precision prevention and treatment of age-related diseases. This review systematically summarizes the patterns of gut microbiota succession across different stages of the human life cycle, including infancy, adolescence, adulthood, and old age, as well as the mechanisms through which the microbiota regulates immune and metabolic functions. Furthermore, the role of the gut microbiota as a key mediator linking aging with an increased risk of chronic inflammation, cardiovascular disease, cognitive impairment, neurodegenerative disorders, and cancer was explored. In addition, this review evaluates the therapeutic potential of microbiota-targeted interventions, such as dietary modification, probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), and lifestyle interventions-in maintaining microbiome homeostasis and mitigating age-related diseases. The feasibility of personalized microbiota-based intervention strategies is also discussed. Finally, we highlight the current challenges and limitations in this field and outline future research directions. In particular, integrating multi-omics approaches with metagenomic sequencing, including emerging spatial and spatiotemporal multi-omics technologies, is crucial for advancing our understanding of the complex interactions within the gut microbiome. These insights provide a theoretical framework for optimizing anti-aging therapeutic strategies and promoting healthy lifespan extension.},
}

@article {pmid42480833,
year = {2026},
author = {Bai, M and Wang, L and Wang, B and Liao, X and Sun, M and Zeng, W and Peng, Y},
title = {Carbon Conversion in Sludge Fermentation Liquid Drives Exogenous-to-Endogenous Transition of Partial Denitrification for Integration with Anammox.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125290},
doi = {10.1016/j.envres.2026.125290},
pmid = {42480833},
issn = {1096-0953},
abstract = {Traditional biological nitrogen removal processes for wastewater characterized by a low carbon-to-nitrogen (C/N) ratio often rely heavily on external carbon sources, resulting in excessively high operational costs. This study investigated the feasibility of using sludge fermentation liquid (SFL) as an alternative carbon source to drive the endogenous partial denitrification-anammox (EnPDA) process for efficient nitrogen removal. A sequencing batch reactor (SBR) was operated for 285 days, consisting of a partial denitrification (PD) phase (183 days) and a subsequent EnPDA phase (102 days). During the PD phase, exogenous PD (ExPD) shifted to endogenous PD (EnPD). After integrating anammox, the single-stage EnPDA system achieved a total inorganic nitrogen removal efficiency of 95.1 ± 1.2%, and maintained 93.8 ± 1.8% efficiency even under elevated ammonium loading. The batch tests revealed the robustness of EnPDA system and its preference for nitrate as the electron acceptor. Microbial community analysis showed a functional shift from Thauera to the endogenous denitrifier Ca. Competibacter, with Ca. Brocadia (1.04%) as the dominant anammox bacterium. Metagenomic analysis revealed 68.6% increased abundance of denitrification-related (narGHI) genes and 7.8-fold enhancement of anammox-related (hzs/hdh) genes. Furthermore, the genes related to carbon metabolism were also upregulated to sustain endogenous electron supply. This work clarifies the microbial and metabolic mechanisms underlying the transition of ExPD to EnPD. The study validates that SFL-driven EnPDA is a cost-effective strategy for advanced nitrogen removal from low C/N wastewater.},
}

@article {pmid42480835,
year = {2026},
author = {Wang, J and Chen, JY and He, YZ and Wu, JJ and Li, ZH},
title = {Functional instability and community-level compensatory mechanisms in the anammox system under long-term acetamiprid stress.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125298},
doi = {10.1016/j.envres.2026.125298},
pmid = {42480835},
issn = {1096-0953},
abstract = {Acetamiprid is a frequently detected neonicotinoid insecticide that is widely present in water bodies and may disrupt the stability of the anaerobic ammonium oxidation (anammox) process. This study investigated the response threshold and mechanistic transition of the anammox system under long-term acetamiprid stress. The system remained stable at 0-2.5 mg/L acetamiprid, and nitrogen removal efficiency (NRE) did not change significantly. At 5-15 mg/L acetamiprid, NRE was maintained at approximately 80%, whereas the NO3[-]-N/NH4[+]-N ratio increased to 0.40, and specific anammox activity (SAA) declined. This apparent maintenance of reactor performance was likely sustained by community-level functional compensation. At 50 mg/L acetamiprid, reactive oxygen species (ROS) levels increased by 74%, the protective effect of extracellular polymeric substances (EPS) weakened, and NRE decreased by 9.11%, indicating that the compensatory capacity of the microbial community had been exceeded and that the reactor had entered an unstable state. Overall, the reactor exhibited a stage-dependent transition from apparent stability to latent functional impairment and ultimately to overt instability. Community and metagenomic analyses further suggested that acetamiprid exposure reduced the ecological dominance and functional contributions of Candidatus Kuenenia and Candidatus Jettenia, while increasing the relative importance of Candidatus Brocadia and associated populations such as Ignavibacterium, and enhancing their stress response and xenobiotic-related functions. This transition indicates that the system shifted from a mode dominated by core anammox bacteria to a more distributed, multispecies compensatory state. These findings provide new insights into the stability boundaries and failure transitions of the anammox system under pesticide stress.},
}

@article {pmid42480947,
year = {2026},
author = {Zhang, J and Li, L and Yang, X and Chen, S and Li, Z and Li, R and Wang, C and Tian, Y},
title = {Efficient sludge reduction and phosphorus recovery in innovative coupled sequencing batch and worm reactor Process: Performance, mass balance and metagenomic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135478},
doi = {10.1016/j.biortech.2026.135478},
pmid = {42480947},
issn = {1873-2976},
abstract = {The efficient release and phosphorus recovery (PR) are core to enhancing the sustainable operation of municipal wastewater treatment systems. To address this issue, this study constructed an innovative coupled sequencing batch reactor (SBR)-worm reactor (WR)-PR process. By leveraging the synergistic regulation between worm predation and microbial activity, the process achieved the dual objectives of sludge reduction and the efficient release and targeted recovery of phosphorus from the solid phase to the liquid phase. By subjecting only approximately 6% of the influent flow to chemical phosphorus recovery, an efficient recovery of 45% of the influent total phosphorus (TP) was achieved. During 160 days of continuous operation, the coupled process exhibited excellent stability in pollutant removal, with removal rates of chemical oxygen demand (COD), total nitrogen (TN), and TP reaching 95%, 71%, and 97%, respectively. Sludge reduction of 49% was achieved through worm predation, with direct worm predation contributing 69%. Sludge characteristics were significantly improved, with the sludge volume index (SVI) decreasing by 46% and dewaterability increasing by 20%. Extracellular polymeric substance (EPS) analysis revealed that side‑stream predation reduced total EPS content, increased the protein/polysaccharide (PN/PS) ratio. Metagenomic analysis confirmed that side-stream biological predation significantly enriched key functional microbial groups and intensified the expression of genes related to phosphorus transport and metabolism. This work elucidates the microbial synergistic mechanisms within the coupled process, providing a novel pathway for the simultaneous achievement of efficient sludge reduction and PR in municipal wastewater treatment.},
}

@article {pmid42481505,
year = {2026},
author = {Song, W and Wang, Z and Liu, Y and Wang, Q and Li, M and Shi, W and Gao, Z and Chen, Y},
title = {Kocuria rosea LAT6 enhances wheat salt tolerance via modulation of rhizosphere microbial function and nitrogen cycling.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01103-7},
pmid = {42481505},
issn = {2055-5008},
support = {ZR2025QC186//Natural Science Foundation of Shandong Province/ ; SYS202206, ZR2021MC190//Natural Science Foundation of Shandong Province/ ; 2021YFF1000403//National Key R&D Program of China/ ; SKL81103//Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; No. 2022KJ333//Youth Innovation Team of Shandong Provincial Department of Science and Technology/ ; tsqn202103162//Taishan Scholars Program/ ; 2024CXPT072//Key R&D Program of Shandong Province, China/ ; },
abstract = {Pioneer plants in saline-alkali soils support unique rhizosphere microbial communities. Some of these microbes promote plant salt tolerance and growth, although the underlying mechanisms are not yet fully understood. In this study, we isolated Kocuria rosea LAT6 from the rhizosphere of pioneer plants in saline-alkali soils. Genome sequencing revealed genes associated with plant growth promotion and stress adaptation. Inoculation with LAT6 markedly reshaped the rhizosphere microbiota, and metagenomic analysis indicated that specific microbial taxa contributed to enhanced nitrogen-cycling functions. Transcriptome profiling further demonstrated that LAT6 promotes nitrate transport and stimulates phenylpropanoid biosynthesis in wheat. It reveals how microbial reorganization and plant-microbiome interactions enhance nitrogen use under salt stress, highlighting the potential of salt-tolerant consortia for saline-alkaline crops.},
}

@article {pmid42481656,
year = {2026},
author = {Stallhofer, J and Leonhardt, J and Semmler, J and Neugebauer, S and Kiehntopf, M and Löhden, W and Homeister, L and Ungelenk, M and Hübner, CA and Steube, A and Waschina, S and Stallmach, A},
title = {Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42481656},
issn = {2045-2322},
mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Bile Acids and Salts/metabolism/blood ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology ; Female ; Feces/chemistry/microbiology ; Male ; Gastrointestinal Microbiome ; Adult ; Middle Aged ; },
abstract = {The gut microbiota communicates extensively with its host through small metabolites, such as bile acids. Primary bile acids are synthesized by the host and secreted into the intestine, where they are actively converted by the microbiota into secondary bile acids. Depending on the resulting bile acid composition, the host's bile acid receptor, Takeda G protein-coupled receptor 5 (TGR5), is activated and mediates immune tolerance. It has been suggested that a disturbed bile acid profile in inflammatory bowel disease (IBD) might lead to inflammation via reduced activation of TGR5. Our study is the first to investigate whether bile acid-induced TGR5 activation differs between healthy individuals and patients with IBD. Bile acid profiles in stool and plasma were quantified by mass spectrometry, and TGR5 bioactivity was assessed from these profiles. In parallel, metagenomic sequencing was performed on fecal samples. We demonstrate that reduced alpha diversity in IBD is associated with a loss of microbial capacity for bile acid transformation, resulting in a significantly decreased secondary-to-primary bile acid ratio (sBA/pBA) in both stool and circulation. TGR5 bioactivity induced by bile acid profiles was substantially reduced in IBD patients, and a lower TGR5 bioactivity correlated with increased inflammatory activity.},
}

Humans
*Receptors, G-Protein-Coupled/metabolism/genetics
*Bile Acids and Salts/metabolism/blood
*Inflammatory Bowel Diseases/metabolism/microbiology/pathology
Female
Feces/chemistry/microbiology
Male
Gastrointestinal Microbiome
Adult
Middle Aged

@article {pmid42481973,
year = {2026},
author = {Wang, Y and Fu, X and Liu, Y and Li, R and Zhu, G and Chen, Z},
title = {Household cluster of psittacosis caused by Chlamydia psittaci ST388 in China: a case report and genomic analysis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13940-0},
pmid = {42481973},
issn = {1471-2334},
support = {2026JKP-07//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; 2026JKY035//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK104//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; },
abstract = {In March 2025, a married couple in Jiaxing City, Zhejiang Province, China, presented with fever and pneumonia. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Chlamydia psittaci (C. psittaci) infection. Epidemiological investigation revealed exposure to a pet budgerigar purchased one month prior. Environmental sampling detected C. psittaci in the bird's feces and the patients' living spaces. Phylogenetic analysis of the ompA gene identified the strains as genotype A, and multilocus sequence typing (MLST) determined the sequence type (ST) as ST388. Two cohabiting elderly parents without bird exposure remained asymptomatic and PCR-negative. Phylogenetic analysis showed the avian and environmental isolates formed a distinct clonal cluster. This report highlights the risk of zoonotic transmission from asymptomatic avian carriers and the utility of genomic surveillance in outbreak investigation. Clinicians should consider psittacosis in atypical pneumonia cases with bird exposure.},
}

@article {pmid42482126,
year = {2026},
author = {Zhai, Y and Kim, Y and Ban, GH and Kim, YM and Kim, SC and Bae, D and Jeong, KC and Kim, SA},
title = {Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02444-3},
pmid = {42482126},
issn = {2049-2618},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health, yet the contribution of food production environments to resistance transmission remains poorly understood.

RESULTS: We conducted a longitudinal shotgun metagenomic study across the pork production continuum from farm to retail to identify environmental AMR reservoirs and transmission pathways of antimicrobial resistance genes (ARGs). Assembly-based, genome-resolved, and source-tracking analyses were integrated to characterize resistomes, microbial communities, and horizontal gene transfer dynamics. ARG abundance and diversity were highest at farms, slaughterhouses, and processing plants and declined toward retail, although clinically relevant resistance determinants persisted throughout processing. Slaughterhouse environments emerged as major contributors to ARG contamination on carcasses, highlighting the importance of environmental exposure at intermediate stages. Resistome structure was closely linked to microbial community composition, with persistent taxa such as Acinetobacter and Pseudomonas serving as key ARG carriers, including genes conferring resistance to tetracycline, aminoglycosides, macrolide-lincosamide-streptogramin, and β-lactams, multidrug efflux. Co-localization of ARGs with mobile genetic elements demonstrated ongoing potential for horizontal transfer across production stages, and genome-resolved metagenome-assembled genome analyses revealed overlapping resistance and virulence profiles between slaughterhouse- and processing plant-associated bacteria, indicating adaptive persistence within pork production environments.

CONCLUSIONS: Resistome composition across the pork production chain is largely shaped by stage-specific environmental sources, highlighting potential intervention points to mitigate AMR transmission. Video Abstract.},
}

@article {pmid42482889,
year = {2026},
author = {Zhang, XY and Huang, J and Gao, YE and Li, J and Wen, Y},
title = {Sympathetic ophthalmia induced by vitrectomy for endogenous fungal endophthalmitis: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1863685},
pmid = {42482889},
issn = {2296-858X},
abstract = {INTRODUCTION: Sympathetic ophthalmia (SO) is a rare but serious inflammatory ocular disorder. We report a case of endogenous fungal endophthalmitis caused by Aspergillus flavus infection, which resulted in SO in the contralateral eye after two vitrectomy procedures.

CASE REPORT: A 22-year-old man presented to our hospital with a 2-week history of redness and blurred vision in his right eye. Three months earlier, he had undergone two vitrectomy procedures for fungal endophthalmitis in his left eye, with culture results positive for Aspergillus flavus. Upon admission, antifungal therapy was administered; however, his health condition did not improve and progressively deteriorated. Metagenomic sequencing and microbial culture of intraocular fluid from the right eye revealed no fungi. Multimodal imaging, including optical coherence tomography (OCT), ocular B-scan ultrasonography, fundus examination, and indocyanine green angiography (ICGA), supported a definitive diagnosis of sympathetic ophthalmia. Treatment with prednisone and adalimumab stabilized the patient's condition. During the 13-month follow-up period, the patient's best-corrected visual acuity (BCVA) was 1.0 in the right eye and 0.04 in the left eye, with no observed recurrences.

CONCLUSION: Sympathetic ophthalmia is a complex ocular disorder characterized by diverse clinical and imaging features, making early diagnosis and treatment challenging. This case underscores the importance of timely intervention and aggressive therapeutic strategies for managing this condition.},
}

@article {pmid42482921,
year = {2026},
author = {Kumari, BSS and Golla, N},
title = {Bacterial ligninolytic enzymes and their applications in bioremediation.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {342},
pmid = {42482921},
issn = {2190-572X},
abstract = {UNLABELLED: Bacterial ligninolytic enzymes demonstrate high stability and catalytic efficiency across a wide range of environmental conditions, with production strongly influenced by strain-specific and process parameters. Enzyme yields vary significantly depending on the fermentation strategy, with solid-state fermentation (SSF) consistently producing higher activities than submerged fermentation (SmF) due to enhanced substrate-microbe interactions and stronger induction by lignocellulosic materials. In contrast, SmF provides improved control over pH, temperature, and aeration, enabling greater process reproducibility and scalability despite comparatively lower enzyme yields. Comparative analysis further indicates that enzyme production is highly strain-dependent and influenced by environmental parameters, including pH, temperature, substrate type, and incubation time. Among bacterial genera, Bacillus, Streptomyces, Acinetobacter, and Micrococcus exhibit consistently high enzyme production, with certain strains showing significantly elevated manganese peroxidase (MnP) and lignin peroxidase (LiP) activities under optimized conditions. Xenobiotic compounds, including synthetic dyes, pesticides, and Maillard reaction products, act as both substrates and inducers, stimulating enzyme production through oxidative stress-mediated pathways. Reactive oxygen species generated during pollutant exposure enhance the expression of bacterial ligninolytic enzymes, while structural similarities between xenobiotics and lignin-derived compounds facilitate their degradation. Sequential enzyme activity is observed, with MnP initiating early-stage oxidation followed by laccase-mediated transformation, indicating synergistic degradation mechanisms. Bacterial ligninolytic enzymes achieve degradation efficiencies exceeding 90% for a wide range of pollutants, including dyes, pesticides, and plastic-associated compounds. Spectroscopic and chromatographic analyses (UV-Vis, FT-IR, GC-MS, and LC-MS) confirm the conversion of complex aromatic compounds into simpler, less toxic intermediates. The integration of advanced omics-based approaches, including metagenomics, metatranscriptomics, and metaproteomics, is increasingly recognized as a powerful strategy for the discovery and functional characterization of novel ligninolytic bacteria and their enzymes. These findings demonstrate that bacterial ligninolytic enzymes are efficient and robust systems for pollutant degradation and lignin valorization, with strong potential for large-scale biotechnological applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04859-z.},
}

@article {pmid42482932,
year = {2026},
author = {Yan, Z and Zhou, F and Lin, D and Ruan, D and Liu, Y and Yang, M and Meng, F and Huang, S and Liu, L and Zheng, E and Cai, G and Yang, J and Zhang, Z},
title = {Domestication reshapes the swine gut microbiome: metagenomic insights into taxonomic and functional divergence across wild and domestic populations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1854568},
pmid = {42482932},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a highly diverse, complex, and dynamically evolving ecosystem within the host. However, the domestication process may alter microbial community composition and function. Here, we investigate these shifts using metagenomic analysis.

METHODS: Microbial diversity was evaluated using alpha and beta-diversity analysis. Furthermore, LEfSe and Functional analyses were employed to delineate significant disparities in microbial abundance and functional potential between wild boars (WB), Chinese domestic pigs (CDP), and Western domestic pigs (WDP).

RESULTS: Our analysis revealed distinct microbial signatures across populations. WB exhibit greater diversity differentiation from WDP, while showing higher similarity to CDP. WB were significantly enriched in the genera Treponema, Oscillibacter, and Pseudoflavonifractor. In contrast, Chinese domestic breeds were characterized by Lactobacillus, Prevotella and Ruminococcus, while WDP retained high abundances of Alistipes, Bacteroides and Clostridium. Functionally, the wild boar microbiome showed significantly higher activity in pathways related to plant secondary metabolite degradation and nutrient biosynthesis. Conversely, domestic pig microbiomes showed significant enrichment in antimicrobial resistance genes and DNA damage repair pathways.

CONCLUSIONS: These findings indicate that domestication has influenced the swine gut microbiota, contributing to distinct compositional and functional divergences. Future research may explore the potential of reintroducing wild-derived probiotics to enhance domestic pig health.},
}

@article {pmid42483398,
year = {2026},
author = {Zhao, Y and Liu, Z and Chen, X and Huang, Y and Li, S and Mao, X and Zheng, X and Yao, X and Hu, B and Zhu, L and Zhang, T},
title = {Environmental effectiveness of the National Action Plan to Contain Antimicrobial Resistance: evidence from Chinese soil.},
journal = {National science review},
volume = {13},
number = {14},
pages = {nwag387},
pmid = {42483398},
issn = {2053-714X},
abstract = {Soil antibiotic resistance genes (ARGs) represent an emerging planetary health threat. However, the environmental impacts of antimicrobial resistance (AMR) control policies remain unclear. Based on 2243 Chinese metagenomes, we generated a 14-year (2009-2022) spatiotemporal profile of Chinese soil ARGs and developed an open-access platform based on the interactive map. Relative to pre-2015 samples, the relative abundance of total ARGs (52.6%) and Rank I ARGs (77.0%) in croplands decreased markedly after 2016, coinciding with the national AMR control policy period (2016-2020). Comparing soil resistomes globally (2556 metagenomes) revealed homogenization in croplands, reflecting convergent ARG profiles under similar agricultural pressures across regions. This underscores the need for a shift from national to global intervention. Our findings highlight the importance of coordinated strategies that combined chemical pollution control with agricultural best practices to curb ARGs' dissemination under the One Health framework.},
}

@article {pmid42483952,
year = {2026},
author = {Oyama, LB},
title = {From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250036},
pmid = {42483952},
issn = {1744-1358},
support = {BB/X012794/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; BB/Z515346/1//UK Research and Innovation (UKRI)/ ; },
abstract = {Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.},
}

@article {pmid42484256,
year = {2026},
author = {Chavarría, KJS and Gomes, EO and Chaves, BA and Sampaio, VS and Silva-Neto, AV and Brito, D and Silva, LFAD and Dias, MYO and Sacchetto, L and Bernardi, V and Marques, BC and Buenemann, M and Vasilakis, N and Nogueira, ML and Lacerda, MVG and Mourão, MPG and Baía-da-Silva, DC},
title = {Integrated surveillance of arboviruses in febrile patients from the Brazilian Amazon reveals complex co-circulation dynamics and hidden viral diversity.},
journal = {Revista da Sociedade Brasileira de Medicina Tropical},
volume = {59},
number = {suppl 1},
pages = {e00422026},
doi = {10.1590/0037-8682-0042-2026},
pmid = {42484256},
issn = {1678-9849},
mesh = {Humans ; Brazil/epidemiology ; Cross-Sectional Studies ; Male ; Female ; *Arboviruses/genetics/classification/isolation & purification ; *Arbovirus Infections/epidemiology/virology/diagnosis ; Child, Preschool ; Adult ; Phylogeny ; Middle Aged ; Adolescent ; Enzyme-Linked Immunosorbent Assay ; Child ; *Fever/virology ; Coinfection/virology ; Young Adult ; Aged ; },
abstract = {BACKGROUND: Arboviral infections continue to be a significant public health challenge in the Brazilian Amazon. Overlapping symptoms, limited laboratory access, and the circulation of multiple arboviruses hamper clinical diagnosis. This study aimed to characterize the epidemiological, clinical, laboratory and genomic profiles of arboviral infections in febrile patients in Manaus, Brazil, and explore additional viral agents using metagenomic sequencing.

METHODS: A cross-sectional study was conducted between February 2021 and February 2023 at a tertiary reference center in Manaus, Brazil. Patients aged ≥ 5 years of age presenting with a rash and either a fever or a history of fever lasting <7 days and a negative thick blood smear for malaria were enrolled. Serum samples were tested for dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHIKV), yellow fever virus (YF), Oropouche virus (OROV), and Mayaro virus (MAYV) using ELISA and RT-qPCR. Positive samples were subjected to amplicon-based genome sequencing for phylogenetic analysis. A subset of RT-qPCR negative samples was analyzed using de novo shotgun metagenomic sequencing.

RESULTS: Among the 708 enrolled participants, 243 (34.3%) had a laboratory-confirmed arboviral infection: 92 (37.9%) DENV, 64 (26.3%) CHIKV, and 4 (1.6%) ZIKV, while 83 (34.2%) laboratory profiles were compatible with coinfection, predominantly DENV+CHIKV (55/83; 66.3%). Circulation of DENV-1 genotype V and DENV-2 genotypes III (Asian American) and II (Cosmopolitan) was identified. Metagenomic analysis of 35 samples detected Pegivirus hominis and Erythroparvovirus primate 1.

CONCLUSIONS: These findings demonstrate complex arbovirus co-circulation in Manaus and support integrated surveillance strategies combining molecular, serological, and genomic approaches.},
}

Humans
Brazil/epidemiology
Cross-Sectional Studies
Male
Female
*Arboviruses/genetics/classification/isolation & purification
*Arbovirus Infections/epidemiology/virology/diagnosis
Child, Preschool
Adult
Phylogeny
Middle Aged
Adolescent
Enzyme-Linked Immunosorbent Assay
Child
*Fever/virology
Coinfection/virology
Young Adult
Aged

@article {pmid42484341,
year = {2026},
author = {Sato, Y and Uda, Y and Nagao, Y},
title = {Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0167726},
doi = {10.1128/spectrum.01677-26},
pmid = {42484341},
issn = {2165-0497},
abstract = {Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.},
}

@article {pmid42484489,
year = {2026},
author = {Xu, C and Ling, W and Xiao, X and Wang, M and Lu, J and Tang, J},
title = {Integrating Cerebrospinal Fluid Metagenomic Next-Generation Sequencing and Immune Profiling in Recurrent HSV-1 Encephalitis: A Case Report and Narrative Review.},
journal = {Journal of child neurology},
volume = {},
number = {},
pages = {8830738261465526},
doi = {10.1177/08830738261465526},
pmid = {42484489},
issn = {1708-8283},
abstract = {BackgroundRecurrent herpes simplex virus type 1 (HSV-1) encephalitis in children is rare, and its pathophysiology remains incompletely understood. Both viral reactivation and host immune dysregulation have been implicated. Advances in metagenomic next-generation sequencing (mNGS) and immune profiling provide new opportunities to elucidate disease mechanisms.Case Presentation: We detail a 13-year-old boy of Qiang ethnicity who experienced 3 neurologic episodes, including 2 virologically confirmed HSV-1 encephalitis events over 7 years. The third recurrence involved fever, seizures, and progressive bilateral temporal lobe lesions visible on magnetic resonance imaging. Cerebrospinal fluid (CSF) mNGS confirmed HSV-1 reactivation, and viral genomic sequencing demonstrated a highly conserved viral genome without high-confidence nonsynonymous mutations. Immune profiling showed compartmentalized central nervous system inflammation with elevated CSF cytokines (interleukin [IL]-6, IL-8, IL-10, interferon [IFN]-α, IFN-γ) and altered lymphocyte subsets, despite normal serum results. The patient was treated with acyclovir, intravenous immunoglobulin, and low-dose corticosteroids, which controlled seizures but left persistent neurocognitive deficits. Multidisciplinary follow-up is crucial to mitigate long-term neurocognitive sequelae.Literature Review: We reviewed 10 previously published pediatric cases of recurrent HSV-1 encephalitis, which demonstrated heterogeneous recurrence intervals, contralateral or novel lesion involvement, and frequent cognitive sequelae. Few studies integrated viral genomics or immune profiling.ConclusionsThe findings suggest that recurrent pediatric HSV-1 encephalitis may be driven by viral reactivation in the context of CNS-restricted immune dysregulation, rather than reinfection or viral evolution.},
}

@article {pmid42477351,
year = {2026},
author = {Hu, L and Hou, B and Yan, S and Tai, W and Xia, Y and Wu, J and Li, D and Shi, B},
title = {Lacticaseibacillus rhamnosus OF44 alleviates allergic rhinitis by rebalancing host immunity and gut microbial function.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00974-6},
pmid = {42477351},
issn = {2396-8370},
abstract = {Allergic rhinitis (AR) involves a maladaptive type 2 inflammatory response driven by systemic immune imbalance and gut dysbiosis. Here, we identify a probiotic strain, Lacticaseibacillus rhamnosus OF44, with significant probiotic potential that alleviates allergic pathology and is associated with coordinated immunological and microbial reprogramming. In an ovalbumin-induced AR rat model, OF44 administration markedly reduced nasal allergic symptoms, normalized serum and nasal immunoglobulin and cytokine levels, and restored the balance of Th1/Th2/Th17/Treg cell populations. Metagenomic profiling revealed that OF44 reshaped the gut microbial structure by enriching beneficial commensals (Rikenellaceae, Alistipes) and suppressing the proinflammatory family Enterobacteriaceae. Functional profiling further demonstrated that OF44 reversed the AR-associated enrichment of pro-inflammatory pathways, including biofilm formation, flagellar assembly, and multidrug resistance, while restoring metabolic pathways related to amino acid metabolism, energy metabolism, and short-chain fatty acid production. Integrated taxonomic-functional correlation analysis suggested that butanoate and lipoic acid metabolic pathways were microbial functions potentially associated with enhanced immune regulation. Collectively, these findings demonstrate that OF44 attenuates AR by reprogramming gut microbial composition and functional capacity, providing mechanistic support for its application as a functional probiotic for the management of allergic disease.},
}

@article {pmid42477402,
year = {2026},
author = {Guo, F and Li, B and Song, P and Zhang, M and Hu, T and Lin, Z and Gao, H and Liang, C and Zhang, T and Cai, Z},
title = {Gut microbiota mediates dietary adaptation across spatially varying diets in the endangered Przewalski's gazelle (Procapra przewalskii).},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10717-8},
pmid = {42477402},
issn = {2399-3642},
support = {2024-SF-146//QingHai Department of Science and Technology (Bureau of Science and Technology of Qinghai Province)/ ; 32570609//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The extreme and heterogeneous Qinghai-Tibet Plateau challenges wildlife survival. Przewalski's gazelle (Procapra przewalskii) is confined to the northeastern Plateau around Qinghai Lake, where habitat fragmentation exposes isolated populations to distinct plant resources. How this species adapts to dietary heterogeneity via internal physiology remains unclear. Here, we integrated dietary analysis, shotgun metagenomics, and untargeted metabolomics to examine relationships among diet, gut microbiome function, and metabolic outputs across three regions. We observed population-specific differences in plant consumption, gut microbial composition, and functional potential, notably in carbohydrate degradation, plant secondary metabolite transformation, and energy metabolism. Metabolomics revealed shifts in short-chain fatty acids and lipid- and energy-related pathways. Co-occurrence networks and partial least squares path modeling (PLS-PM) indicated diet influences metabolites indirectly via the gut microbiome as a key mediator. Our findings establish a "diet-gut microbiome-metabolic output" framework, highlighting microbial mechanisms underpinning local adaptation and informing conservation of endangered plateau species.},
}

@article {pmid42477662,
year = {2026},
author = {Chao-Chao, Q and Zhi-Ruo, L and Xiao-Qing, L and Yan-Hong, M and Yue-Ying, Z and Ning, P and Ji-Chan, S and Xian-Gao, J},
title = {Exploring differences in alveolar microbiome between pulmonary tuberculosis patients with different treatment outcomes: a metagenomic study from China.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04500-y},
pmid = {42477662},
issn = {1471-2466},
abstract = {This study aimed to investigate differences in the composition and functional characteristics of alveolar microbiota in patients with pulmonary tuberculosis (PTB) exhibiting differential therapeutic responses. Thirty-two patients with drug-sensitive PTB who had completed standard anti-tuberculosis therapy were enrolled and classified into good-response (n = 16) and poor-response (n = 16) groups. Bronchoalveolar lavage fluid (BALF) samples were collected and analysed using metagenomic sequencing to characterize microbial community and functional pathways. No significant differences were observed in α-diversity between the two groups; however, β-diversity analysis demonstrated moderate but significant in microbial community structure (ANOSIM, R = 0.381, P < 0.001). The good efficacy group was characterized by enrichment of Prevotella, Staphylococcus, and oral commensal bacteria including Fusobacterium and Rothia, together with significantly increased pathways related to peptidoglycan biosynthesis, glutathione metabolism, energy production, and DNA repair. In contrast, the poor efficacy group was characterised by enrichment of Microbacterium and activation of functional pathways associated with biofilm formation. These findings suggest that both the taxonomic composition and functional activity of the pulmonary microbiome are closely associated with anti-tuberculosis treatment outcomes.},
}

@article {pmid42477714,
year = {2026},
author = {Zhang, Y and Chang, ZH and Gan, S and Wang, SH and Luo, JX and Jin, L and Zhai, XF and Sun, YB},
title = {Hologenomic rewiring facilitates dietary adaptation to chitin-rich marine resources in the crab-eating frog.},
journal = {Frontiers in zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12983-026-00626-1},
pmid = {42477714},
issn = {1742-9994},
support = {XNYB24-07//Foundation of Key Laboratory of Southwest China Wildlife Rsources Conservation (Ministry of Education)/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 202401BC070011//Yunnan Fundamental Research Projects/ ; },
abstract = {BACKGROUND: Secondary adaptation of amphibians to marine environments is exceptionally rare. The crab-eating frog, Fejervarya cancrivora, is the only known amphibian capable of completing its life cycle in intertidal zones, where it faces dual challenges: high salinity stress and a diet rich in chitinous crab exoskeletons. While osmoregulatory adaptations have been well documented, the synergistic roles of the host's digestive system and its gut microbiota in this dietary specialization remain unclear.

RESULTS: Here, we integrated histological analysis, comparative transcriptomics, chitinase activity assays, and gut metagenomics to compare F. cancrivora with its freshwater congener, F. multistriata. We found that F. cancrivora has evolved a thicker gastric muscularis and longer gastric villi, consistent with enhanced processing of hard prey. Comparative transcriptomic analysis revealed an expanded repertoire of putative chitinase encoding transcripts (15 vs. 8 non-redundant transcripts), and both gastric and intestinal tissues exhibit significantly higher and more pH-tolerant chitinase activity. In contrast, the gut microbiota of F. cancrivora is not enriched for microbial chitin degradation genes, but instead is functionally specialized for lipid metabolism and DNA repair pathways. A controlled feeding experiment confirmed that the microbial enrichment in lipid metabolism is diet-driven, while the DNA repair pathways is largely independent of diet and likely reflects microbiome-intrinsic adaptation to chronic saline stress.

CONCLUSIONS: Together, these findings suggest a partially partitioned host-microbiome strategy in which host manages chitin breakdown, while the microbiota optimizes energy harvest and intrinsic stress tolerance. Our findings provide a new paradigm for amphibian marine adaptation, and highlights host-microbiome functional differentiation during niche expansion.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42477746,
year = {2026},
author = {Jiang, P and Zhou, M and Wen, Y and Hu, Z and Hu, Y and Liu, M},
title = {Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00601-5},
pmid = {42477746},
issn = {2524-4671},
support = {2022YFA1304204//National Key R&D Program of China/ ; },
abstract = {Post-weaning estrus return is critical for sow reproductive efficiency. The gut microbiota is associated with post-weaning estrus of sows, potentially through effects on nutrient utilization and metabolic regulation. However, current microbial signatures associated with estrus return remain poorly resolved at the strain-level. Here, we explored the relationship between the gut microbiome and post-weaning estrus in sows using metagenomics and metabolomics profiling of 85 fecal samples. From 2,704 non-redundant metagenome-assembled genomes (MAGs), 608 estrus-associated MAGs were identified by LEfSe analysis. Among these, 48 high-quality MAGs were selected for co-abundance network analysis, which revealed two competing microbial functional guilds. Guild 1 was significantly enriched in the normal group, harboring more β-glucosidase and folate biosynthesis genes, but fewer antibiotic resistance genes and virulence factors than Guild 2. A random forest model based on these 48 MAGs demonstrated excellent performance in distinguishing between the normal and non-return sows (AUROC = 0.946) and was validated in an independent dataset (n = 29, AUROC = 0.818). Additionally, the guild-level microbiome index (GMI) derived from abundance differences between the two guilds also showed good discriminatory power (AUROC = 0.799). Integrated multi-omics analysis revealed alterations in fecal bile acid metabolism in non-return sows, characterized by a significantly increased ratio of secondary to primary bile acids and the accumulation of specific secondary bile acids. Notably, the enrichment of the Clostridia strain SFHK01 sp016296675, a member of Guild 2, and its encoded 12α-HSDH gene was positively associated with specific secondary bile acids, suggesting that this specific strain is involved in the distinct metabolic alterations observed in non-return sows. These findings provide the genome-resolved and guild-based insights into the gut microbial signatures associated with post-weaning estrus return, offering a basis for potential microbiota-targeted interventions to improve sow reproductive performance.},
}

@article {pmid42477864,
year = {2026},
author = {Lakamp, AD and Adams, S and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML},
title = {Influence of host genetics on the functional composition of the rumen metagenome in beef cattle1.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag224},
pmid = {42477864},
issn = {1525-3163},
abstract = {Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.},
}

@article {pmid42477955,
year = {2026},
author = {Fariba, E and Rosanna, V and Domenico, C and Gaetano, S and Mauro, L and Lucio, LR},
title = {Oral and Pancreatobiliary Microbiota in Cancer: A Systematic Review of Compositional Alterations and Their Clinical Implications.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70172},
pmid = {42477955},
issn = {1600-0714},
abstract = {BACKGROUND: Associations between microbial dysbiosis and malignancies of the pancreatobiliary system have been described in recent studies. As a result of the limited number of studies that have been done specifically on the malignancies of the biliary tract, information regarding oral, biliary and tumour-related microbial alterations was combined to provide an overview of the microbial changes that may occur.

METHODS: Studies that involved observations on the composition or presence of dysbiosis of the microbiota from oral (saliva, oral rinse, dental plaque) or other non-oral specimens (bile, pancreatic tissue, duodenal tissue and bacteria-derived extracellular vesicles from plasma) in patients with pancreatobiliary malignancies were considered. The risk of bias was evaluated using the Newcastle-Ottawa Scale (NOS) for case-control study designs and the JBI Checklist for cross-sectional studies.

RESULTS: There were a total of 16 studies involving 1426 participants that were conducted using both case-control and cross-sectional study designs. Samples were collected from saliva, oral wash, bile, pancreatic and duodenal tissues and bacterial extracellular vesicles isolated from plasma samples. The most common method used was 16S rRNA sequencing, and two used shotgun metagenomics. In all the studies, patients with pancreatobiliary cancers, especially PDAC, had a significantly higher abundance of opportunistic microbes like Streptococcus, Veillonella, Fusobacterium, Prevotella and a lower abundance of commensal bacteria like Neisseria and Corynebacterium. There was overlap of microbial profile in the oral cavity and tumour/bile compartments in a few studies.

CONCLUSIONS: Although the current data is preliminary and observational in nature, there are consistent findings linking microbiota dysbiosis with cancers of the pancreatobiliary region within both oral and non-oral body sites. Causality has not been established yet. The use of microbial signatures as a basis for biomarker development is a promising research direction.},
}

@article {pmid42478129,
year = {2026},
author = {Zhou, Y and Xu, J and Zhou, W and Wu, P and Yang, S and Ji, L and Shen, Q and Wang, X and Liu, Y and Zhou, C and Zhang, W and Xu, M},
title = {Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.},
journal = {Journal of medical virology},
volume = {98},
number = {7},
pages = {e71063},
doi = {10.1002/jmv.71063},
pmid = {42478129},
issn = {1096-9071},
support = {2023YFD1801300//National Key Research and Development Programs of China/ ; 82550118//National Natural Science Foundation of China/ ; 82341106//National Natural Science Foundation of China/ ; BK20241926//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Humans ; *Genetic Variation ; *Virome/genetics ; *Genome, Viral ; *Respiratory Tract Infections/virology/microbiology ; Sputum/virology ; Metagenomics ; Phylogeny ; *Mycoses/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Sequence Analysis, DNA ; },
abstract = {Respiratory tract infections represent a leading cause of morbidity and mortality globally, with viral pathogens accounting for a substantial proportion of these cases. However, research on the human respiratory virome is still in its infancy, and our understanding of this field remains relatively limited. In the present study, viral metagenomic sequencing was conducted on 65 sputum samples obtained from patients with severe fungal infections. We successfully assembled viral genome sequences belonging to four distinct viral families: Anelloviridae, Genomoviridae, Microviridae, and Inoviridae. Through systematic analysis of the virome composition, this study characterized the structural features of the respiratory virome in patients with severe fungal infections. The findings provide a foundational description of viral diversity in this specific clinical context. These findings lay a theoretical foundation for clinical pathogen detection, targeted interventions, and the development of future prevention strategies.},
}

Humans
*Genetic Variation
*Virome/genetics
*Genome, Viral
*Respiratory Tract Infections/virology/microbiology
Sputum/virology
Metagenomics
Phylogeny
*Mycoses/virology/microbiology
*Viruses/genetics/classification/isolation & purification
Female
Male
Middle Aged
Adult
Sequence Analysis, DNA

@article {pmid42478355,
year = {2026},
author = {Mu, M and Mu, C and Liu, H and Song, J and Du, X and Ge, Y and Lei, P and Mo, X and Wei, Y and Zhang, C and Zhao, C},
title = {Microbial Reduction of Methane Emissions from High-Altitude Thermokarst Lakes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17973},
pmid = {42478355},
issn = {1520-5851},
abstract = {Thermokarst lakes, a typical landscape resulting from abrupt permafrost thaw, are expected to be a substantial CH4 source. Climate change perturbs CH4 dynamics in these systems, particularly through increasingly frequent wet-dry cycles in small thermokarst lakes. However, how wet-dry alternation alters microbial communities remains poorly understood, and quantifying the effects of microbial shifts on CH4 emissions from these lakes represents a key challenge. Here, by integrating field observations, laboratory incubation experiments, and amplicon sequencing, we show that seasonal thermokarst lakes with wet-dry alternation exhibit a 41-70% decrease in diffusive CH4 emissions compared with perennial lakes. Alternating wet-dry cycles lead to a 33-37% decrease in the relative abundances of methanogens and a 39-59% decline in syntrophic partners in lake sediments, while the anaerobic methanotrophic archaea Candidatus Methanoperedens increased from 0.2% to 20.8%. Functional gene analyses indicate acetoclastic methanogenesis, dominated by Methanosaeta, is the primary pathway of CH4 production. The reduction in CH4 emissions is associated with changes in sediment properties, as well as decreased abundances of methylotrophic Methanomassiliicoccaceae and syntrophs. Moreover, denitrifying anaerobic CH4 oxidation processes mediated by Candidatus Methanoperedens lead to a further decline in CH4 emissions. This study provides novel insights into the microbial changes and pathways regulating diffusive CH4 emissions from seasonal thermokarst lakes, which is crucial for assessing permafrost carbon-climate feedback and prioritizing CH4 mitigation strategies.},
}

@article {pmid42478812,
year = {2026},
author = {Henige, M and Anklam, K and Yoon, I and Wheeler, J and Dawson, G and Döpfer, D},
title = {Effect of Saccharomyces cerevisiae fermentation postbiotic supplementation on metagenomics of digital dermatitis lesions in lactating Holstein cows.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0030426},
doi = {10.1128/spectrum.00304-26},
pmid = {42478812},
issn = {2165-0497},
abstract = {Digital dermatitis (DD) is the leading cause of lameness in cattle, posing major animal welfare and economic concerns. Effective prevention strategies are increasingly important given emerging antimicrobial resistance associated with common DD treatments. Supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has been shown to enhance innate immunity and reduce DD lesion development. This study evaluated the effect of a commercial SCFP supplement on the microbial composition of DD lesions using shotgun metagenomic sequencing to characterize microbial communities and associated antimicrobial resistance genes. Beta diversity analysis revealed that stage M4 DD lesions from SCFP-supplemented cows had a trend for different microbial compositions compared with controls (P = 0.051). At the genus level, M2 lesions were found to have statistically significant lower abundance of the genera Desulfovibrio, Pseudomonas, Staphylococcus, Anaerotignum, Caproicibacterium, and Bacteroides in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the genera Fusobacterium, Citricoccus, Listeria, and Fundicoccus as compared with the control (P < 0.05). M4 lesions were found to have statistically significant lower abundance of the genera Blautia and Petrimonas in the SCFP treatment group compared with the control (P < 0.05). At the species level, M2 lesions were found to have statistically significant lower abundance of the species Desulfovibrio sp. G11, Anaerotignum sp. MB30-C6, Caproicibacterium argilliputei, and Prevotella intermedia in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the species Fundicoccus culcitae and Helcococcus ovis as compared with the control (P < 0.05). Metagenomic analysis identified antimicrobial resistance genes associated with multiple antibiotics commonly used for DD treatment, including tetracyclines, lincosamides, and pleuromutilins. These findings demonstrate the potential for SCFP supplementation to alter the microbial composition of DD lesions while highlighting the ongoing concerns regarding antimicrobial resistance in DD management.IMPORTANCEDigital dermatitis (DD) causes substantial economic loss and welfare concerns in cattle production systems worldwide. Our findings show that dietary supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has the potential to alter the microbial ecology of DD lesions. Importantly, this work identifies antimicrobial resistance genes within DD lesions, underscoring the limitations of antibiotic-based control strategies. By linking nutritional supplementation to changes in microbial communities and resistance gene profiles, this study advances understanding of non-antibiotic approaches to disease mitigation and supports the development of sustainable, microbiome-informed management practices in food animal production.},
}

@article {pmid42478878,
year = {2026},
author = {Davis, EC and Jackson, CM and Diaz, NS and Susana, J and Nelson, A and Insel, R and Seppo, AE and Järvinen, KM},
title = {Maternal Perinatal Gut Microbiome Is Shaped by Traditional Farming Lifestyle and Associated With Early Childhood Atopic Disease.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70446},
pmid = {42478878},
issn = {1398-9995},
support = {U01 AI131344/AI/NIAID NIH HHS/United States ; //University of Rochester University Research Award/ ; NIFA 67012-35010//U.S. Department of Agriculture/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; T32 HL066988/HL/NHLBI NIH HHS/United States ; },
abstract = {Maternal exposure to a traditional farming lifestyle during pregnancy is associated with protection against allergic disease in childhood; however, the mechanism remains unclear. Pre-clinical work has demonstrated a role for the maternal gut microbiome in fetal immune programming. Given the diverse microbial exposure on farms, we sought to assess whether the maternal gut microbiome may mediate the relationship between maternal farm exposure and protection against offspring allergic disease. Deep shotgun metagenomic analysis of the perinatal fecal microbiome showed that women from an Old Order Mennonite traditional farming community (OOM, n = 68) harbored a more diverse gut microbiome relative to women from urban/suburban Rochester, NY (ROC, n = 55). We identified several bacterial species differentially abundant between lifestyle groups, including those from Dorea, Anaerobutyricum, Bifidobacterium, and Bacteroides genera, which translated to marked differences in microbiome functional capacity. These differences in the gut microbiome composition were accompanied by targeted metabolite findings indicating higher serum acetate and isobutyrate levels in OOM women that were positively correlated with cord plasma levels and infant systemic IgA concentrations. Among urban women, maternal microbiome composition was associated with early childhood atopic disease outcomes. Specifically, Dorea longicatena and Segatella copri were least abundant in urban mothers whose infants developed atopic disease (atopic dermatitis) or IgE-mediated food allergy alone, respectively, and were most abundant in the OOM mothers. Together, these findings highlight the maternal gut microbiome and metabolites as potential contributors to prenatal farming lifestyle protection against early childhood allergic disease.},
}

@article {pmid42471440,
year = {2026},
author = {Xiang, ZF and Wang, H and Yang, F and Chen, SJ and Huang, TS and Wang, SQ and Jiang, ZH and Hu, YY and Xiang, M and Wang, KX and Wang, YZ and Huang, YL and Li, YR and Shi, M and Hou, W and Chen, LJ},
title = {Metatranscriptomics reveals urbanization-driven divergence in rodent viromes and zoonotic risks in Chinese megacities.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10711-0},
pmid = {42471440},
issn = {2399-3642},
support = {2023KF003//State Key Laboratory of Virology (SKLV)/ ; U20A20396//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Metagenomic sequencing has advanced our understanding of wildlife-associated viruses and enabled identification of potential zoonotic pathogens. However, most studies remain geographically limited, with few systematic comparisons of virome compositions across urbanization gradients. To address this gap, we conducted large-scale sampling in two densely populated Chinese megacities-Wuhan and Shenzhen-with distinct climates. We collected 1,072 rodents from four species that frequently interact with humans, enabling comparative analysis of urban rectal virome dynamics and zoonotic risks in rodents. We identified 35 vertebrate-associated viruses. Among them, 9 were potentially novel species, including Norovirus and Orthopicobirnavirus species, and 3 had zoonotic potential, namely Orthohantavirus seoulense and human coronavirus OC43 (HCoV_OC43). We also discovered two viruses previously unreported in rodents, Erinaceus hedgehog Seoul orthohantavirus and Canine astrovirus, which revealed cross-order transmission risk. Additionally, 22 high-risk viruses were identified, with Wuhan and Shenzhen showing distinct prevalence patterns. Our analysis shows that inter-city rectal virome divergence is structured by meteorological variables, independently explaining 5.0% of the variation in viral community composition. Our findings highlight the importance of spatial distance in shaping the distribution and transmission of rodent-borne viruses. These insights are essential for proactive surveillance and mitigation of emerging zoonotic threats in high-density urban environments.},
}

@article {pmid42472228,
year = {2026},
author = {Li, X and Fan, M and Yue, J and Xie, J and Zhang, Y and Lu, X and Liu, L and Li, X and Huang, Y},
title = {Metagenomic Next-Generation Sequencing for Brain Abscess: Improved Pathogen Detection, Targeted Antimicrobial Therapy, and Association with Fewer Surgical Interventions.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {617362},
pmid = {42472228},
issn = {1178-6973},
abstract = {BACKGROUND: Brain abscesses demand prompt, accurate pathogen identification; however, identification using conventional culture is limited, especially for anaerobic and polymicrobial infections. We compared the diagnostic and clinical utility of metagenomic next-generation sequencing (mNGS) with that of conventional culture in patients with brain abscess.

METHODS: We retrospectively included 115 patients with confirmed brain abscess pathogens. Seventy-two patients underwent both mNGS and conventional culture, and 43 underwent culture alone. We evaluated diagnostic performance, pathogen profiles, adjustments to antimicrobial regimens, and clinical outcomes.

RESULTS: mNGS detected pathogens in 86.1% of patients versus 44.4% for culture (Cohen's kappa test p=0.004; McNemar's test p=0.0001). It identified mixed infections in 53.2% of cases, whereas culture predominantly revealed single pathogens. mNGS produced substantially higher detection rates than culture for anaerobic bacteria (50.0% vs 16.7%) and oral-derived bacteria (77.6% vs 61.1%). Antimicrobial regimens were adjusted in 54.2% of patients based on mNGS results; 61.5% of these adjustments involved de-escalation, and vancomycin was discontinued in 77.8% of patients. mNGS use was associated with a lower surgical intervention rate (47.2% vs 65.1%, P = 0.002). There were no differences in length of hospital stay, fever duration, Glasgow Outcome Scale score, or hospitalization costs. In eight patients without reported dental history, mNGS revealed occult odontogenic foci, enabling source control and potentially reducing recurrence risk.

CONCLUSION: mNGS outperformed conventional culture for detecting mixed infections, anaerobes, and pathogens of d origin. It may inform targeted antimicrobial therapy and assist in identifying the infection source. In this single‑center retrospective study, which is subject to potential selection bias, mNGS use was associated with a lower rate of surgical intervention; however, this finding should be interpreted as an association rather than causation, and prospective studies are needed to confirm this observation. These findings support the integration of mNGS into diagnostic algorithms for brain abscess.},
}

@article {pmid42472698,
year = {2026},
author = {Zhong, Y and Peng, L},
title = {Immune-guided calibration of metagenomic next-generation sequencing (mNGS) results in a pregnant patient with Listeria infection: a case report.},
journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {39},
number = {1},
pages = {2698915},
doi = {10.1080/14767058.2026.2698915},
pmid = {42472698},
issn = {1476-4954},
mesh = {Humans ; Female ; Pregnancy ; *Listeriosis/diagnosis/immunology/drug therapy ; Adult ; *Pregnancy Complications, Infectious/diagnosis/immunology/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; Listeria monocytogenes/genetics/isolation & purification ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Listeriosis during pregnancy is a rare but life-threatening infection that often presents with nonspecific symptoms, making timely diagnosis difficult. This article reports a case in which the clinical presentation and immune profile were highly consistent with Listeria monocytogenes infection, leading to a presumptive clinical diagnosis. The patient was successfully treated following a diagnostic approach that integrated host immune profiling with AI-assisted decision-making, despite dual interference from Ureaplasma urealyticum detected by metagenomic next-generation sequencing (mNGS) and Staphylococcus capitis detected by blood culture.

CASE PRESENTATION: A 25-year-old female patient, at 37[+6 ]weeks of gestation, presented with persistent high fever following induced labor due to intrauterine fetal death. External hospital blood culture and our hospital's reproductive tract mNGS suggested Staphylococcus capitis and Ureaplasma urealyticum, respectively. However, intensified treatment targeting these pathogens was ineffective.

DIAGNOSTIC PROCESS: Further investigation revealed a characteristic immune imbalance in the patient: a concurrent significant elevation of IFN-γ and IL-10, accompanied by activated CD8+ T cells. With AI-assisted analysis, this immune profile was found to be highly consistent with Listeria monocytogenes infection.

TREATMENT AND OUTCOME: After switching to ampicillin combined with gentamicin, the patient's body temperature rapidly normalized, and she recovered and was discharged.

CONCLUSION: When etiological diagnosis reaches an impasse, integrating host immune characteristics with AI-assisted decision-making can provide crucial diagnostic clues for infections caused by rare pathogens when microbiological confirmation is unavailable.},
}

Humans
Female
Pregnancy
*Listeriosis/diagnosis/immunology/drug therapy
Adult
*Pregnancy Complications, Infectious/diagnosis/immunology/drug therapy/microbiology
High-Throughput Nucleotide Sequencing
Listeria monocytogenes/genetics/isolation & purification
Metagenomics/methods
Anti-Bacterial Agents/therapeutic use

@article {pmid42472835,
year = {2026},
author = {Contreras-Martinez, H and la Hoz, DE and López, Y and López, Y and Hoyos, R and Romero, L and Alemán, M and Martínez, C and Gastelbondo, B and Álvarez, K and Borja, G and Galeano, K and García, A and Fragoso, P and Arrieta, G and Mattar, S},
title = {First molecular detection of the genus Almendravirus in Johnbelkinia ulopus and Anopheles apicimacula mosquitoes from the Colombian Caribbean.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07432-y},
pmid = {42472835},
issn = {1756-3305},
abstract = {BACKGROUND: Rhabdoviridae includes many viruses, among which rabies virus is notable. Other genera in this family can infect mammals, birds, reptiles, fish, and plants.

METHODS: Between October 2022 and July 2023, mosquitoes were collected from some municipalities in the Córdoba and Cesar departments, Colombian Caribbean. Pools were formed according to taxonomic identification and geographic area. RNA was extracted, and sequencing was performed using MGI-G50 platform. Bioinformatics analyses were performed using the Galaxy platform and the Diamond-MEGAN program. The MAFFT program was used for sequence alignment. The Prokka program was used for genome annotation, IQ-TREE was used for phylogenetic reconstruction, and iTOL was used to visualize and edit the tree. The Clustal Omega program of the European Molecular Biology Laboratory (EMBL-EBI) was used to construct a percent similarity matrix, and Unipro UGENE was used to align the amino acids of the L protein with the conserved consensus sequence (GDNQ).

RESULTS: Two new genomes showing high similarity to Almendravirus arboretum (ABTV), and Almendravirus chico (RCHV) were identified in a single pool of Johnbelkinia ulopus mosquitoes collected in Córdoba. Additionally, a third genome with a low similarity percentage to the L segment of the Almendravirus menghai (MRV) from China was detected in Anopheles apicimacula from Cesar.

CONCLUSIONS: This is the first study in Colombia that reports the ABTV and RCHV in Jb. ulopus mosquitoes and the first report of a phylogenetically similar sequence to the MRV, which could be a new virus of the Rhabdoviridae family.},
}

@article {pmid42473456,
year = {2026},
author = {Nwaiwu, O and Onyeaka, H and Ibekwe, VI and Okorondu, SI and Nnokwe, JC and Edward, KC and Chikezie, PC and Offor-Emenike, IU and Ewelike, NC and Anyanwu, NJ and Nwachukwu, IN and Chinakwe, EC and Okorondu, MM},
title = {Molecular phylogeny of 16S rRNA sequences from Ugba (Pentaclethra macrophylla) seeds.},
journal = {Access microbiology},
volume = {8},
number = {7},
pages = {},
pmid = {42473456},
issn = {2516-8290},
abstract = {The evolutionary analysis of bacterial species harbouring 16S rRNA sequences detected in the oil bean seeds of Ugba (Pentaclethra macrophylla) was carried out. The food product has a high socio-economic relevance to communities where it is consumed. Species such as Kurthia gibsonii, Stenotrophomonas geniculata and Alcaligenes nematophilus found in Ugba may have occurred in the environment and entered the sample in the field during or before harvest. The phylogenetic analysis of 35 sequences showed that some strains of the same species resolved into different monophyletic groups, suggesting species divergence or distinct evolutionary lineages. The species K. gibsonii was found to be the earliest ancestor following sequence-based ancestral analysis, suggesting that it was present in the analysed samples before other bacteria. The Ugba seeds appear to harbour a diverse group of bacteria and will benefit from metagenomic investigations as well as studies of the mechanism of survival and succession to reveal the true nature of the resident flora. This will help safeguard public health and highlight the organism's relevance to food safety surveillance and microbial evolution. Increased knowledge of the resident organisms will also lead to the improvement of fermentation techniques and enhance the quality of the final product.},
}

@article {pmid42473567,
year = {2026},
author = {Yan, J and Yang, H and Wan, L and Zhao, C},
title = {Oral Histoplasmosis in an Immunocompetent Male Diagnosed by Culture, Histopathology, and MetaCAP.},
journal = {International medical case reports journal},
volume = {19},
number = {},
pages = {596732},
pmid = {42473567},
issn = {1179-142X},
abstract = {BACKGROUND: Histoplasmosis is a systemic fungal infection caused by the dimorphic fungus Histoplasma capsulatum, commonly found in soil contaminated by bird or bat excrement. Oral granulomatous histoplasmosis is a relatively rare presentation that often lacks typical clinical features. Patients may experience persistent oral pain or lesions lasting several weeks, and clinical presentations can mimic malignant tumors or other infectious pathogens, leading to diagnostic challenges.

CASE PRESENTATION: We report a case of oral granulomatous histoplasmosis in a 53-year-old immunocompetent male, initially suspected of having lymphoma or tuberculosis. To our knowledge, this is an exceptional case of oral histoplasmosis diagnosed in an immunocompetent patient through a combination of tissue fungal culture, pathological biopsy, and metagenomic capture sequencing (metaCAP).

CONCLUSION: The case highlights the importance of considering fungal infections in persistent oral lesions of immunocompetent patients. It also demonstrates that metaCAP, alongside conventional culture and histopathology, can facilitate a definitive diagnosis in challenging cases.},
}

@article {pmid42473611,
year = {2026},
author = {Liu, M and Chen, Y and Xie, P and Xu, W and Huang, S and Liu, B},
title = {A Case of Listeria monocytogenes Meningitis (Complicated) with Hydrocephalus and Occipital Lobe Infarction.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {624063},
pmid = {42473611},
issn = {1178-6973},
abstract = {BACKGROUND: Listeria monocytogenes (LM) meningitis is a rare but severe infection, particularly in immunocompromised patients, often leading to complications such as hydrocephalus, markedly increasing treatment complexity and the risk of poor outcomes.

CASE PRESENTATION: We report a case of LM meningitis in an immunocompromised patient. The illness began with fever and gastrointestinal symptoms, followed by neck stiffness and altered consciousness. LM was identified via blood culture, cerebrospinal fluid (CSF) culture, and metagenomic next-generation sequencing (mNGS). During hospitalization, the patient developed decompensated hydrocephalus and a right occipital lobe infarction, emergent external ventricular drainage (hospital day 4) and subsequent ventriculoperitoneal shunting (hospital day 44) were performed, which were potentially life-saving. After comprehensive treatment and rehabilitation, the patient was discharged on day 85 without significant neurological deficits.

CONCLUSION: Clinical presentation of LM meningitis may be atypical, especially in immunocompromised patients. In such patients, aggressive management of hydrocephalus-including timely CSF diversion-is potentially life-saving. Early pathogen detection through combined blood culture, CSF culture, and mNGS, together with prompt, targeted antimicrobial therapy and dynamic management of neurological complications such as hydrocephalus, is essential for improving clinical outcomes.},
}

@article {pmid42474014,
year = {2026},
author = {Yu, Y and Zhao, H and He, Y and Zhao, J and Yang, X and Liu, X and Cheng, X},
title = {Therapeutic Effects of the Traditional Chinese Formula Qifuyin on Cognition, Lipid Metabolism, and Gut Microbiota in ApoE4 Mice.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073453341260621182306},
pmid = {42474014},
issn = {1875-5402},
abstract = {INTRODUCTION: Apolipoprotein E4 (ApoE4) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Qifuyin is a promising herbal formula used clinically for cognitive decline, but its effects on ApoE4-associated cognitive and systemic phenotypes remain unclear. This study aimed to evaluate the effects of Qifuyin on cognitive performance in ApoE4 transgenic mice and to preliminarily explore its associations with lipid metabolism and gut microbiota alterations.

METHODS: Ten-month-old ApoE4 transgenic mice were treated with Qifuyin by gavage for 321 days, once daily for the first 123 days and once every two days thereafter. Cognitive function was assessed using the step-down test, novel object recognition test (NORT), and Morris water maze test (MWM). Aging- and frailty-related phenotypes were evaluated using senescence grading scores. Serum triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and apolipoprotein B (ApoB) levels were measured to assess lipid metabolism. Gut microbiota composition and functional profiles were analyzed by 16S rRNA and metagenomic sequencing.

RESULTS: Qifuyin treatment significantly reduced error counts and prolonged latency in the stepdown test, increased the 24h preference index in the NORT, shortened escape latency, and increased platform crossings in the MWM in ApoE4 transgenic mice. High-dose Qifuyin reduced aging scores in males and in all doses in females and in the pooled dataset. Qifuyin decreased serum TG and ApoB levels, and increased serum HDL-C levels. 16S rRNA sequencing indicated that Qifuyin increased alpha diversity and shifted beta diversity toward the control profile. At the phylum level, Qifuyin altered the relative abundances of Firmicutes, Bacteroidota, Cyanobacteria, and Synergistota. At the family and genus levels, Qifuyin treatment was associated with increased abundances of Helicobacteraceae, Bacteroidaceae, Helicobacter, and Bacteroides, and a reduced abundance of Ruminococcaceae. Metagenomic annotation analysis showed altered abundances of K02003, K06147, COG1961, CBM37, and GH35-related features.

DISCUSSION: These findings suggest that Qifuyin may benefit ApoE4-associated cognitive and systemic dysfunction through its integrated effects on lipid metabolism and gut microbiota alterations. The microbiota-related changes observed in this study may provide a potential link between peripheral metabolic regulation and cognitive improvement, although their mechanistic significance requires further validation.

CONCLUSIONS: Qifuyin improved cognitive performance and lipid metabolism, and was associated with alterations in gut microbiota composition in ApoE4 transgenic mice. These findings suggest that Qifuyin may exert beneficial effects on cognitive and systemic phenotypes in this model, while the biological significance of specific microbial changes warrants further investigation.},
}

@article {pmid42474149,
year = {2026},
author = {Liu, H and Chen, M and Zhang, D},
title = {Lactobacillus-fermented feed alters growth performance, fecal short-chain fatty acid contents, metagenomics, and metabolomics in growing pigs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040426},
doi = {10.1128/msystems.00404-26},
pmid = {42474149},
issn = {2379-5077},
abstract = {UNLABELLED: This study sought to comprehensively evaluate the impact of Lactobacillus-fermented feed produced with Latilactobacillus curvatus SQ13 on the growth and fecal short-chain fatty acid (SCFA) contents, as well as metagenomic and metabolomic parameters, in growing pigs. One hundred crossbred pigs were randomized into two dietary treatment groups. Animals were given either a basal diet (CON) or a diet containing Lactobacillus-fermented feed (LP) over a 32-day period. The LP group exhibited a significantly reduced feed conversion ratio (FCR) and lower fecal valeric acid concentration compared with the CON group (P < 0.05). Microbial community analysis revealed that the relative abundance levels of Candidatus_Eremiobacterota, Cyanobacteriota, Lacrimispora, and Candidatus_Onthomorpha were markedly increased in the LP group (P < 0.05), whereas Actinomycetota, Pseudomonadota, Solobacterium, and Mitsuokella were significantly decreased (P < 0.05). KEGG pathway analyses indicated that arachidonic acid metabolism, phototransduction-fly, and Th17 cell differentiation were the three most significantly altered pathways. Correlation analysis further demonstrated that FCR was positively associated with Solobacterium abundance and downregulated metabolites, while showing negative correlations with Alistipes and upregulated metabolites. Collectively, these findings suggest that Lactobacillus-fermented feed improves growth efficiency and modulates valeric acid levels in growing pigs, likely through coordinated alterations in gut microbial composition and host metabolic processes. These results offer a potential foundation for the application of fermented feed in swine production systems. .

IMPORTANCE: Our study demonstrated that fermented feed produced by Latilactobacillus curvatus ZLA031 could improve growth efficiency, decrease valeric acid levels in growing pigs, likely through coordinated alterations in fecal microbiota composition, and host metabolic processes. Our work provided both experimental evidence and a theoretical framework supporting the application of Lactobacillus-fermented feed in swine production, while highlighting the need for further mechanistic research.},
}

@article {pmid42474199,
year = {2026},
author = {Xu, Y and Ren, R and Liu, W and Liu, L and Cui, X and Guo, J and Li, S},
title = {Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0037426},
doi = {10.1128/spectrum.00374-26},
pmid = {42474199},
issn = {2165-0497},
abstract = {UNLABELLED: To explore the diagnostic efficiency, clinical concordance, and precision treatment value of metagenomic next-generation sequencing (mNGS) for severe pulmonary infections in children in the pediatric intensive care unit (PICU), and to provide evidence for improving microbiological diagnosis and optimizing anti-infective strategies. A retrospective cohort study included 89 children with severe pneumonia in the PICU in 2024. All underwent routine microbiological testing and mNGS of bronchoalveolar lavage fluid (BALF). Detection rates, pathogen composition, co-infection identification, diagnostic concordance, and treatment impact were analyzed. Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, achieving a positive detection rate of 90.0% (80/89) and identifying a diverse spectrum of 103 pathogens, including 50.5% viruses, 43.7% bacteria, 38.8% co-infections (vs 11.6%), and 86.3% diagnostic concordance (vs 55.8%, P < 0.01). Among 46 patients included in the therapeutic outcome analysis (22 in the mNGS-guided group), 21 patients in the mNGS-guided group improved. Multivariate logistic regression analysis, adjusting for confounding factors (age, underlying diseases, PaO2/FiO2 ratio, PRISM III score, and preoperative antibiotic use duration), confirmed that mNGS-guided therapy was an independent protective factor for achieving the primary outcome (OR = 5.23, 95% CI: 1.87-14.61, P = 0.002) and secondary outcomes (C-reactive protein reduction ≥50%: OR = 4.89, 95% CI: 1.72-13.93, P = 0.003; oxygenation improvement: OR = 5.67, 95% CI: 1.98-16.21, P = 0.001). Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, guiding precision therapy, and improving prognosis.

IMPORTANCE: It supports metagenomic next-generation sequencing (mNGS) as a supplementary tool for pediatric intensive care unit (PICU) refractory infections, guides anti-infective adjustments, and informs tiered diagnostic pathways for resource-limited settings to optimize cost-effectiveness.},
}

@article {pmid42474201,
year = {2026},
author = {Palmer, B and Couradeau, EM and Johansen, JR and Kurbessoian, T and Carranza, JO and Stajich, JE and Ward, R and Pietrasiak, N},
title = {Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0104326},
doi = {10.1128/aem.01043-26},
pmid = {42474201},
issn = {1098-5336},
abstract = {The cyanosphere is composed of non-cyanobacterial microorganisms living within the exopolysaccharide sheath of cyanobacteria, interacting with the cyanobacterial hosts and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres can help predict the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity and functions within the cyanosphere remains limited. Here, we used metagenomic sequencing to reconstruct 415 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 terrestrial cyanobacteria cultures, representing 12 cyanobacterial orders. Our findings showed that the composition of cyanosphere microbial communities was significantly shaped by environmental factors such as habitat of host origin, including precipitation and temperature. Three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, suggesting a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, an anaerobic process that retains nitrogen in the host-cyanosphere system in contrast to denitrification. While nitrogen fixation was more common in the cyanobacteria, 15 cyanospheres also contained nitrogen fixation genes, including in hosts that were nitrogen fixation capable themselves. The cyanosphere also contained genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities.IMPORTANCEOur study identifies members of an understudied and under-valued microbial community, the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a novel approach to studying the cyanosphere, providing insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.},
}

@article {pmid42474235,
year = {2026},
author = {Pettersson, KJ and Demina, T and Eronen-Rasimus, E and Roux, S and Viitamäki, S and Pessi, IS and Oksanen, HM and Assmy, P and Kaartokallio, H and Hultman, J},
title = {Viral genetic diversity and functional potential in polar and subarctic sea ice.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag077},
pmid = {42474235},
issn = {1574-6941},
abstract = {Sea ice plays a critical role in regulating the global climate and serves as a unique habitat for diverse microbial communities. Still, our understanding of viruses in these communities remains limited. To further uncover the diversity and functional potential of viruses in polar and subarctic sea ice, we explored the viral component of Arctic, Baltic Sea, and Antarctic sea ice metagenomes. Altogether, 550 viral operational taxonomic units (vOTUs) were recovered, most of which were putatively classified within the class Caudoviricetes, which comprises bacterial and archaeal tailed double-stranded DNA viruses. Hosts were predicted for 187 vOTUs, with Gammaproteobacteria and Bacteroidia being the most prevalent viral host groups. Potential functions were assigned for 56% of predicted viral gene products, including putative auxiliary metabolic genes (AMGs) involved in oxidative metabolism, photosynthesis, and metabolism regulation under stress conditions. Related viral genomes carrying similar AMGs were detected in other Arctic and more geographically distant freshwater, marine, and ice environments. Genus- and/or family-level links between the studied vOTUs were detected across samples. Our results suggest diverse and complex virus-host interactions in sea ice and highlight the essential roles viruses may play in sea ice ecosystem dynamics across polar and subpolar environments.},
}

@article {pmid42474352,
year = {2026},
author = {Bergada-Pijuan, J and Pichler, I and Zaheri, M and Kufner, V and Huber, M},
title = {Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0039726},
doi = {10.1128/jcm.00397-26},
pmid = {42474352},
issn = {1098-660X},
abstract = {Viral metagenomic next-generation sequencing (mNGS) is a powerful approach for pathogen detection in clinical diagnostics; however, accurate virus identification depends critically on the quality of reference databases. Diagnostic specificity is frequently compromised by erroneous viral classifications, which occur when host- or reagent-derived sequences align to non-viral contaminant regions (such as ribosomal RNA, vector contamination like cytomegalovirus enhancers, and sequencing adapters) embedded within the viral reference sequences. To address this, we present VirMask, a novel computational strategy to systematically identify and mask recurrent contaminant regions within the viral reference sequences. In a first step, VirMask aligns simulated human reads against a viral database and masks host-derived regions. Second, it identifies and masks persistent contaminant regions based on their high prevalence across independent metagenomic data sets. Finally, VirMask employs alignment-based similarity searches to detect and mask homologous regions across multiple reference sequences, thereby reducing noise in mNGS outputs and improving diagnostic specificity. Using data from clinical mNGS runs, we demonstrate that VirMask usefully reduces artefactual detections without impacting true pathogen identification. Specifically, reads erroneously assigned to human viruses decreased by up to 30%, and those assigned to non-human viruses and bacteriophages by more than 99%. Furthermore, validation with a standardized international quality control panel confirmed 100% preservation of true-positive detections, while reducing false-positive human virus calls by up to 89% and overall erroneous assignments by 40%-94%. These results underscore the necessity of rigorous viral database curation and offer a reproducible framework for enhancing diagnostic confidence in mNGS-based clinical virology.IMPORTANCEThe importance of this study lies in addressing a critical bottleneck in clinical metagenomic next-generation sequencing (mNGS): the presence of systematic false-positive viral detections caused by contaminant regions within reference databases. While mNGS is a powerful, unbiased tool for pathogen discovery, its diagnostic reliability is often compromised by "kitome-derived" sequences that align to non-viral segments embedded in viral reference genomes. By introducing VirMask, this research provides a reproducible framework to systematically identify and mask these recurrent artifacts without sacrificing the sensitivity required to detect true pathogens. This targeted refinement of viral databases significantly reduces "noise" in diagnostic outputs, ensuring that clinicians can interpret metagenomic data with higher confidence and avoid misidentifying persistent laboratory contaminants as clinically significant infections.},
}

@article {pmid42475242,
year = {2026},
author = {Shi, W and Cen, L and Huang, J and Lei, X and Wang, Y and Wang, S and Ying, J and Li, Y and Ma, Y and Fang, Y and Liu, A and Lu, C and Dai, M},
title = {LECT2 deficiency contributes to bile acid metabolic reprogramming and cholestatic liver injury.},
journal = {Hepatology communications},
volume = {10},
number = {8},
pages = {},
doi = {10.1097/HC9.0000000000001007},
pmid = {42475242},
issn = {2471-254X},
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Knockout ; Mice ; *Intercellular Signaling Peptides and Proteins/deficiency/genetics/metabolism ; Liver/metabolism/pathology ; Disease Models, Animal ; Receptor, Farnesoid X-Activated ; Gastrointestinal Microbiome ; Male ; Receptors, Cytoplasmic and Nuclear/metabolism ; Metabolic Reprogramming ; Fibroblast Growth Factors/metabolism ; *Cholestasis, Intrahepatic/metabolism ; *Cholestasis/metabolism ; Signal Transduction ; Mice, Inbred C57BL ; Humans ; },
abstract = {BACKGROUND: Cholestatic liver injury involves impaired bile acid (BA) formation or flow, leading to toxic hepatic BA accumulation, yet the underlying mechanisms remain poorly understood. Leukocyte cell-derived chemotaxin 2 (LECT2) has been implicated in liver metabolic disorders; however, its specific role in cholestasis remains incompletely understood.

METHODS: ANIT was administered to wild-type (WT) and LECT2 knockout (KO) mice to establish an intrahepatic cholestasis model. Metabolomics and metagenomics were performed to discover the role of BA metabolism and the gut-liver axis in cholestatic liver injury. Clinical samples were analyzed to assess the relationship between LECT2 and cholestatic liver injury.

RESULTS: LECT2 deletion was associated with altered BA synthesis, characterized by a shift toward the classical pathway with upregulation of CYP7A1 and CYP8B1. Under cholestatic conditions, LECT2 deficiency was associated with aggravated liver injury, accompanied by alterations in gut microbiota composition, changes in intestinal FXR-FGF15 signaling, and increased hepatic JNK activation. In KO mice, HDCA supplementation restored the alternative synthesis pathway, FMT reshaped gut microbiota, and antibiotic cocktail treatment suppressed intestinal FXR signaling, each of which was associated with improved cholestatic liver injury. In clinical samples, LECT2 levels were negatively correlated with markers of cholestasis, supporting its potential relevance to disease severity.

CONCLUSION: LECT2 deficiency is associated with aggravated cholestatic liver injury, which may involve altered BA synthesis, gut microbiota dysbiosis, and modulation of intestinal FXR-hepatic JNK signaling. These findings offer new insights into the role of LECT2 in regulating metabolism and identify potential therapeutic targets for managing cholestatic liver injury.},
}

Animals
*Bile Acids and Salts/metabolism
Mice, Knockout
Mice
*Intercellular Signaling Peptides and Proteins/deficiency/genetics/metabolism
Liver/metabolism/pathology
Disease Models, Animal
Receptor, Farnesoid X-Activated
Gastrointestinal Microbiome
Male
Receptors, Cytoplasmic and Nuclear/metabolism
Metabolic Reprogramming
Fibroblast Growth Factors/metabolism
*Cholestasis, Intrahepatic/metabolism
*Cholestasis/metabolism
Signal Transduction
Mice, Inbred C57BL
Humans

@article {pmid42475475,
year = {2026},
author = {Durán-Viseras, A and Cha, G and Hatt, JK and Lindner, BG and Benvenuto, EM and Zhang, Y and Kunjapur, AM and Konstantinidis, KT},
title = {A Metagenome-Based Methodology to Track Genomically Recoded Strains and Assess Their Effects on Indigenous Microbes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15663},
pmid = {42475475},
issn = {1520-5851},
abstract = {Assessing the effects of the release of biologically contained microorganisms into the environment represents a challenging task as it requires both the tracking of escape events as well as the changes that result in the indigenous microbes, which cannot be effectively determined based on conventional culture-based methodologies. Toward closing this gap, we set up closed, laboratory mesocosms with water from a nearby recreational-use freshwater reservoir that were subsequently spiked with the Escherichia coli strain DEP to simulate an accidental spill of a synthetic organism into the environment. Strain DEP is a chloramphenicol-resistant synthetic auxotroph harboring three redesigned genes encoding nonstandard amino acid (nsAA)-dependent gene products for l-4,4'-biphenylalanine (BipA) dependence. Shotgun metagenome sequencing of the mesocosms revealed a sharp decline in the relative abundance of strain DEP over time, with minimal impact on the indigenous freshwater microbial communities as evidenced by the recovery of these communities to the preperturbation state after 2 days of incubation. Further, there were no observations of transfer of the nsAA-dependent genes to the indigenous populations at the limit of detection of our metagenome sequencing effort or based on culturing on BipA-supplemented media. Collectively, our results show that this particular strain DEP may not pose a serious environmental threat if accidentally released into the environment due to low competitiveness against the indigenous freshwater microbes and the lack of escape mutants. Notably, this work establishes a holistic approach to assess biocontainment efficacy that should be applicable to additional genetically modified organisms.},
}

@article {pmid42475510,
year = {2026},
author = {Li, R and Dong, W and Yang, Z and Wang, M and Xiong, J and Ma, Y and Hu, X and Yang, Y and Wan, J and Wu, R and Ye, R and Liu, B and Nguyen-Viet, H and Peng, Z and Wang, S and Li, J},
title = {MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored "Dark Matter" Discovery.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzag059},
pmid = {42475510},
issn = {2210-3244},
abstract = {The large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacology has increased the complexity of data analysis and interpretation. However, the microbiome and virome fields still lack a user-friendly and programming-free desktop application for comprehensive analysis of microbiome and virome data, with a particular gap in virome analysis and "dark matter" exploration. To address this gap, we introduce MicroWorldOmics, a plugin-based desktop application designed to offer a streamlined one-stop solution for life sciences and biomedical research. Its plugin-based architecture allows users to analyze data interactively and in parallel, simplifying tasks that typically require advanced bioinformatics skills. MicroWorldOmics is a comprehensive software suite tailored for microbiome and virome research, featuring 92 sub-applications across four main modules: epidemiology analysis, in-depth metagenomic/amplicon and virome profiling, and "dark matter" exploration. MicroWorldOmics leverages over 80 Python modules and 600 R packages for diverse bioinformatics, statistics, deep learning, and visualization tasks, accommodating multiple input and output formats including GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT. To enhance user productivity, the software is compatible with Windows, Linux, and macOS systems, and includes demo data for easy benchmarking. In summary, MicroWorldOmics is intended to facilitate microbiome and virome data analysis for life sciences and biomedicine researchers without a programming background. It is available at https://hzaurzli.github.io/.},
}

@article {pmid42475793,
year = {2026},
author = {Lyu, Y and Wu, S and Fan, X and Zhang, Y and Zhang, Q and Wang, S and Feng, Z},
title = {Discovery and characterization of a novel GH6 multifunctional enzyme from soil metagenomic library.},
journal = {Carbohydrate research},
volume = {568},
number = {},
pages = {110046},
doi = {10.1016/j.carres.2026.110046},
pmid = {42475793},
issn = {1873-426X},
abstract = {Cellulases are crucial for converting biomass into renewable energy. Despite extensive research, there remains a significant industrial demand for novel cellulases, particularly those with multi-substrates catalytic activity. This study aimed to identify and characterize a novel cellulase from a high-altitude soil metagenome library using functional screening method. A novel 1218-bp GH6 family hydrolase gene, designated zfy1641, was identified from a Mount Everest soil library. Bioinformatics analysis indicated that it encoded a 405-amino-acid protein (43.7 kDa) and was classified into glycoside hydrolase family 6 (GH6). The target glycoside hydrolase gene was cloned and heterologously expressed, then the recombinant protein was purified, and its biochemical properties and kinetic parameters were characterized. The purified recombinant enzyme exhibited broad substrate specificity, demonstrating significant activity against carboxymethyl cellulose (CMC-Na; 69.87 ± 0.13 U/mg), locust bean gum (125.56 ± 0.18 U/mg) and chitin (77.06 ± 0.08 U/mg). ZFY1641 represented a novel member of the GH6 family, that exhibited detectable reducing sugar release from chitin-a function not previously documented for this family. Moreover, ZFY1641 demonstrated optimal activity at 50°C and pH 5.0, and exhibited moderate thermal stability, tolerance to selected metal ions, and halophilicity under the conditions tested. These characteristics suggest potential utility of ZFY1641 in industrial processes, though further validation is required. This work expanded the substrate diversity of GH6 family enzymes and provided a foundation for the development of new enzymatic preparations with a novel multi-functional GH6 family enzyme.},
}

@article {pmid42476086,
year = {2026},
author = {Jurvansuu, J and Sipponen, E and Salmivirta, E and Lehto, KM and Havulinna, A and Pitkänen, T and Oikarinen, S},
title = {Wastewater viromics reveals host-structured viral signals and non-human pathogens.},
journal = {Water research},
volume = {305},
number = {},
pages = {126485},
doi = {10.1016/j.watres.2026.126485},
pmid = {42476086},
issn = {1879-2448},
abstract = {Wastewater represents a powerful platform for human virus surveillance. However, the entry of animal- and plant-associated viruses into sewage is heterogeneous and incompletely understood, creating uncertainty about how reliably wastewater reflects non-human virus circulation. Here, we address this by analysing monthly wastewater metagenomic data from two distinct periods (2020-2021 and 2024-2025) across five major Finnish wastewater treatment plant catchments using a targeted hybrid-capture approach to characterise the composition, host range, and spatial distribution of the non-human wastewater virome. Nearly half of the detected viral accessions were non-human, indicating substantial diversity, despite human-associated viruses accounting for 83% of normalised viral reads. Rodent-, livestock-, and bird-associated viruses showed spatial structuring consistent with regional host populations. The wastewater viromics also detected four EU-regulated plant pathogens, including tomato brown rugose fruit virus, which was highly prevalent in wastewater two years before its first official detection in Finland. Together, these results show that wastewater contains structured, host-linked viral signals, supporting its use as an ecological proxy for non-human virus circulation.},
}