@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.},
}

@article {pmid42120383,
year = {2026},
author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW},
title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42120383},
issn = {2041-1723},
support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Carrageenan/metabolism
*Ruminants/microbiology
Rumen/microbiology
Glycoside Hydrolases/metabolism/genetics
Feces/microbiology
Bacteria/metabolism/genetics/classification/isolation & purification
Seaweed/metabolism
Bacteroides/metabolism/genetics/isolation & purification
Metagenomics
Phylogeny

@article {pmid42120665,
year = {2026},
author = {Chen, LG and Zhou, L and Wang, BW and Javed, M and Liu, YF and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial assembly and metabolic restructuring following CO2 injection in subsurface oil reservoir.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02066-w},
pmid = {42120665},
issn = {2191-0855},
support = {Grant No. 42473082//National Natural Science Foundation of China/ ; No. 42173076//National Natural Science Foundation of China/ ; No. 52074129//the National Natural Science Foundation of China/ ; 21ZR1417400//the Natural Science Foundation of Shanghai/ ; JKJ01231714//the Fundamental Research Funds for the Central Universities of China/ ; },
abstract = {Carbon dioxide (CO2) injection into oil reservoirs is a well-established and promising strategy for enhancing oil recovery while simultaneously sequestering carbon, whose effectiveness is increasingly recognized to be influenced by microbial-mediated mechanisms and biogeochemical processes. However, the impact of CO2-injected and storage on functional microbial communities and their metabolic potential remains poorly understood. The study employed high-throughput sequencing to analyze the composition and diversity of microbial communities in produced water from three production wells with a long-term (> 20 years) history of CO2 injection and two adjacent water-flooding ones in Xinli Oilfield, China. The results showed that CO2-injected wells had significantly higher microbial diversity and distinct metabolic potential relative to the adjacent water-flooding wells. A metabolic difference in the archaeal communities towards hydrogenotrophic and heterotrophic metabolisms, alongside an enrichment of bacterial taxa associated with sulfur and nitrogen cycling was observed. Correlation analysis revealed that microbial differentiation was strong associated with geochemical alteration (especially pH and some inorganic ions), with NH4[+] and S[2-] identified as key factors in this process. Metagenomic analysis based on high-quality metagenome-assembled genomes (MAGs) further demonstrated that CO2 injection led to a different profile of microbial metabolic functions relative to the water-flooding condition, characterized by significantly enhancing hydrogenotrophic methanogenesis, dissimilatory sulfate reduction, and denitrification, while diminishing methylotrophic methanogenesis and Wood-Ljungdahl pathway activity. These findings provide new insights into the microbial mechanisms driving carbon transformation in CO2-flooded oil reservoirs.},
}

@article {pmid42120930,
year = {2026},
author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X},
title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51805-3},
pmid = {42120930},
issn = {2045-2322},
support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; },
abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.},
}

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04958-7},
pmid = {42121077},
issn = {1471-2377},
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

@article {pmid42121260,
year = {2026},
author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E},
title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02369-x},
pmid = {42121260},
issn = {2049-2618},
support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; },
abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.

RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.

CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.},
}

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02410-z},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

@article {pmid42121750,
year = {2026},
author = {Moharam, I and Brüggemann, J and Schmitt, F and Schade, B and Böhm, B and Kappe, E and Emmrich, F and Najar, FZ and El-Mayet, FS},
title = {Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091331},
pmid = {42121750},
issn = {2076-2615},
abstract = {Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting-stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity.},
}

@article {pmid42121788,
year = {2026},
author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L},
title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091369},
pmid = {42121788},
issn = {2076-2615},
support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; },
abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.},
}

@article {pmid42122064,
year = {2026},
author = {Hussain, A and Abbas, Q and Nadeem, M and Nazar, A and Athar, A and Rahman, HUU},
title = {Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/diagnostics16091360},
pmid = {42122064},
issn = {2075-4418},
abstract = {Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4-104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future.},
}

@article {pmid42122249,
year = {2026},
author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI},
title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.},
journal = {Cancers},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/cancers18091453},
pmid = {42122249},
issn = {2072-6694},
support = {No Grant Number//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.},
}

@article {pmid42122826,
year = {2026},
author = {Pardo, JM and Suwannarach, N and Malichan, S and Cuellar, WJ and Siriwan, W},
title = {Mixed-Pathogen Infections in Vegetatively Propagated Crops: From Biological Synergism to Integrated Management.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/plants15091332},
pmid = {42122826},
issn = {2223-7747},
support = {000//Ministry of Higher Education, Science, Research and Innovation/ ; 000//Kasetsart University/ ; CROP-2023-157//Australian Centre for International Agricultural Research/ ; 000//National Research Council of Thailand/ ; },
abstract = {Vegetatively propagated crops, including cassava, sweet potato, banana, and potato, are susceptible to mixed-pathogen infections resulting from the continuous use of clonal planting material and infrequent seed replacement. A diverse array of viruses, bacteria, and fungi can accumulate within these materials over successive cultivation cycles, precipitating seed degeneration and complex disease syndromes that complicate diagnosis and management. Mixed infections frequently trigger synergistic interactions that exacerbate disease severity and yield losses. This review synthesizes data on mixed-pathogen complexes in vegetatively propagated crops, with particular focus on vascular and systemically colonizing pathogens and analyzing starch crops to highlight the epidemiological, biological, and ecological drivers of synergism and antagonism. Furthermore, the review examines host defense responses during coinfection, including the modulation of plant immune pathways, and evaluates how interpathogen dynamics influence pathological outcomes. Although advancements in molecular diagnostics-notably next-generation sequencing and metagenomics-have revolutionized the detection of mixed infections, they have also introduced challenges in differentiating causal agents from commensal microorganisms. Finally, we discuss the implications for integrated disease management, emphasizing clean seed systems, resistance breeding, and phenotyping strategies tailored to multipathogen environments. The dynamics of mixed infections is critical for resilient and sustainable management strategies amidst increasingly complex agricultural and climatic shifts.},
}

@article {pmid42122957,
year = {2026},
author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ},
title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093225},
pmid = {42122957},
issn = {2077-0383},
abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.},
}

@article {pmid42123237,
year = {2026},
author = {Liu, JW and Ma, X and Qian, YT and Wang, JW and Zhu, CY and Ma, DL},
title = {Detection of Nontuberculous Mycobacterial Skin Infection by Next-Generation Sequencing: A Pilot Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093504},
pmid = {42123237},
issn = {2077-0383},
support = {2022- PUMCH-161//National High Level Hospital Clinical Research Funding/ ; 3332024006//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Background: Nontuberculous mycobacteria (NTM) skin infections pose significant diagnostic challenges in clinical practice, due to nonspecific clinical/histopathological features and limitations of conventional pathogenic detection methods. Metagenomic next-generation sequencing (mNGS) offers a promising approach but requires further evaluation. Methods: A prospective pilot study at Peking Union Medical College Hospital enrolled 20 patients with cutaneous NTM infection, confirmed by positive skin culture or mNGS. All patients underwent thorough clinical assessment, skin biopsy for histopathology and culture, and mNGS testing of skin tissue. Treatment was based on identified species and disease extent. Treatment outcomes were tracked. Results: Among 20 patients (median age 45.5 years), fingers were the most common site affected (n = 10), followed by forearms (n = 7), hands (n = 4), and face (n = 4). Mycobacterium marinum was the predominant pathogen (n = 12), associated with fish bone puncture, followed by M. abscessus (n = 4). mNGS demonstrated a substantially higher positivity rate than culture (95% [19/20] vs. 30% [6/20]) and delivered results faster. Histopathology revealed granulomatous inflammation in all cases. Nineteen patients presented with non-disseminated disease; one immunocompromised patient (GATA2 deficiency) had disseminated M. abscessus infection. Treatment success was achieved in 17 patients (85%) with tailored antibiotic regimens. Adverse drug effects occurred in seven patients. Conclusions: In this pilot study of cutaneous NTM infections, mNGS enabled more rapid diagnosis relative to conventional culture. Clinical presentation and exposure history correlate with specific NTM species. Integrating mNGS with clinical assessment significantly improves diagnosis and management.},
}

@article {pmid42123326,
year = {2026},
author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS},
title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093741},
pmid = {42123326},
issn = {1422-0067},
mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; },
abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.},
}

Animals
Chickens/microbiology
*Manure/microbiology
*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Metagenome
Microbiota/genetics
Biodiversity

@article {pmid42123473,
year = {2026},
author = {Cheng, R and Liu, T and Liao, C and Wu, X and Zhu, L and Zhang, S},
title = {Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093891},
pmid = {42123473},
issn = {1422-0067},
support = {No. 32401056//National Natural Science Foundation of China/ ; 2024RC3144//Hunan Province Science and Technology Innovation Program/ ; },
mesh = {*Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Humans ; Molecular Sequence Annotation ; },
abstract = {Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening "sequence-function gap" exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function.},
}

*Proteins/chemistry/metabolism
*Computational Biology/methods
Databases, Protein
Humans
Molecular Sequence Annotation

@article {pmid42123477,
year = {2026},
author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M},
title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093893},
pmid = {42123477},
issn = {1422-0067},
mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; },
abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.},
}

Humans
*Mineral Waters/therapeutic use
Balneology/methods
Animals
Skin/drug effects

@article {pmid42123517,
year = {2026},
author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ},
title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093935},
pmid = {42123517},
issn = {1422-0067},
support = {10180//United States Department of Agriculture/ ; },
mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration & dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; },
abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.},
}

Humans
*Saliva/microbiology/drug effects
Female
Male
*Vaccinium macrocarpon/chemistry
*Polyphenols/pharmacology/administration & dosage/chemistry
*Microbiota/drug effects
Adult
Propylthiouracil
*Plant Extracts/pharmacology/chemistry/administration & dosage
*Photinia/chemistry
Taste/drug effects
*Mouthwashes/pharmacology/chemistry
*Fruit and Vegetable Juices
Young Adult

@article {pmid42124595,
year = {2026},
author = {Mejía-Pitta, A and Zhang, Z and Hossain, AA and Bartosik, K and Baca, CF and Peralta, C and Molina, H and Teplova, M and Brady, SF and Micura, R and Patel, DJ and Marraffini, LA},
title = {A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.25.707755},
pmid = {42124595},
issn = {2692-8205},
abstract = {The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.},
}

@article {pmid42125129,
year = {2026},
author = {Khantsi, M and Babalola, OO},
title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {},
pages = {e70157},
pmid = {42125129},
issn = {2575-6265},
abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.},
}

@article {pmid42125266,
year = {2026},
author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Devarajan, AK and Petrich, C and O'Sadnick, M and Tiirik, K and Truu, J},
title = {Microbial succession and hydrocarbon-degrading potential in Arctic sea ice exposed to dispersed crude oil and chemical dispersant.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag022},
pmid = {42125266},
issn = {2633-6685},
abstract = {The increasing oil exploration and transport activities in the Arctic amplify the risk of oil spills in ice-containing marine environments. Chemical dispersants, intended to promote oil biodegradation by breaking hydrocarbons into small droplets, are potential tools in cold marine oil spill mitigation; however, their fate and effectiveness within sea ice remain uncertain. This study examined the influence of dispersed crude oil and the chemical dispersant (FinasolOSR 51) on microbial community dynamics and hydrocarbon-degrading potential compared to clean ice during an 89-day sea-ice mesocosm experiment using shotgun metagenomics and metagenome-assembled genomes. Dispersant addition markedly reshaped microbial communities in both dispersed-oil and dispersant containing ice, causing similar shifts toward psychrophilic hydrocarbon degraders such as Oleispira, Bermanella, and Pseudoalteromonas. Although aliphatic hydrocarbon degradation genes were enriched, several dominant taxa exhibited limited hydrocarbon metabolic capacity yet possessed extensive stress-response traits. Oil hydrocarbon loss in ice remained modest despite the presence of degraders, likely due to the very low microbial abundance. These findings demonstrate that dispersants can strongly shape microbial communities in Arctic sea ice, without necessarily enhancing the biodegradation of oil hydrocarbons. This highlights the need for careful evaluation of dispersants as remediation tools in ice-containing Arctic marine environments.},
}

@article {pmid42125370,
year = {2014},
author = {, },
title = {Schmallenberg virus: State of Art.},
journal = {EFSA journal. European Food Safety Authority},
volume = {12},
number = {5},
pages = {3681},
pmid = {42125370},
issn = {1831-4732},
abstract = {This scientific report provides an overview of all research carried out on Schmallenberg virus (SBV), reviewing the current knowledge on SBV regarding genotyping findings, susceptible species, pathogenesis, transmission routes, immunity, seroprevalence, geographical and temporal SBV spread, improved within-herd transmission model, SBV impact assessment and within-herd and regional spread models. Metagenomic analysis identified SBV as a novel orthobunyavirus emerged in 2011 and it has been detected in domestic cattle, sheep, goats and 12 wild species. Seroprevalence studies indicate that SBV has probably spread over the whole of Europe, showing high seroprevalence at national scale, while larger variability is observed at regional scales. Clinical disease frequency is low and experimental infection on pregnant ewes and cows suggest that SBV rarely induces malformations. SBV may be detected from semen with a low frequency though there is no scientific evidence of transmission through insemination. Vector competence studies suggest that Culicoides are likely to be able to transmit SBV but found no evidence that mosquitoes are likely to be able to transmit it. SBV vertical transmission has not yet been identified as a major route. SBV has successfully overwintered, despite lengthy period of minimal vector activity and duration of immunity in cattle lasts for at least one year. A farm-to-farm spread model for SBV shows a rapid spread of infection across the study region and latent period, duration of viraemia, probability of transmission from host to vector and virus replication are sufficient to account for the rapid SBV spread. The between-farm SBV transmission model indicates that the application of movement restrictions has little effect on SBV spread. An impact assessment based on limited data suggests a probable effect of SBV infection on abortion, short gestation, non-return and the number of artificial inseminations required per animal. International trade restrictions by third countries represent the main SBV impact.},
}

@article {pmid42125413,
year = {2026},
author = {Wang, J and Qiu, J and Zhang, C},
title = {Crusted scabies complicated by septic shock: a fatal case report with incidental detection of Sarcoptes scabiei DNA in peripheral blood.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02577},
pmid = {42125413},
issn = {2214-2509},
abstract = {Crusted scabies is a severe form of scabies characterized by massive mite burden and profound immune dysregulation. Secondary bacterial infection is common and may progress to sepsis with fatal outcomes. We report a fatal case of crusted scabies complicated by septic shock in a 58-year-old man with diabetes mellitus and chronic dermatitis. The patient presented with diffuse erythroderma, extensive hyperkeratotic crusts, and deep skin fissures, and several household members had similar pruritic skin lesions. Laboratory investigations revealed marked eosinophilia, extremely elevated serum immunoglobulin E levels, and multiorgan dysfunction. Peripheral blood metagenomic next-generation sequencing identified multiple bacterial pathogens and incidentally detected Sarcoptes scabiei DNA. Despite broad-spectrum antimicrobial therapy, antiparasitic treatment, and intensive supportive care, the patient deteriorated and died. This case highlights crusted scabies as a potentially lethal condition when complicated by severe bacterial infection and underscores the need for cautious interpretation of parasitic DNA detected in blood, particularly in non-invasive ectoparasitic diseases.},
}

@article {pmid42125597,
year = {2026},
author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK},
title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112791},
pmid = {42125597},
issn = {2352-3409},
abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.},
}

@article {pmid42125669,
year = {2026},
author = {Szaraz, D and Bohm, J and Machacek, C and Salokova, G and Gachova, D and Ruzicka, F and Danek, Z and Gheit, T and Zavadil, J and Borilova Linhartova, P},
title = {Bacteriome-based oral dysbiosis index in patients with oral squamous cell carcinoma.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2668149},
pmid = {42125669},
issn = {2000-2297},
abstract = {BACKGROUND: Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs other oral samples and evaluate the association of a novel bacteriome-based Oral Dysbiosis Index (bbODI) with the OSCC surface.

MATERIALS AND METHODS: This pilot observational study used 84 patient-matched samples from the OSCC tumoral surface (swabs and biopsies), healthy oral mucosa (tongue and buccal swabs), and supragingival dental plaque swabs. Bacteriomes were analyzed by 16S rRNA amplicon sequencing. The presence of microscopic fungi and selected viruses was also evaluated.

RESULTS: The relative abundance of the genus Fusobacterium, the ratio of the relative abundances of gram-negative to gram-positive bacterial genera, and the bbODI on the tumour surface significantly differed from patient-matched healthy oral mucosa (both buccal and tongue swabs) and supragingival dental plaque samples. Oral candidosis was found in 25% of patients; all patients were negative for cytomegalovirus and Epstein-Barr virus.

CONCLUSIONS: Certain characteristics of the bacteriome composition of the OSCC surface differ from patient-matched samples of healthy oral mucosa and supragingival dental plaque. The proposed bbODI appears to be a promising non-invasive tool for the identification of bacteriome disruption on the OSCC surface.},
}

@article {pmid42125783,
year = {2026},
author = {Hu, X and Han, L and Ochoa-Hueso, R and Song, J and Yang, X and Wang, G},
title = {From Microbes to Molecules: Biodegradable Microplastics Reshape Soil Carbon Metabolism and Composition of Dissolved Organic Matter.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01030},
pmid = {42125783},
issn = {1520-5118},
abstract = {Microplastics (MPs) are ubiquitous in the environment, yet how conventional MPs (CMPs) and biodegradable MPs (BMPs) alter microbial carbon (C) metabolism and dissolved organic matter (DOM) remains unclear. Using metagenomic sequencing and Fourier transform ion cyclotron resonance mass spectrometry, we found that BMPs altered microbial C cycling profiles more profoundly than CMPs. This was driven by a significant enrichment of functional genes involved in aerobic respiration, C fixation, intracellular C decomposition, and fermentation. In addition, BMPs exerted stronger influences on prokaryotic and viral community structures than CMPs. Notably, BMPs specifically enriched unique microbial taxa and virus-host linkages carrying diverse C-cycling genes, coregulating key metabolic pathways, and promoting a "viral shuttle" mechanism that accelerated DOM turnover. These effects were mediated through enhanced accumulation of labile and recalcitrant C components in relation to fertilization regimes. These findings revealed mechanisms by which BMPs reshape soil carbon dynamics through microbial-viral interactions.},
}

@article {pmid42125851,
year = {2026},
author = {Fisher, CJ and Khrongsee, P and Subramaniam, K and Pushinsky, AD and Stevenson, V and Crawford, C and Goncalves, R},
title = {Acute Respiratory Distress Syndrome in a Dog With Canine Respiratory Coronavirus Infection.},
journal = {Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)},
volume = {},
number = {},
pages = {},
doi = {10.1111/vec.70113},
pmid = {42125851},
issn = {1476-4431},
abstract = {OBJECTIVE: To describe the clinical progression of acute respiratory distress syndrome (ARDS) associated with canine respiratory coronavirus and suspected aspiration in a previously healthy young dog.

CASE SUMMARY: A 1.5-year-old neutered male Rottweiler was presented for acute respiratory distress. The dog had a productive cough 2 weeks prior that was reported to have improved. While at a boarding facility, the dog developed decreased appetite and lethargy, regurgitated, and became acutely dyspneic. The dog was taken to the veterinarian on site, where thoracic radiographs revealed severe consolidation of the cranioventral lung lobes. The dog was presented to a university referral hospital approximately 12 h after regurgitation with fever, hypotension, hypoglycemia, and leukopenia, and was treated with positive pressure ventilation after failing high-flow oxygen therapy. The dog remained profoundly hypoxemic, developed acute kidney injury, and was euthanized after 24 h. Necropsy revealed diffuse alveolar damage consistent with a diagnosis of ARDS. Bacterial cultures were negative. Real-time polymerase chain reaction results from upper respiratory and fresh lung samples, as well as metagenomics analysis from a lung sample, confirmed the presence of canine respiratory coronavirus.

Canine respiratory coronavirus is primarily associated with mild upper respiratory signs and has not been previously associated with ARDS. Direct pulmonary damage from the virus, decreased mucociliary clearance secondary to viral ciliary damage followed by aspiration, and secondary pulmonary damage from systemic inflammation and coagulation disturbances are all possible in this case. The practical use of metagenomics, an emerging diagnostic screening tool that provides characterization of a virus's entire genome, is also demonstrated here. Metagenomics has not been previously described in small animal clinical medicine and may aid in surveillance of infectious canine respiratory disease and provide better understanding of the role of "milder" pathogens in patients with multifactorial respiratory failure.},
}

@article {pmid42126224,
year = {2026},
author = {Abuah, CY and Sipes, K and Buongiorno, J and Steen, AD and Bradley, JA and Giovannelli, D and Abramov, A and Peters, SL and Giannone, RJ and Hettich, RL and Liang, R and Boike, J and Vishnivetskaya, TA and Lloyd, KG},
title = {Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0045626},
doi = {10.1128/spectrum.00456-26},
pmid = {42126224},
issn = {2165-0497},
abstract = {The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches-metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics-we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass-remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.IMPORTANCEPermafrost thaw may be a critical climate feedback because microbial degradation of organic matter (OM) can release greenhouse gases. While fjords serve as major carbon burial sites, our results show that burial of terrestrial-derived OM in these sediments does not ensure protection from microbial degradation. Microbial communities in both active layer soils and fjord sediments harbor a broad arsenal of carbohydrate-active enzymes, with evidence of activity across diverse taxa. This functional continuity indicates that once terrestrial material is washed into fjords, it remains vulnerable to microbial breakdown despite different environmental conditions. Understanding these cross-system continuities in microbial function is essential for predicting the fate of OM in a rapidly warming Arctic and highlights the importance of including fjord sediments in global carbon cycle models.},
}

@article {pmid42126240,
year = {2026},
author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Javornik Cregeen, SJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW},
title = {Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0054726},
doi = {10.1128/aem.00547-26},
pmid = {42126240},
issn = {1098-5336},
abstract = {Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exist in the realm of wastewater-based viral epidemiology (WBE) for cancer-causing viruses, with existing studies using targeted approaches (i.e., PCR-based approaches) that lack genomic resolution. In this study, we used a hybrid-capture approach to detect, filter, and sequence all known oncogenic virus signals from wastewater samples collected over 3 years (May 2022-May 2025) in 16 Texas cities, covering nearly 25% of the state's population. Once sequenced, we used custom computational tools designed for wastewater metagenomics to assign reads into their respective virus of origin, estimate viral abundances over time, and measure genomic read coverage. Our data indicate that we successfully detected oncogenic viruses, including six known oncogenic viruses, and three suspected oncogenic viruses, across all sampling locations within Texas. We observed a gradual increase in the viral abundance of oncogenic viruses over 3 years, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as human papillomavirus (HPV) and Epstein-Barr virus (EBV) rose, with sharp increases in viral abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using this hybrid-capture technique for nearly all oncogenic viruses, with resolution down to the species and type taxonomic levels in some cases, such as that of HPV. Our study showcases the utility of hybrid-capture techniques to detect and track multiple oncogenic viruses simultaneously.IMPORTANCECancer-causing viruses are of major clinical significance, responsible for nearly 20% of all recorded cancer incidences in humans worldwide. There is a need for improved detection, tracking, and control of oncogenic viruses across the globe. To our knowledge, this work is the first comprehensive WBE approach used to detect all known oncogenic viruses concurrently, demonstrating the feasibility of monitoring the presence and levels of cancer-causing viruses and enabling the possibility of public health interventions in the future. Using this method, we obtain broad genomic coverage at strong depth and specificity, coupled with consistent real-time tracking dynamics of multiple oncogenic viruses. Furthermore, we showcase the ability to identify genomic regions on viral reference genomes from which sequenced reads originate. This information can be an invaluable tool toward understanding the viral prevalence dynamics in general populations, their relationship to cancer incidences in humans, and their mechanisms of viral evolution, including mutations.},
}

@article {pmid42126253,
year = {2026},
author = {Hambücken, L and Sudianto, E and Verleyen, E and Saw, JH and Baurain, D and Cornet, L},
title = {An early diverging SQR enzyme in Antarctic Gloeobacterales indicates sulfide tolerance in thylakoid-lacking cyanobacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042326},
doi = {10.1128/spectrum.00423-26},
pmid = {42126253},
issn = {2165-0497},
abstract = {Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions-characterized by sulfidic, anoxic oceans-posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of a sulfide-quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage. Phylogenetic analyses consistently position these SQR sequences at the base of the cyanobacterial clade, likely predating the multiple lateral transfers reported for this gene in the phylum. Additional searches in metagenomic data sets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions.IMPORTANCEThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic), a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an early diverging cyanobacterium lacking thylakoids, isolated from Antarctica, suggests that oxygenic and anoxygenic photosynthesis coexisted early on in cyanobacterial evolution. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.},
}

@article {pmid42126918,
year = {2026},
author = {Smith, DB and Simmonds, P and Siddell, SG},
title = {Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist.},
journal = {The Journal of general virology},
volume = {107},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002243},
pmid = {42126918},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Virology ; *Classification/methods ; Terminology as Topic ; },
abstract = {Just over 125 years has passed since the 'filterable' agents of tobacco mosaic disease and foot-and-mouth disease were first described as infectious, replicating entities smaller than bacteria. Today, viruses are formally classified into more than 16,000 species ranked into genera, families and higher taxa. The development of an official virus taxonomy has been overseen by an International Committee, first constituted in 1966 and renamed as the International Committee on Taxonomy of Viruses (ICTV) in 1975. Despite the engagement of the ICTV in virus taxonomy over the last 60 years, many aspects of virus classification and nomenclature may seem odd or sometimes incomprehensible to virologists more familiar with the taxonomy of cellular organisms. Who runs the ICTV? What are virus species demarcation criteria? Why have all virus species names become binomial? How can a sequence in a metagenomic dataset be assigned to a virus species? This article attempts to answer several such questions and outlines how a large, inclusive and global community of virologists has developed new and responsive policies for virus taxonomy in a decade when the pace of virus discovery has dramatically accelerated.},
}

*Viruses/classification/genetics
*Virology
*Classification/methods
Terminology as Topic

@article {pmid42127418,
year = {2026},
author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC},
title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag124},
pmid = {42127418},
issn = {1751-7370},
abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.},
}

@article {pmid42127818,
year = {2026},
author = {Mahler, M and Yuping, L},
title = {Predicting phage anti-defenses that shoot the messenger.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {811-813},
doi = {10.1016/j.chom.2026.04.014},
pmid = {42127818},
issn = {1934-6069},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Viral Proteins/metabolism/genetics ; Metagenomics ; Signal Transduction ; },
abstract = {Locked in a constant arms race, bacteria and their phage predators have evolved various defenses and counter-defenses. Compared to the numerous identified defenses, phage-encoded counter-defenses are understudied. In a recent Science paper, Tal et al. developed a structure-guided approach to identify phage proteins counteracting nucleotide signaling defenses using metagenomic data.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*Viral Proteins/metabolism/genetics
Metagenomics
Signal Transduction

@article {pmid42127820,
year = {2026},
author = {Bickel, S and Berg, G},
title = {Microbial diversity creates a global firewall against pathogens in soil.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {817-819},
doi = {10.1016/j.chom.2026.04.016},
pmid = {42127820},
issn = {1934-6069},
mesh = {*Soil Microbiology ; Humans ; Metagenomics ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Melioidosis/microbiology ; *Microbiota ; Tuberculosis/microbiology ; Soil ; Animals ; },
abstract = {Soil is a critical ecological contributor to plant and animal health. In this issue of Cell Host & Microbe, Xiong et al. use global metagenomic data to show that human pathogens linked to diseases like tuberculosis, melioidosis, and sepsis are widespread in humid and agricultural soils harboring reduced microbial diversity.},
}

*Soil Microbiology
Humans
Metagenomics
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Melioidosis/microbiology
*Microbiota
Tuberculosis/microbiology
Soil
Animals

@article {pmid42127824,
year = {2026},
author = {Bouzek, DC},
title = {What the nose knows of cystic fibrosis microbes and hypertonic saline.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {827-829},
doi = {10.1016/j.chom.2026.04.017},
pmid = {42127824},
issn = {1934-6069},
mesh = {*Cystic Fibrosis/microbiology/drug therapy ; Humans ; Saline Solution, Hypertonic/pharmacology ; *Nasopharynx/microbiology ; *Microbiota ; Metagenomics ; Infant ; *Nose/microbiology ; },
abstract = {In this issue of Cell Host & Microbe, Steinberg et al.[1] present a microbial gene atlas of nasopharyngeal swabs in infants with cystic fibrosis and healthy controls using shotgun metagenomic sequencing. The impacts of clinical interventions on respiratory microbial function can be identified and experimentally validated using the atlas.},
}

*Cystic Fibrosis/microbiology/drug therapy
Humans
Saline Solution, Hypertonic/pharmacology
*Nasopharynx/microbiology
*Microbiota
Metagenomics
Infant
*Nose/microbiology

@article {pmid42127855,
year = {2026},
author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y},
title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {107056},
doi = {10.1016/j.psj.2026.107056},
pmid = {42127855},
issn = {1525-3171},
abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.},
}

@article {pmid42127905,
year = {2026},
author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y},
title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102797},
doi = {10.1016/j.xcrm.2026.102797},
pmid = {42127905},
issn = {2666-3791},
abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.},
}

@article {pmid42128151,
year = {2026},
author = {Yang, F and Sui, C and Tian, H and Ao, J},
title = {Metagenomic next-generation sequencing reveals the clinicopathological features of mucormycosis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108553},
doi = {10.1016/j.micpath.2026.108553},
pmid = {42128151},
issn = {1096-1208},
abstract = {BACKGROUND: Mucormycosis is a rare but highly lethal opportunistic infection driven by mucor fungi, which mainly affects individuals with compromised immune systems, such as diabetic patients and organ transplant recipients. This study aims to investigate the clinicopathological features of patients with mucormycosis diagnosed by metagenomic next-generation sequencing (mNGS).

METHODS: A systematic analysis was conducted in 15 cases of mucormycosis diagnosed and treated at Hunan Provincial People's Hospital between January 2019 and July 2024. Various detection methods were utilized, including hematoxylin-eosin staining, fungal fluorescence staining, fungal culture, and high-throughput mNGS technology to ensure an accurate diagnosis. Furthermore, we conducted a literature review and analyzed 311 cases of mucormycosis published in the public databases between 2021 and 2024 to assess the underlying pathological characteristics.

RESULTS: Of the 15 cases treated in our institute, ten (66.7%) were males, with a median age of 41 (range 4-78),five (33.3%) were females, with a median age of 58.5 (range 32-85). Compared to other detection methods including PAS/PASM staining, mNGS proved effective in diagnosing typical mucormycosis infections in 15 of the patients in this study. The literature review of 311 cases indicated that the lungs and bronchi were the main sites of infection, followed by the nasal cavity, brain, and skin. Diabetes emerged as the most prevalent underlying condition, present in more than 40% of cases. Other internal and immune system disorders, such as immunodeficiency disease, were also associated with an increased risk of infection.

CONCLUSIONS: MNGS is an effective diagnostic tool for mucormycosis.},
}

@article {pmid42128673,
year = {2026},
author = {, and , and , },
title = {[Expert consensus on laboratory identification of emerging pathogens based on metagenomic next-generation sequencing technology(2025 edition)].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {5},
pages = {669-684},
doi = {10.3760/cma.j.cn112150-20251117-01086},
pmid = {42128673},
issn = {0253-9624},
support = {2024ZD0532804//National Science and Technology Major Special Project for Noncommunicable Chronic Diseases/ ; 2025ZD01903400//National Science and Technology Major Special Project for Prevention and Control of New Emergencies and Major Infectious Diseases/ ; 2025-I2M-KJ-001, 2025-I2M-XHJC-004//CAMS Innovation Fund for Medical Sciences(CIFMS)/ ; },
mesh = {*High-Throughput Nucleotide Sequencing ; *Metagenomics ; Humans ; Consensus ; *Communicable Diseases, Emerging/diagnosis ; Computational Biology ; },
abstract = {Emerging pathogen infections pose a significant challenge to global public health security. Pathogen metagenomic next-generation sequencing (mNGS), characterized by its hypothesis-free, culture-independent, and unbiased nature, provides a powerful tool for the timely detection and precise identification of emerging pathogens. This consensus was jointly developed by multidisciplinary experts from clinical laboratories, infectious diseases, disease prevention and control, and other relevant fields. It aims to standardize the identification process for clinically suspected emerging pathogen infections, as well as specimen submission, technical requirements, bioinformatic analysis, and reporting and interpretation procedures for the laboratory identification of emerging pathogens using clinical mNGS technology. This framework provides systematic guidance for clinical early warning and practice.},
}

*High-Throughput Nucleotide Sequencing
*Metagenomics
Humans
Consensus
*Communicable Diseases, Emerging/diagnosis
Computational Biology

@article {pmid42128675,
year = {2026},
author = {Zhou, HJ and Ma, JX and Hu, JR and Han, YX and Yang, B and Zhou, ZM and Li, LL and Liu, JY and Du, XL and Cui, ZG and Kan, B},
title = {[Analysis on the epidemiological characteristics of legionnaires' disease in China based on multi-source data].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {5},
pages = {714-720},
doi = {10.3760/cma.j.cn112150-20260306-00178},
pmid = {42128675},
issn = {0253-9624},
support = {GZNL2024A01025//Special Project of Guangzhou National Laboratory/ ; 2022YFC2305300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; China/epidemiology ; *Legionnaires' Disease/epidemiology/microbiology ; Male ; Middle Aged ; Aged ; Female ; Genotype ; High-Throughput Nucleotide Sequencing ; Legionella pneumophila ; Legionella/genetics ; Adult ; Incidence ; },
abstract = {Objective: To analyze the epidemiological characteristics of Legionnaires' disease in China based on multi-source data. Methods: Based on the metagenomic next-generation sequencing (mNGS) data of bronchoalveolar lavage specimens collected from a third-party medical testing institution from March 2024 to September 2025, this study aggregated nucleic acid detection data for multiple pathogens from the National Pathogenic Bacteria Identification Network's respiratory syndrome surveillance and conducted a meta-analysis by combining published literature. Descriptive epidemiological methods were used to analyze the demographic characteristics, spatiotemporal distribution, and Legionella species and genotype of Legionnaires' disease in China. Results: By integrating three types of data sources, a total of 1 866 Legionnaires' disease cases were included in the study. Chinese Legionnaires' disease patients were predominantly middle-aged and elderly males, accounting for 64.31% of cases. The age distribution of cases exhibited a bimodal pattern, with a significant concentration in the middle-aged and elderly population. The 60-65 age group had the highest incidence. However, in addition to the peak in the middle-aged and elderly population, there was also a peak in the 0-5 age group. The number of cases showed a peak occurring from July to August. The cases exhibited significant regional distribution disparities across the country. Legionella pneumophila infection was predominant (accounting for 95.70%), with other species including Legionella macleodii (20 cases) and Legionella longbeachae (18 cases). Among 412 samples, L. pneumophila genotypes were obtained, divided into 7 sequence types, including ST36 (n=148), ST1 (n=60), ST23 (n=58), ST51 (n=51), ST734 (n=51), ST42 (n=32), and ST47 (n=12). The distribution of STs in different geographical regions had commonalities, but there were also certain regional differences. The results of universal core genome multi-locus sequence typing showed that each ST formed relatively independent branch clusters, indicating clear genetic differentiation between different STs. The overall genetic diversity of Legionella in China was high. Conclusion: Legionella-positive cases have been detected throughout the year in China, with a wide distribution and regional differences. L. pneumophila has a high proportion and a large genetic diversity in its genome.},
}

Humans
China/epidemiology
*Legionnaires' Disease/epidemiology/microbiology
Male
Middle Aged
Aged
Female
Genotype
High-Throughput Nucleotide Sequencing
Legionella pneumophila
Legionella/genetics
Adult
Incidence

@article {pmid42114750,
year = {2026},
author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E},
title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28157},
pmid = {42114750},
issn = {1525-3198},
abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.},
}

@article {pmid42115187,
year = {2026},
author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X},
title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04095-2},
pmid = {42115187},
issn = {2158-3188},
abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.},
}

@article {pmid42115271,
year = {2026},
author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W},
title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52084-8},
pmid = {42115271},
issn = {2045-2322},
support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; },
abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.},
}

@article {pmid42115921,
year = {2026},
author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F},
title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05117-1},
pmid = {42115921},
issn = {1471-2180},
abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.},
}

@article {pmid42116123,
year = {2026},
author = {Zhou, J and Cheng, H and Zhang, Y and Liu, T and Chen, X and Lea-Smith, DJ and Todd, JD and Liu, J and He, X and Liu, R and Zhang, XH},
title = {Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00908-5},
pmid = {42116123},
issn = {2524-6372},
support = {BB/Y008332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/X014428//Natural Environmental Research Council/ ; NE/P012671//Natural Environmental Research Council/ ; RPG-2020-413//Leverhulme Trust/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2025YFF0516900&2025YFF0516903//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.

RESULTS: To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4[+] and SiO3[2-]) based on Pearson's correlation analysis.

CONCLUSION: This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.},
}

@article {pmid42116193,
year = {2026},
author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS},
title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00909-4},
pmid = {42116193},
issn = {2524-6372},
support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; },
abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.

METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.

RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.

CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.},
}

@article {pmid42116465,
year = {2026},
author = {Ozaki, GEDN and Maciel, ESO and Souza, BP and da Silva-Padilha, MP and Santos, NMMO and Oliveira, JCS and Souza, VB and Tulini, FL},
title = {Development and characterization of seriguela (Spondias purpurea) water kefir: metagenomic insights and functional potential of a spray-dried probiotic powder.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119194},
doi = {10.1016/j.foodres.2026.119194},
pmid = {42116465},
issn = {1873-7145},
mesh = {*Kefir/microbiology/analysis ; *Probiotics/analysis ; Powders ; Fermentation ; *Metagenomics ; *Spray Drying ; Food Microbiology ; Hydrogen-Ion Concentration ; Antioxidants/analysis ; Fruit/chemistry/microbiology ; Bacteria/classification/genetics ; },
abstract = {Water kefir is a fermented probiotic beverage suitable for those with lactose intolerance, dairy allergies, or vegan diets. Adding fruits during fermentation can modulate microbial dynamics, sensory attributes, and biochemical composition, thereby enhancing functional properties. In this context, Spondias purpurea (seriguela), a bioactive-rich fruit native to the Americas, represents a promising yet underexplored substrate for the development of functional beverages. Therefore, this study investigated the composition of seriguela and its application in water kefir production, followed by physicochemical and metagenomic characterization and the evaluation of spray-dried formulations. Seriguela fruits exhibited an acidic pH (3.63), the presence of coumarins, steroids, and tannins, and remarkable antioxidant activity. Seriguela-flavored kefir maintained microbial levels comparable to those of traditional kefir (7.1 and 6.8 log CFU/mL for bacteria and yeasts, respectively), promoting a predominance of Komagataeibacter saccharivorans, Acetobacter aceti, A. lovaniensis, Liquorilactobacillus mali, Clostridium pasteurianum, and yeasts from the Saccharomyces genus. This change in the microbiota of seriguela-flavored kefir indicates a more homogeneous fermentation with pronounced acetic characteristics and probiotic potential. Furthermore, the spray-dried kefir demonstrated good physical properties, remarkable resistance under simulated gastrointestinal conditions, and moderate stability during refrigerated storage throughout 30 days (75.7% and 82.9% of survival for bacteria and yeasts, respectively, enumerated on De Man, Rogosa & Sharpe agar and potato dextrose agar), highlighting its potential as a stable probiotic product. Overall, these results demonstrate the suitability of seriguela as a functional ingredient in water kefir and confirm spray-drying as a viable strategy for producing stable fermented powders with potential health-promoting properties.},
}

*Kefir/microbiology/analysis
*Probiotics/analysis
Powders
Fermentation
*Metagenomics
*Spray Drying
Food Microbiology
Hydrogen-Ion Concentration
Antioxidants/analysis
Fruit/chemistry/microbiology
Bacteria/classification/genetics

@article {pmid42116469,
year = {2026},
author = {Liu, D and Li, J and Zhang, J and Zhang, C},
title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119201},
doi = {10.1016/j.foodres.2026.119201},
pmid = {42116469},
issn = {1873-7145},
mesh = {*Carbon Dioxide/chemistry ; *Taste ; *Microbiota ; *Vegetables/microbiology/metabolism/chemistry ; *Food Microbiology ; *Atmosphere ; Biogenic Amines/analysis/metabolism ; Food Handling/methods ; Volatile Organic Compounds/analysis ; },
abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.},
}

*Carbon Dioxide/chemistry
*Taste
*Microbiota
*Vegetables/microbiology/metabolism/chemistry
*Food Microbiology
*Atmosphere
Biogenic Amines/analysis/metabolism
Food Handling/methods
Volatile Organic Compounds/analysis

@article {pmid42116470,
year = {2026},
author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W},
title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119200},
doi = {10.1016/j.foodres.2026.119200},
pmid = {42116470},
issn = {1873-7145},
mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Indoles/metabolism ; *Oligosaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Mice ; *Propionates/metabolism ; *Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy ; *Receptors, Aryl Hydrocarbon/metabolism ; *Anti-Bacterial Agents/adverse effects ; Humans ; Male ; Female ; Prospective Studies ; Dysbiosis/chemically induced ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.

OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.

METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.

RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.

CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.},
}

*NF-E2-Related Factor 2/metabolism
Animals
*Indoles/metabolism
*Oligosaccharides/pharmacology
Gastrointestinal Microbiome/drug effects
Mice
*Propionates/metabolism
*Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy
*Receptors, Aryl Hydrocarbon/metabolism
*Anti-Bacterial Agents/adverse effects
Humans
Male
Female
Prospective Studies
Dysbiosis/chemically induced
Oxidative Stress/drug effects
Multiomics

@article {pmid42116511,
year = {2026},
author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W},
title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119274},
doi = {10.1016/j.foodres.2026.119274},
pmid = {42116511},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; },
abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.},
}

*Fermentation
*Microbiota
*Metabolome
Food Microbiology
Taste
Volatile Organic Compounds/analysis
Bacteria/metabolism/classification/genetics
*Wine/microbiology/analysis
Fungi/metabolism/classification
Metabolomics
Flavoring Agents
China

@article {pmid42116518,
year = {2026},
author = {Zhou, H and Xu, B and Zhang, L and Yan, L and Wang, R and Xu, Q and Jiang, C and Chen, A and Wu, X and Li, X},
title = {Ecological dominance and genomic features of bacterial generalists during pit fermentation of three distinct baijiu types in Anhui Province.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119296},
doi = {10.1016/j.foodres.2026.119296},
pmid = {42116518},
issn = {1873-7145},
mesh = {*Fermentation ; China ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Wine/microbiology/analysis ; Lactobacillus/genetics/metabolism ; },
abstract = {Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.},
}

*Fermentation
China
*Food Microbiology
*Bacteria/genetics/classification/metabolism
*Wine/microbiology/analysis
Lactobacillus/genetics/metabolism

@article {pmid42116534,
year = {2026},
author = {Veyrenche, N and Boluda, S and Pérot, P and Malissin, I and Leruez-Ville, M and Jamet, A and Ferroni, A and Regnault, B and Salmona, M and Feghoul, L and Robert-Capraro, L and Leroux, A and Grasland, B and Niqueux, E and Briand, FX and Plu, I and Seilhean, D and Megarbane, B and Fourgeaud, J and Dheilly, NM},
title = {One Health Investigation into Fatal Encephalitis Caused by Pigeon Paramyxovirus Type 1, France.},
journal = {Emerging infectious diseases},
volume = {32},
number = {5},
pages = {753},
doi = {10.3201/eid3205.251576},
pmid = {42116534},
issn = {1080-6059},
mesh = {Humans ; France/epidemiology ; *Newcastle disease virus/genetics/classification/isolation & purification ; Fatal Outcome ; *Newcastle Disease/virology/diagnosis/epidemiology ; Animals ; Male ; Phylogeny ; Columbidae/virology ; *Encephalitis, Viral/diagnosis/virology/epidemiology ; },
abstract = {Pigeon paramyxovirus type 1 (PPMV-1) is a genotype of avian paramyxovirus type 1 that uses species of the family Columbidae as reservoir species. We report fatal PPMV-1 encephalitis in a human without immunosuppression or travel history outside metropolitan France. Postmortem analyses revealed PPMV-1 in tissues, underscoring that physicians should consider this potential diagnosis.},
}

Humans
France/epidemiology
*Newcastle disease virus/genetics/classification/isolation & purification
Fatal Outcome
*Newcastle Disease/virology/diagnosis/epidemiology
Animals
Male
Phylogeny
Columbidae/virology
*Encephalitis, Viral/diagnosis/virology/epidemiology

@article {pmid42116592,
year = {2026},
author = {Andreani, J and Boschi, C and Decoppet, A and Delerce, J and Penant, G and Karadeniz, A and Grimaldier, C and Jardot, P and Zangoli, L and Mandy, M and Vigroux, N and Polesso, F and Edouard, S and Cano, P and Lagier, JC and La Scola, B and Colson, P},
title = {Severe Respiratory Illness and Death Associated with Outbreak of Human Rhinovirus B14 among Older Adults, France, 2024.},
journal = {Emerging infectious diseases},
volume = {32},
number = {5},
pages = {768-773},
doi = {10.3201/eid3205.250981},
pmid = {42116592},
issn = {1080-6059},
mesh = {Humans ; France/epidemiology ; *Rhinovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; *Picornaviridae Infections/epidemiology/virology/mortality ; Aged ; Male ; Female ; Aged, 80 and over ; *Respiratory Tract Infections/epidemiology/virology/mortality ; Phylogeny ; Genome, Viral ; },
abstract = {We investigated an outbreak of unknown respiratory disease and 8 deaths among older adults in a long-term care facility in France. We identified human rhinovirus (HRV) by quantitative PCR and HRV-B14 by metagenomics. We obtained 5 HRV-B14 genomes that diverged from 5 publicly available genomes. Real-time metagenomics could enable rapid clinical diagnoses.},
}

Humans
France/epidemiology
*Rhinovirus/genetics/classification/isolation & purification
*Disease Outbreaks
*Picornaviridae Infections/epidemiology/virology/mortality
Aged
Male
Female
Aged, 80 and over
*Respiratory Tract Infections/epidemiology/virology/mortality
Phylogeny
Genome, Viral

@article {pmid42116727,
year = {2026},
author = {Kutter, JS and Cuevas-Lobato, O and Fernandez-Pacheco-Gonzalez-Echavarri, BE and Moreno-Gomila, C and Garcia-Ibañez, N and Camacho, J and Ruiz-Pedro, E and Cabrerizo, M and Alós, JI and Diez-Fuertes, F and Fernandez-Garcia, MD},
title = {Unraveling the Transmission Dynamics of a Novel Norovirus GII.17[P17] Lineage During Two Consecutive Outbreaks in a Spanish Hospital.},
journal = {Journal of medical virology},
volume = {98},
number = {5},
pages = {e70966},
doi = {10.1002/jmv.70966},
pmid = {42116727},
issn = {1096-9071},
support = {PI23CIII-00009//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Caliciviridae Infections/epidemiology/transmission/virology ; *Norovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; Spain/epidemiology ; Phylogeny ; *Cross Infection/epidemiology/virology/transmission ; Feces/virology ; *Genotype ; Male ; Female ; Middle Aged ; Adult ; Molecular Epidemiology ; Aged ; Hospitals ; High-Throughput Nucleotide Sequencing ; *Gastroenteritis/epidemiology/virology ; Young Adult ; Genome, Viral ; },
abstract = {Norovirus outbreaks in healthcare settings pose significant challenges to infection prevention and control (IPC). To prevent and control such outbreaks efficiently, identifying sources and transmission clusters (TCs) is crucial but often limited by traditional outbreak investigations. Here, we examined two consecutive hospital norovirus outbreaks employing a genomic epidemiology approach to elucidate transmission dynamics and guide IPC strategies. Stool samples of 54 symptomatic patients were analyzed with different diagnostic methods, and 26 norovirus-positive samples underwent metagenomic next-generation sequencing (mNGS) for phylodynamic and phylogenetic analyses. All infections belonged to the novel GII.17[P17] lineage, circulating globally since 2023/2024. LiquidArray® outperformed fluorescence immunoassay (FIA, 28.6%) and RT-PCR (85.7%) with FIA's low sensitivity leading to missed cases highlighting the need for molecular confirmation for accurate outbreak management. Genomic analysis revealed multiple introductions, with two TCs identified in Outbreak-1 and one in Outbreak-2, as well as inter-hospital-unit spread. Reconstruction of transmission trees indicated sustained person-to-person spread with 0-3 unobserved intermediate cases in both outbreaks. Identical sequences in patients without clear epidemiological links suggested possible fomite transmission. These analyses provided key insights into infection sources and TCs that would have remained unknown using epidemiological investigations alone, supporting more targeted IPC resource allocation and intervention strategies.},
}

Humans
*Caliciviridae Infections/epidemiology/transmission/virology
*Norovirus/genetics/classification/isolation & purification
*Disease Outbreaks
Spain/epidemiology
Phylogeny
*Cross Infection/epidemiology/virology/transmission
Feces/virology
*Genotype
Male
Female
Middle Aged
Adult
Molecular Epidemiology
Aged
Hospitals
High-Throughput Nucleotide Sequencing
*Gastroenteritis/epidemiology/virology
Young Adult
Genome, Viral

@article {pmid42116832,
year = {2026},
author = {Dawson, MN and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {189},
pmid = {42116832},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Aurelia sp. 4 Dawson et al., 2005 (moon jellyfish; Cnidaria; Scyphozoa; Semaeostomeae; Ulmaridae). The genome sequence has a total length of 462.10 megabases. Most of the assembly (99.99%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.88 kilobases. From the metagenome data, we recovered 3 bins, of which 2 were high-quality MAGs.},
}

@article {pmid42116847,
year = {2026},
author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA},
title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag081},
pmid = {42116847},
issn = {2730-6151},
abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.},
}

@article {pmid42117813,
year = {2026},
author = {Qi, W and Lü, L and Huang, K and Qi, J and Li, M and Shi, M and Wang, H},
title = {Effects of Rotary Tillage and Fertilization on Chemical Properties and Microbial Communities of Soil Under Continuous Morchella Mushroom Cultivation.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090674},
pmid = {42117813},
issn = {2079-7737},
support = {2024XTCX0403//Liaoning Academy of Agricultural Sciences Collaborative Innovation Project/ ; 2026NYGG010//Key Core Technology Research and Development in Shaanxi Province Agriculture/ ; },
abstract = {The severe continuous cropping obstacles in Morchella cultivation, driven primarily by soil microecological imbalance, critically constrain the sustainable development of the industry. To address this challenge, this study evaluated the efficacy of rotary tillage, calcium cyanamide (CaCN2), and organic fertilizer, applied individually and in combination, in mitigating these obstacles and explored the underlying microbial mechanisms. The soil was treated on 5 August 2024, and soil samples were collected on 5 October 2024. Four treatments were established: continuous cropping control (CK), rotary tillage (XGX), rotary tillage combined with calcium cyanamide (MPD), and rotary tillage combined with calcium cyanamide and organic fertilizer (MPX). Soil chemical properties were analyzed in conjunction with metagenomic sequencing to characterize the responses of soil properties and microbial communities, including both eukaryotic and bacterial taxa. The results indicated that the MPD treatment showed a relatively pronounced effect in enhancing key soil fertility indicators, including soil organic matter (OM), total nitrogen (TN), available nitrogen (AN), available potassium (AK), and total phosphorus (TP). All amendments significantly altered microbial community structures. Specifically, the integrated MPX treatment effectively reduced the relative abundance of the pathogenic fungus Olpidium while maintaining higher overall microbial diversity. It also significantly promoted the abundance of Morchella itself and beneficial bacterial phyla such as Actinomycetota and Pseudomonadota. Redundancy analysis identified AN and AK as the primary drivers of eukaryotic community variation, whereas Availa-ble phosphorus (AP) and potential of hydrogen (pH) were the key factors shaping the bacterial community. The results indicated that MPD was the showed relatively pronounced effectiveness in rapidly improving soil fertility and suppressing pathogenic fungi. In contrast, MPX showed relatively better performance in optimizing microbial community structure, enhancing microbial diversity, and strengthening overall ecological stability. These two treatments exhibited distinct advantages in soil chemical improvement and microbial community regulation, respectively, thereby providing alternative practical strategies and a theoretical basis for the ecological management of continuous-cropping obstacles in Morchella cultivation. It should be noted that this study did not include treatments with calcium cyanamide alone, organic fertilizer alone, or their combined application without rotary tillage. This is primarily because rotary tillage is a standard land preparation practice in Morchella cultivation, and the use of soil amendments without accompanying tillage is rarely adopted under practical production conditions.},
}

@article {pmid42118424,
year = {2026},
author = {Devi, P and Nath, SK and Barua, B and Saha, T},
title = {Big data and artificial intelligence in animal nutrition: a new era of precision feeding.},
journal = {Tropical animal health and production},
volume = {58},
number = {4},
pages = {},
pmid = {42118424},
issn = {1573-7438},
mesh = {Animals ; *Big Data ; *Artificial Intelligence ; *Animal Feed/analysis ; *Animal Husbandry/methods ; *Animal Nutritional Physiological Phenomena ; *Livestock/physiology ; Dairying/methods ; },
abstract = {The convergence of Big Data and Artificial Intelligence (AI) is redefining animal nutrition by enabling precision feeding systems that are individualized, data-driven, and sustainability-oriented. This review synthesizes recent advances in multi-omics technologies, sensor-based monitoring, and machine learning applications across feed formulation, health surveillance, and production optimization. Precision feeding in pigs has been shown to reduce production costs by more than 8%, decrease protein and phosphorus intake by approximately 25%, lower nutrient excretion by up to 40%, and reduce greenhouse gas (GHGs) emissions by 6%, while maintaining or improving performance. In dairy systems, precision feed management strategies have achieved approximately 9.7% lower dietary crude protein levels, 14% reductions in manure nitrogen excretion, and annual net income gains of USD 137 per cow. AI-driven models have enhanced prediction of milk yield, feed conversion ratio (R[2] = 0.74), and residual feed intake (R[2] = 0.76), while enabling 96.26% accuracy in detecting microplastics in poultry feed. Integration of genomic, phenotypic, and sensor-derived datasets supports real-time monitoring, with wearable and IoT technologies transforming livestock management through continuous tracking of feeding behavior, emissions, and welfare indicators. Despite significant progress, current systems remain constrained by data heterogeneity, limited interoperability, and insufficient prescriptive decision-support frameworks. This article identifies methodological, technological, and adoption-related gaps, while highlighting future directions including nutrigenomics- and metagenomics-informed diet design, adaptive precision nutrition, and cost-effective solutions for smallholder systems. Collectively, these innovations establish Big Data and AI-enabled precision nutrition as a cornerstone of sustainable livestock production, advancing food security, climate resilience, and ethical animal management.},
}

Animals
*Big Data
*Artificial Intelligence
*Animal Feed/analysis
*Animal Husbandry/methods
*Animal Nutritional Physiological Phenomena
*Livestock/physiology
Dairying/methods

@article {pmid42118429,
year = {2026},
author = {Tekin, B and Gurbanov, R},
title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42118429},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Aging/physiology
Biomarkers/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
Animals
Host Microbial Interactions
Fatty Acids, Volatile/metabolism

@article {pmid42119030,
year = {2026},
author = {Yu, J and Tang, SN and Lee, PKH},
title = {Host-Linked Virome Assembly and Turnover Predict Bacterial Community Structure in Wastewater Treatment Systems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag120},
pmid = {42119030},
issn = {1751-7370},
abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1,046 and 1,386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.},
}

@article {pmid42119140,
year = {2026},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13903},
pmid = {42119140},
issn = {1520-5851},
abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.},
}

@article {pmid42119184,
year = {2026},
author = {Pilliol, V and Beye, M and Boualam, MA and Tellissi, L and Slimani, A and Drancourt, M and Aboudharam, G and Tassery, H and Grine, G and Terrer, E},
title = {Evidence of a millennia-old association between a methanogenic archaeon and a bacterium in dental calculus: A re-analysis of ancient and modern metagenomic datasets.},
journal = {Archives of oral biology},
volume = {188},
number = {},
pages = {106622},
doi = {10.1016/j.archoralbio.2026.106622},
pmid = {42119184},
issn = {1879-1506},
abstract = {OBJECTIVES: Granehäll et al. (2021) identified TS-2 as an unknown Methanobrevibacter lineage abundant in ancient dental calculus, less prevalent in modern samples, and not linked to any cultivated representative. We aimed (i) to determine whether TS-2 corresponds to the cultivated oral archaeon Methanobrevibacter massiliense using genome-based species delineation, and (ii) to assess the antiquity of the association between M. massiliense and Pyramidobacter piscolens in ancient and modern dental calculus.

DESIGN: This fully in silico study combined comparative genomics with re-analysis of 97 ancient and modern dental calculus metagenomic datasets. Species-level relationships were assessed using average nucleotide identity, digital DNA-DNA hybridization, and 16S rRNA phylogeny. Metagenomic associations were examined using Kraken2-based taxonomic profiling, with Methanobrevibacter sp. YE315 as a proxy because M. massiliense was absent from the classifier database, and direct competitive read mapping to M. massiliense. Associations with P. piscolens were evaluated using Spearman correlation and negative binomial regression.

RESULTS: Comparative genomics supported TS-2 and M. massiliense as the same species-level taxon, with > 95% average nucleotide identity and > 90% digital DNA-DNA hybridization. In metagenomic analyses, the YE315 proxy was positively associated with P. piscolens in Kraken2 Spearman analysis (ρ = 0.3506, q = 0.0026), and mapped M. massiliense reproduced this pattern (ρ = 0.2939, q = 0.0153). Negative binomial models showed concordant but weaker support, whereas the signal for M. oralis was less consistent.

CONCLUSION: These results identify M. massiliense as the cultivated representative of TS-2 and support an ancient, recurrent association between M. massiliense and P. piscolens in dental calculus.},
}

@article {pmid42119293,
year = {2026},
author = {Li, H and Xu, Y and Lin, T and Hu, C and Yang, Z and Su, H},
title = {Overwintering waterbirds are important reservoirs for the spread of antibiotic resistance genes (ARGs): Shared patterns at the waterbird-environment interface and the risk of horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142298},
doi = {10.1016/j.jhazmat.2026.142298},
pmid = {42119293},
issn = {1873-3336},
abstract = {The global spread of antibiotic resistance genes (ARGs) has become a critical challenge to public health. Long-distance migratory waterbirds are recognized as important biological vectors in the transregional spread of ARGs. However, the sharing patterns of ARGs and the horizontal transfer risks between these birds and their habitats during the wintering period remain poorly understood. This limits a comprehensive understanding of their role in ARG transmission. This study investigated a typical wintering wetland in southwestern China along the East Asian-Australasian Flyway, using metagenomic approaches to systematically characterize the distribution patterns, sharing profiles, and horizontal transfer risks of ARGs in the guts of overwintering waterbirds and their associated aquatic and terrestrial habitats. The results show that multidrug resistance genes are the predominant type of resistance observed both in the guts of overwintering waterbirds and in their habitats. Extensive sharing of ARGs occurs between the guts of overwintering waterbirds and their habitats, with approximately 50% of the 1250 identified ARG subtypes shared by both. We detected 55 high-risk ARG subtypes belonging to 10 resistance categories. Among these, β-lactam resistance genes (e.g., blaNDM-5 and blaCTX-M-15) were the predominant types. In addition, the co-localization of ARGs with mobile genetic elements (MGEs) (e.g., transposons and plasmids) suggests that the gut of waterbirds and aquatic environments may represent potential hotspots for horizontal transfer of ARGs. This study highlights the high connectivity of ARGs between overwintering waterbirds and their habitats, offering important insights into ecological and public health risks related to ARG spread.},
}

@article {pmid42119385,
year = {2026},
author = {Pan, L and Huang, Y and Chen, Y and Peng, T and Yang, J and Qiu, Y and Ji, M and Wu, X},
title = {Responses of soil microbes to antimony stress and coupled nutrient cycling in karst mining areas of Southwest China.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120248},
doi = {10.1016/j.ecoenv.2026.120248},
pmid = {42119385},
issn = {1090-2414},
abstract = {Persistent and poorly mobile heavy metals in soil present a widespread environmental challenge. Among these, antimony (Sb) is a contaminant of emerging concern whose transformation and migration in soil require further investigation to inform effective remediation strategies. Microbial processes are central to these dynamics, yet the mechanisms underlying Sb-microbe interactions remain poorly defined. In this study, we used integrated geochemical and metagenomic analyses to assess Sb contamination and microbial community responses systematically in an abandoned Sb mining area in Southwest China. The data reveal how microbial communities respond to low and moderate levels of Sb contamination. Contamination was highest in the mining area, followed by the smelting and tailings areas; the control area exhibited the lowest levels. Community structure analysis revealed significant enrichment of Thiobacillus, Geothrix, and Anaeromyxobacter in the mining area, while Nocardioides and Sphingomonas were more abundant in the smelting area. Bradyrhizobium dominated in the control area. These patterns reflect distinct microbial responses to the Sb contamination gradient. Critically, partial least squares path modeling revealed that Sb contamination did not directly affect microbial α-diversity. Instead, its influence was indirectly mediated through disruptions in sulfur cycling functions-a novel finding highlighting the indirect ecological impact of Sb. Sb, along with co-occurring copper, may drive adaptive microbial succession by interfering with sulfate respiration. This process enriches microbial groups with sulfur-cycling-related detoxification functions, resulting in simplified community structure and reduced diversity. Thus, the primary mechanism by which Sb alters microbial communities in karst soils is indirect, operating via perturbation of the sulfur cycle rather than direct toxicity. These findings offer a theoretical basis for developing targeted microbial remediation strategies and restoring ecological functions in Sb-contaminated environments by regulating key elemental cycles.},
}

@article {pmid42119482,
year = {2026},
author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS},
title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.},
journal = {Chemosphere},
volume = {405},
number = {},
pages = {144948},
doi = {10.1016/j.chemosphere.2026.144948},
pmid = {42119482},
issn = {1879-1298},
abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.},
}

@article {pmid42119567,
year = {2026},
author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W},
title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102777},
doi = {10.1016/j.xcrm.2026.102777},
pmid = {42119567},
issn = {2666-3791},
abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.},
}

@article {pmid42119613,
year = {2026},
author = {Liu, Y and Cheng, C and Xie, H and Nie, W and Chen, Y and Yu, C and Pavlostathis, SG and Zhang, J and He, Q},
title = {New insights into nitrous oxide-driven anaerobic methane oxidation mediated by Methylococcales and Gemmatimonadales.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134844},
doi = {10.1016/j.biortech.2026.134844},
pmid = {42119613},
issn = {1873-2976},
abstract = {The simultaneous biogeochemical transformation of methane (CH4) and nitrous oxide (N2O) in anoxic environments is a recently proposed pathway for decreasing carbon emission in wetlands. However, the mechanisms underlying this coupled process have yet to be elucidated. Here, two systems with CH4 to N2O molar ratios of 1:1 (R1) and 1:2 (R2) were established. Isotopic tracing showed that the production rate of [13]CO2 in R2 consistently exceeded than that in R1, with a maximum N2O-driven AOM rate of 2.29 μmol∙g[-1]dw∙d[-1], demonstrating the superior performance of R2. Microbial community analysis revealed that Methylococcales and Rhizobiales were the dominant methanotrophs, whereas Gemmatimonadales and Sphingobacteriales represented the primary denitrifiers involved in N2O reduction. Metagenomic binning further indicated that Methylococcales and Gemmatimonadales harbor complementary genomic potentials for CH4 oxidation and N2O reduction, supporting a synergistic interaction driving N2O-dependent AOM. This cooperation appears to rely on electron transfer between the methanotrophic and denitrifiers. Collectively, these findings provide mechanistic evidence for N2O-driven AOM, advancing the understanding of coupled carbon-nitrogen transformations and offering new insights into microbial strategies for mitigating greenhouse gas emissions in wetland systems.},
}

@article {pmid42119614,
year = {2026},
author = {Zhang, Y and Yu, W and Chen, B and Lu, D and Guo, R and Fu, S},
title = {Harnessing microbial resource Rhodopseudomonas palustris for saline-alkaline paddy soil amelioration: key role of extracellular polymeric substances.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134777},
doi = {10.1016/j.biortech.2026.134777},
pmid = {42119614},
issn = {1873-2976},
abstract = {Bioremediation offers an eco-friendly solution for soil salinization, yet few salt-alkali-tolerant microorganisms can adapt to redox fluctuations induced by wet-dry alternation in paddy soil. Rhodopseudomonas palustris (R. palustris) holds promise for addressing this challenge, while the mechanism is still poorly understood. This study established a microcosm experiment mimicking paddy wet-dry alternation by regulating redox conditions to investigate the mechanisms of R. palustris and its extracellular polymeric substances (EPS) in soil amelioration. R. palustris adapted well to redox alternation and significantly reduced soil pH and electrical conductivity (EC) by 3-7% and 7-28%. In anaerobic phase, R. palustris secreted organic acids and promoted EPS synthesis, which directly complexed salt ions and drove soil acidification. Upon transition to aerobic conditions, it accumulated glycogen and polyhydroxyalkanoate (PHA) to sustain growth and EPS secretion. In the subsequent aerobic phase, EPS gradually transformed into amino acids, fulvic acid, and humic-like substances, as revealed by excitation-emission matrix (EEM) spectra, thereby improving soil fertility. Metagenomic analysis further revealed R. palustris and its EPS reshaped the microbial community and regulated the expression of related functional genes. Collectively, this study demonstrates R. palustris serves as an effective microbial resource for sodic-saline paddy soil amelioration, with EPS acting as a key bioactive component that drives this process toward biotechnology-driven remediation strategies.},
}

@article {pmid42119617,
year = {2026},
author = {Yang, C and Cao, Y and Yang, Q and Li, J and Dong, T and Liu, Y and Li, X and Liu, F},
title = {Hematite-enhanced denitrification in bioelectrochemical system at low current density: kinetics, biofilm chemistry and metagenomic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134852},
doi = {10.1016/j.biortech.2026.134852},
pmid = {42119617},
issn = {1873-2976},
abstract = {Nitrate contamination of groundwater threatens drinking-water safety and necessitates the development of sustainable, low-energy remediation technologies. Bioelectrochemical systems (BESs) can enhance denitrification; however, their performance is constrained by low cathodic electron efficiency and ammonium accumulation. We developed a hematite-enhanced BES (HBES) and evaluated denitrification at different current densities (0-400 mA/m[2]). Hematite shifted the optimal current density from 200 to 100 mA/m[2], achieving complete nitrate removal within 72 h while suppressing ammonium formation to 0.38 ± 0.02 mg-N/L. Mechanistically, hematite improved cathodic kinetics and minimized activation losses, increased nitrate reductase activity, and promoted extracellular polymeric substance (EPS) enrichment with higher redox-active fulvic- and humic-like fractions. Community profiling revealed hematite-associated enrichment of Thauera, Acinetobacter, Hydrogenophaga, and Alishewanella, consistent with enhanced denitrification and electroactivity. Metagenomic analyses further revealed enhanced modules for sequential nitrate reduction to N2, suppression of dissimilatory nitrate reduction to ammonium (DNRA) marker genes, and elevated potentials for cytochrome-associated extracellular electron transfer (EET) and oxidative phosphorylation. Overall, hematite restructures electron-transfer networks and microbial metabolism at the mineral-biofilm-electrode interface, facilitating efficient and cleaner denitrification at relatively low current density and offering operational insights for BES-based groundwater nitrate remediation.},
}

@article {pmid42119682,
year = {2026},
author = {Mardirossian, JM and Abdallah, B and Douglas, GM and Barbour, J and Shapiro, BJ and El Chaar, M},
title = {Early-life acquisition of antimicrobial resistance genes and strain-level genomic concordance across maternal-infant compartments.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105956},
doi = {10.1016/j.meegid.2026.105956},
pmid = {42119682},
issn = {1567-7257},
abstract = {BACKGROUND: Early-life microbial colonization and antimicrobial resistance gene (ARG) acquisition may influence long-term health outcomes. High-resolution genomic studies assessing strain-level concordance and resistome overlap across maternal-infant interfaces during the immediate postnatal period remain limited.

METHODS: We analyzed 32 healthy mother-newborn dyads in Lebanon (91 samples), including maternal colostrum and breast milk and neonatal meconium and stool. Culture-based isolation, antimicrobial susceptibility testing, shotgun metagenomics, and whole-genome sequencing were used to characterize microbial composition, resistome profiles, and strain-level relatedness.

RESULTS: Viable bacteria were recovered from 80% of meconium samples, with Escherichia coli and Enterococcus faecalis among the most frequent isolates. Whole-genome sequencing identified highly similar strains (≥99.9% average nucleotide identity) of E. coli, Klebsiella pneumoniae, and K. oxytoca across maternal and neonatal samples in six dyads. Metagenomic profiling demonstrated early acquisition of multidrug resistance genes, including blaCTX-M-15, tet(M), and oqxA/B, alongside mobile genetic elements such as IncF and Col-type plasmids. The colistin resistance gene mcr-10 was detected in one neonatal stool sample.

CONCLUSION: These findings demonstrate early-life resistome establishment and strain-level genomic concordance across maternal-infant compartments within the first week of life. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared ARGs are consistent with potential maternal or shared environmental contributions to neonatal microbial and resistance gene acquisition, although the direction of transfer cannot be definitively established. This work underscores the importance of integrating genomic surveillance of maternal and neonatal resistomes in perinatal health research.

IMPORTANCE: This study provides high-resolution genomic insight into early-life microbial colonization and antimicrobial resistance gene acquisition by integrating culture-based microbiology, shotgun metagenomics, and whole-genome sequencing across matched maternal (colostrum, breast milk) and neonatal (meconium, stool) samples. The identification of viable bacteria and clinically relevant resistance determinants within the first week of life, including instances of strain-level genomic concordance between maternal and neonatal samples, contributes to understanding the early establishment of the neonatal resistome. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared mobile genetic elements suggest potential maternal or shared environmental influences on early colonization dynamics. These findings highlight the value of considering maternal reservoirs in studies of neonatal microbial and resistance gene evolution and underscore the need for genomic surveillance of early-life resistome development in perinatal settings.},
}

@article {pmid42119744,
year = {2026},
author = {Mao, N and Liao, C and Hao, J and Sun, H and Zheng, Y and Yin, H and Xie, Y},
title = {Late-window oxygen pulsing unlocks lignin-carbohydrate shielding and enhances fiber deconstruction during maize stover fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134854},
doi = {10.1016/j.biortech.2026.134854},
pmid = {42119744},
issn = {1873-2976},
abstract = {Staged aeration offers a controllable lever to relax the strict-anaerobic paradigm in lignocellulosic fermentation. We compared single-dose air injection at early, mid, and late windows with a cellulase benchmark and anaerobic control, integrating fiber fractions, fermentation products, FTIR metrics, metagenomic functional profiles (CAZy and nitrogen cycling), microbial succession, and network topology. Mid and late aeration promoted ADL reduction and fiber deconstruction, lowering acid detergent lignin and acid detergent fiber by 23-34% and 13-15% versus the control, reaching cellulase-comparable levels. Late aeration produced the strongest structural unlocking, with attenuation of carbohydrate- and lignin-aromatic FTIR regions and reduced carbonyl-associated bands, consistent with disrupted lignin shielding and improved substrate accessibility. Late aeration increased glycosyltransferases yet showed the lowest glycoside hydrolases and auxiliary activities while achieving the largest net ADL and fiber losses, indicating that accessibility rather than terminal hydrolytic potential governs deconstruction intensity. Network analysis showed reduced mean degree and K-core but higher modularity under late aeration, consistent with a more compartmentalized interaction structure and reallocated carbon use. Overall, aeration timing is a scalable, low-input lever for process design. Future work should test generality across feedstocks and develop accessibility-based monitoring and control.},
}

@article {pmid42119966,
year = {2026},
author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC},
title = {Metagenomic Characterization of Bacterial Communities on Beach Macroplastics: Insights into Antimicrobial Resistance and Virulence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128213},
doi = {10.1016/j.envpol.2026.128213},
pmid = {42119966},
issn = {1873-6424},
abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1,264-2,046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.},
}

@article {pmid42120015,
year = {2026},
author = {Ito, T and Li, B and Sakaguchi, T and Yagita-Sakamaki, M and Itoi, H and Murakami, M and Wu, R and Fukada, A and Motooka, D and Ogino, T and Nakamura, S and Okuzaki, D and Takeda, K and Kayama, H},
title = {The IL-10/IL-10Rα axis in fibroblasts limits large intestinal pathology by suppressing type I interferon signaling.},
journal = {International immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/intimm/dxag022},
pmid = {42120015},
issn = {1460-2377},
abstract = {Recent studies identified that the dysregulation of fibroblast activity, in addition to impairment in epithelial integrity and uncontrolled immune response, is implicated in the pathogenesis of inflammatory bowel disease (IBD). The anti-inflammatory cytokine IL-10 and its receptors IL-10Rα and IL-10Rβ have IBD-associated single nucleotide polymorphisms. In the intestine, IL-10 signaling is essential for maintaining an anti-inflammatory state of myeloid cells and inducing regulatory T cells, thereby preventing intestinal inflammation linked to IBD development. However, its impact on the physiology and pathophysiology of intestinal fibroblasts is poorly understood. Here, we show that Il10ra deficiency leads to increased expression of a subset of genes in colonic fibroblasts, most of which are associated with the type I interferon (IFN) and type II IFN signaling pathways. In addition, Pdgfra-cre; Il10raf/f mice aged 16 weeks or older develop chronic spontaneous colitis and subsequent fibrosis accompanied by enhanced infiltration of myeloid cells and effector CD4+ T cells in the lamina propria of the colon. Moreover, Pdgfra-cre; Il10raf/f mice at 12 weeks of age exhibit more severe clinical symptoms than those of Il10raf/f mice during dextran sodium sulfate-induced colitis that can be suppressed by the administration of anti-IFNAR1 antibody but not anti-IFNGR1 antibody. Therefore, inhibition of type I IFN pathway via IL-10Rα signaling in fibroblasts is one of the IL-10-dependent mechanisms underlying the prevention of large intestinal pathology.},
}

@article {pmid42120057,
year = {2026},
author = {Owens, LA and Berkman, LK and Pease, BS and Dunn, CD and Nielsen, CK and Groninger, JW and Bosch, K and Hudman, D and Timm, SR and Goldberg, TL},
title = {Viruses and Parasites in Swamp Rabbits (Sylvilagus aquaticus): A Baseline Survey to Aid Conservation Efforts.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
doi = {10.7589/JWD-D-25-00059},
pmid = {42120057},
issn = {1943-3700},
abstract = {Technical advancements have enabled the discovery of potential pathogens in an ever-broadening range of wildlife taxa. To further the scope of this body of knowledge and to inform conservation efforts, we examined potential disease agents present in swamp rabbits (Sylvilagus aquaticus) of southeastern Missouri, USA, during winter 2023. This region represents the northernmost portion of the species' range and is characterized by an intermixed landscape of preferred bottomland hardwood forest and agricultural landcover. Concerns about infectious disease threats to swamp rabbits have increased since the emergence of rabbit hemorrhagic disease, caused by rabbit hemorrhagic disease virus 2 (RHDV2; Caliciviridae, Lagovirus europaeus), that has spread to domestic, wild, and feral rabbits and hares, predominantly in the western and midwestern USA. We applied metagenomic and metabarcoding methods, designed to characterize communities of viruses and parasites, to noninvasively collected rabbit fecal samples. We identified seven viruses and eight parasite genera that probably infect mammals. Although some relatives of these agents cause disease, none are unexpected in lagomorphs, and none are considered a health concern. Notably, RHDV2 was not detected. These results provide baseline data for future conservation and management efforts, especially if RHDV2 or other pathogens become a concern for swamp rabbits.},
}

@article {pmid42108292,
year = {2026},
author = {Guo, JX and Gao, YZ},
title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {91-103},
pmid = {42108292},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.},
}

*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Humans
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid42108294,
year = {2026},
author = {Xia, H and Zhou, C and Fu, B and Han, H},
title = {Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {117-146},
pmid = {42108294},
issn = {1940-6029},
mesh = {*Machine Learning ; *Proteomics/methods ; Metagenomics/methods ; *Enzymes/genetics/metabolism/chemistry ; Lignin/metabolism ; Genomics/methods ; Multiomics ; },
abstract = {Enzymes are fundamental protein catalysts essential to life processes and widely applied in industrial and healthcare sectors. However, the broader application of natural enzymes is constrained by their inherent catalytic limitations, and traditional discovery methods such as microbial enrichment are often slow and low-throughput. Driven by advances in multi-omics and artificial intelligence, a range of novel screening strategies has been developed, enabling significant enhancements in both catalytic efficiency and stability of enzymes. This chapter assesses high-throughput approaches, such as metagenomics, metaproteomics, machine learning, and de novo design, comparing their respective advantages and limitations for enzyme discovery. Furthermore, we discuss the application potential of lignocellulose-degrading and plastic-degrading enzymes in biomass conversion and plastic waste recycling.},
}

*Machine Learning
*Proteomics/methods
Metagenomics/methods
*Enzymes/genetics/metabolism/chemistry
Lignin/metabolism
Genomics/methods
Multiomics

@article {pmid42108295,
year = {2026},
author = {Peng, B and Chang, X},
title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {147-164},
pmid = {42108295},
issn = {1940-6029},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; },
abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.},
}

Humans
*Gastrointestinal Microbiome
*Lung/metabolism
*Metabolomics/methods
Lung Diseases/metabolism/microbiology
Metagenomics/methods
Dysbiosis
Animals
*Genomics/methods
Proteomics/methods

@article {pmid42109826,
year = {2026},
author = {Sun, A and Jin, SL and Liu, JG},
title = {A practical guide for characterization of novel CRISPR-Cas systems with Pro-CRISPR factors.},
journal = {Biophysics reports},
volume = {12},
number = {2},
pages = {85-99},
pmid = {42109826},
issn = {2364-3420},
abstract = {The emergence of advanced genome editing technologies has revolutionized research in life sciences, offering an unprecedented way to uncover unknown biological functions and innovative therapeutic strategies. Among all genome editing tools, CRISPR-Cas-based technologies play a pivotal role in this revolution, particularly Class 2 effectors such as Cas9 and Cas12, owing to their high efficacy and ease of programmability. With the advancements in genome sequencing and metagenomics, an increasing number of novel CRISPR-Cas systems have been discovered, including those found in extreme environments and viruses. Furthermore, recent studies have revealed an unexpected role of non-Cas accessory genes, such as the Tn7-like transposon and Pro-CRISPR factors (Pcr), in conferring additional functionalities to the CRISPR system, providing new insights into the understanding of CRISPR-mediated bacterial immunity and advancing the development of genome editing technologies. Therefore, it is essential to develop comprehensive methods for characterizing the Cas proteins and Pro-CRISPR factors with a growing diversity. In this protocol, we provide a method encompassing protein purification, biochemical characterization, validation of protein-protein interactions, and preliminary in vivo functional assays in bacteria for Cas nuclease and its associated Pro-CRISPR factor. We hope this protocol will not only assist in the characterization of the CRISPR-Cas system, but also provide valuable guidance for the characterization of other nucleases or nucleic acid modification systems.},
}

@article {pmid42109869,
year = {2026},
author = {Gao, Y and Zhu, T and Jiang, Y and Tian, F and Li, Y and Liu, W and Xu, S and Tong, Y and Qin, Z and Hu, F},
title = {Genomic characterization of two duck-origin picornaviruses with seven putative 2A peptides.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1753959},
pmid = {42109869},
issn = {2297-1769},
abstract = {INTRODUCTION: The Picornaviridae family is a large group of viruses comprising 68 genera. Duck-origin picornaviruses are categorized into four genera, however, the taxonomic status of some recently identified strains remains to be determined.

METHODS: In this study, two virus strains isolated from breeding ducks experiencing reduced egg production were identified and characterized through viral metagenomic analysis.

RESULTS: Two viral strains (NC0246 and PX0394) exhibiting the typical picornavirus-like genomic structure were identified and characterized. Notably, both strains exhibit extended 2A sequences that each possesses seven distinct 2A polypeptides considered rare in Picornaviridae family. Specifically, NC0246 exhibits a deletion of 73 amino acids (aa) in the region corresponding to 2A4-2A5 when compared to PX0394 indicating the genetic diversity of picornaviruses. Homology analysis revealed that the P1 region of NC0246 was most closely related to duck aalivirus A1, with aa identity of 37.37%. Conversely, the P1 region of PX0394 was most closely related to duck egg-reducing syndrome virus (DERSV), with aa identity of 64.44%. Furthermore, the 2C and 3D proteins of NC0246 and PX0394 was most closely related to DERSV. Phylogenetic analyses indicate that NC0246 and PX0394 form a sister clade to DERSV and duck aalivirus A1 and display marked heterogeneity in the P1 protein. While NC0246 and PX0394 branch nearest to DERSV and duck aalivirus A1, duck hepatitis A virus types 1 and 3, sharing secondary homology, occupy a separate lineage.

CONCLUSION: Two picornaviruses were identified and characterized from breeding ducks that exhibited decreased egg production. Through genomic structure and homology analysis, these viruses were most closely related to DERSV and duck aalivirus A1. NC0246, PX0394, and the previously reported DERSV show a close evolutionary relationship with the genus Aalivirus based on genomic and phylogenetic analyses, suggesting a potential affiliation with this genus.},
}

@article {pmid42110882,
year = {2026},
author = {Mayne, R and Smith, DB and Brown, K and Chen, YP and Firth, AE and Katayama, K and Knowles, NJ and Simmonds, P},
title = {Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales.},
journal = {Virus evolution},
volume = {12},
number = {1},
pages = {veag023},
pmid = {42110882},
issn = {2057-1577},
abstract = {The order Picornavirales is a group of highly diverse RNA viruses that includes many pathogens of significance to human and veterinary health, agriculture, and the wider environment. However, the wide range of viruses assigned to the order, together with their genomic variability, and the recent description of numerous 'picorna-like' viruses derived from metagenomic analyses of environmental samples, challenge the established taxonomic classification of members of the order and the criteria for their classification. Here, we combine the existing gold standard, hallmark RNA-directed RNA-polymerase (RdRP) gene sequence-based analysis with helicase sequence-based phylogeny, RdRP structural prediction through the use of ColabFold and Fold Tree, and analysis of coding-complete genomes using GRAViTy-V2, to genetically classify 525 picornaviral genomes and recently described 'picorna-like' viruses. All analyses were conducted with a bespoke, fully automated pipeline for retrieval of genome sequences, domain prediction and extraction, phylogenetic analysis, and output conditioning, which is available as open-source software. Our results reveal broad support for established families as well as for 6 novel families, and 32 new genera. In instances where inconsistencies were found between classification methods, we demonstrate how examination of the pipeline's output may be used to reconcile differences with respect to the genomic features quantified by the analysis. Automated multimodal taxonomic analysis may save significant resources over manual methods and better define demarcation criteria for families and genera.},
}

@article {pmid42111070,
year = {2026},
author = {Zurdo-López, M and Sagredo Del Rio, M and Cháfer Rudilla, M and Ibarra, A and Doncel-Pérez, E},
title = {Microbiota and Guillain-Barré syndrome: role of microbial metabolites, biomarkers, and emerging therapeutic strategies.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1815899},
pmid = {42111070},
issn = {1664-2295},
abstract = {Guillain-Barré syndrome (GBS) is an acute autoimmune polyradiculoneuropathy that follows infection and is characterized by immune-mediated demyelination or axonal injury of the peripheral nervous system. While established triggers such as Campylobacter jejuni are well recognized, increasing evidence implicates the gut microbiota as a key modulator of immune responses relevant to GBS pathogenesis. The intestinal microbiota produces a diverse array of bioactive metabolites, including short-chain fatty acids (SCFAs), tryptophan-derived indoles, and neurotransmitter-like molecules, which influence immune tolerance, gut barrier integrity, and neuroinflammatory signaling. SCFAs, particularly butyrate, exert anti-inflammatory effects and support epithelial and blood-nerve barrier function. Microbial tryptophan metabolites regulate astrocyte and microglial activity via aryl hydrocarbon receptor (AHR) signaling, thereby restraining central and peripheral neuroinflammation. In contrast, dysbiosis-associated metabolites such as lipopolysaccharide (LPS) may enhance systemic inflammation, disrupt immune tolerance, and promote autoantibody production through mechanisms including molecular mimicry. Studies suggest that specific microbial taxa and metabolite signatures may serve as diagnostic or prognostic biomarkers in GBS, offering insights into disease susceptibility and progression. Microbiota-targeted therapeutic strategies are emerging as promising adjuncts to immunotherapy. Probiotics and prebiotics may restore beneficial microbial communities and rebalance immunoregulatory metabolite production, while host-directed metabolic interventions such as creatine supplementation may further support mitochondrial function, immunometabolic homeostasis, and neuroprotection. Fecal microbiota transplantation (FMT), though still experimental in GBS, has shown benefit in related neuroinflammatory disorders by reestablishing eubiosis and dampening immune activation. Future studies integrating metagenomic, metabolomic, and immunologic profiling in well-characterized GBS cohorts are essential to validate these findings and advance personalized microbiota-based interventions.},
}

@article {pmid42111291,
year = {2026},
author = {Marcos, S and Odriozola, I and Aizpurua, O and Eisenhofer, R and Mak, SST and Martin-Bideguren, G and Kale, V and Baldi, G and Richardson, LJ and Finn, RD and Tarradas, J and Estonba, A and Gilbert, MTP and Alberdi, A},
title = {Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag091},
pmid = {42111291},
issn = {2730-6151},
abstract = {The early-life development of the gut microbiome in broiler chickens is a dynamic ecological process with significant implications for host physiology and productivity. Using 388 genome-resolved metagenomic and 61 metatranscriptomic samples across two replicated trials, we analysed the compositional and functional succession of the caecal microbiome in chickens from hatching to slaughter age. We reconstructed 822 bacterial genomes and distilled gene annotations into comprehensive metabolic traits that captured the functional capacities of each genome. We observed that the increase in microbial diversity with chicken age was accompanied by a decline in community-level average metabolic capacity, driven by a shift from metabolically versatile generalists (Lachnospiraceae) to hitherto uncultured, genome-reduced specialists (RF39, RF32, and UBA1242). However, the specific identity of the dominant genome-reduced specialists varied among individuals, resulting in contrasting associations with host body weight. At slaughter age, only 10 UBA660 (RF39) bacteria were positively associated with body weight, while other genome-reduced lineages, such as UBA1242 (Christensenellales), were among 190 negatively associated bacteria. Gene expression analyses revealed that despite their reduced functional repertoire, UBA660 exhibited greater metabolic activity than UBA1242, particularly in the production of two key metabolites for host nutrition and intestinal homeostasis: the essential amino acid lysine and the signaling molecule indole-3-acetate. These findings provide new insights into the functional ecology of the chicken gut microbiome and highlight the relevance of cultivation approaches to retrieve underexplored and uncultured bacterial taxa, which could open new avenues for microbiome-based strategies aimed at improving poultry growth and health in intensive production systems.},
}

@article {pmid42111294,
year = {2026},
author = {Yergaliyev, T and Enokela, SO and Eberhardt, G and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A},
title = {Toward reproducible pig gut microbiome profiling through standardized methodologies.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag097},
pmid = {42111294},
issn = {2730-6151},
abstract = {Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.},
}

@article {pmid42111296,
year = {2026},
author = {De Chiara, L and Doughty, R and Estévez-Gómez, N and Gallego-García, P and Alvariño, P and Díez-Martín, A and Dávila Piñón, P and Treangen, TJ and Cubiella, J and Posada, D},
title = {A comparison of methods for the optimal recovery of the human fecal virome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag090},
pmid = {42111296},
issn = {2730-6151},
abstract = {Human virome research is gaining increasing attention as viruses are recognized as critical modulators of microbial communities and human health. Viral metagenomics, however, faces unique challenges, including the low abundance and diversity of viruses in biological samples, the absence of universal marker genes, and biases introduced by experimental protocols. While various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these approaches often fail to capture the complexity and heterogeneity of natural viromes. In this study, we systematically evaluated modifications to key methodological steps in the metagenomic analysis of human fecal samples, including viral enrichment, nucleic acid extraction, genome amplification, and library preparation. Using gold-standard bioinformatic approaches on sequencing datasets generated after amplification, we assessed the impact of these modifications on relative viral taxonomic assignment, contig quality, richness, diversity, and inferred genome structure. Our findings reveal striking trade-offs between recovery of viral genomes and retention of nonviral sequences, demonstrating how methodological choices can shape the inferred virome composition. Based on these observations, we propose an optimized protocol that enhances viral genome recovery while reducing contamination from nonviral sequences. This refined workflow provides a more robust and reliable framework for gut virome studies, paving the way for a deeper exploration of the role of viruses in human health and microbial ecosystems.},
}

@article {pmid42111477,
year = {2025},
author = {Gudenkauf, JC and Wagstaff, E and Arneson, EJ and Gill, C and Gillman, AN and Haim, H and Tan, CS},
title = {Successful Recovery from Meningoencephalitis Associated with Archetype-like JC Virus in a Lung Transplant Recipient: Case Report and Review of the Literature.},
journal = {Annals of clinical case reports},
volume = {10},
number = {1},
pages = {},
pmid = {42111477},
issn = {2474-1655},
abstract = {Meningoencephalitis due to JC polyomavirus (JCV) is rare and delays in diagnosis could lead to potentially fatal outcomes in immunosuppressed patients. We present a case of an HIV-negative lung transplant recipient who presented with neurological deficits, including aphasia and right-sided weakness. Brain imaging lacked demyelination usually diagnostic of progressive multifocal leukoencephalopathy (PML), the disease most often associated with JC virus, however cerebrospinal fluid (CSF) metagenomic analysis confirmed a high JC viral load, suggestive of JCV-associated meningoencephalitis. After reducing immunosuppression, the patient showed significant neurological improvement within three months and full recovery by 6 months. The JCV genome sequenced from patient's plasma and CSF were identical and resembled the "nonpathogenic" archetype in the non-coding region but shared homology in the coding region with the classically-considered neurotropic strains detected in those with PML. These findings suggest that mutations in the virus's noncoding region are not necessary for neuropathogenesis. We also review other cases of JCV-associated meningitis and encephalitis, which, in contrast to our case, were all fatal. Clinicians should consider JCV testing in immunosuppressed patients with encephalopathy and focal neurological deficits, even in the absence of significant brain radiographic abnormalities.},
}

@article {pmid42111802,
year = {2026},
author = {Belkina, DD and Vinogradova, SV},
title = {Plant virome analysis by high-throughput sequencing: concepts and approaches.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {30},
number = {2},
pages = {311-320},
doi = {10.18699/vjgb-26-35},
pmid = {42111802},
issn = {2500-0462},
abstract = {The metagenomic approach based on high-throughput sequencing is becoming increasingly prevalent for the detection of viral infections in plants. This method allows us to study the species composition of viruses associated with the plant, including novel species, describe their population genetic structure, and develop genetic test systems for routine diagnostics. A metagenomic approach to phytosanitary monitoring can help to determine the cause of unknown plant diseases, which is particularly important for preventing the spread of pathogens, such as viruses. Furthermore, as it is impossible to eliminate plant viruses in field conditions, comprehensive diagnostics using high-throughput sequencing is becoming an effective tool for complying with quarantine regulations on the import of foreign material, as well as for producing high-quality local planting material. High-throughput sequencing is becoming more affordable every year, with both the instrumentation and analytical capacity improving. This review summarizes key approaches to analyzing plant virome using high-throughput sequencing. The analysis process, from sample collection to bioinformatic data processing, validation and interpretation, is described in detail. The features of sequencing platforms and the factors affecting sequencing quality, including contamination, are discussed. Three complementary approaches to processing bioinformatic data are described: mapping reads to reference viral sequences; assembling and annotating contigs; taxonomic classification of reads without assembly. The importance of carefully interpreting the results is emphasized, considering the bioinformatic analysis and the validation by molecular genetic methods. This review will be useful for both researchers and specialists who have no experience with high-throughput sequencing, and those who have used this method for other applications.},
}

@article {pmid42111813,
year = {2026},
author = {Mubaraki, FA},
title = {From sequencing to intelligence: how AI is transforming metagenomics.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21137},
pmid = {42111813},
issn = {2167-8359},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Machine Learning ; Deep Learning ; Metagenome ; },
abstract = {Microbial communities are critical in advancing human health. Metagenomics is a technique that analyzes these communities and allows for investigating their composition and functions. Metagenomic shotgun sequencing enables to capture all of the genetic material in environmental samples, such as water, soil, or the human gut. Despite this advantage, one of the main challenges of this technique is the assembling and interpreting of its data, as it produces many short, fragmented reads. Though long-read technologies may change this in the future, artificial intelligence (AI), machine learning (ML) and data science (DS) offer a powerful solution now, enabling scientists to efficiently process and analyze these large and complex datasets. This review explores the latest advancements in AI and ML applications across the metagenomic pipeline. First, it examines the impact of deep learning (DL) on next-generation sequencing, particularly for long-read technologies. Then, it discusses how ML is automating and improving quality control processes, as well as the use of AI applications in metagenome-assembled genome (MAG) assembly, with a focus on contig binning. Finally, this article looks at how AI and ML can improve predictive modeling for phenotype prediction.},
}

*Metagenomics/methods
*Artificial Intelligence
Humans
*High-Throughput Nucleotide Sequencing/methods
Machine Learning
Deep Learning
Metagenome

@article {pmid42112348,
year = {2026},
author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H},
title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1782828},
pmid = {42112348},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; },
abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.},
}

Humans
*Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology
Dysbiosis/immunology
Animals
*Microbiota/immunology
*Gastrointestinal Microbiome/immunology
Autoimmunity

@article {pmid42112399,
year = {2026},
author = {Wang, Y and Dong, W and Qin, J},
title = {Fatal AA-like bone marrow failure and invasive pulmonary aspergillosis after long-term pembrolizumab in squamous NSCLC: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1800904},
pmid = {42112399},
issn = {1664-3224},
mesh = {Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/complications ; *Lung Neoplasms/drug therapy/complications ; *Invasive Pulmonary Aspergillosis/etiology/diagnosis ; *Anemia, Aplastic/chemically induced/diagnosis/etiology ; Fatal Outcome ; *Immune Checkpoint Inhibitors/adverse effects ; *Antineoplastic Agents, Immunological/adverse effects ; },
abstract = {Immune checkpoint inhibitors (ICIs) such as pembrolizumab have substantially improved outcomes in advanced non-small cell lung cancer (NSCLC), including squamous histology, but prolonged exposure may be complicated by immune-related adverse events (irAEs) and opportunistic infections. We report a 58-year-old man with advanced squamous NSCLC who achieved durable tumor control after six cycles of pembrolizumab plus platinum-based chemotherapy, followed by pembrolizumab maintenance monotherapy (18 cycles). During the later course, he developed severe bacterial pneumonia, invasive pulmonary aspergillosis (IPA), and subsequent aplastic anemia (AA)-like bone marrow failure. Despite systemic antifungal therapy and supportive measures, he experienced progressive pancytopenia complicated by massive hemoptysis and ultimately died. This case underscores the dual nature of ICIs: while providing meaningful and sustained antitumor benefit, they may rarely precipitate life-threatening hematologic toxicity and facilitate severe opportunistic infections in a complex immunologic milieu. Close surveillance of blood counts and infectious complications is warranted during long-term ICI therapy; unexplained cytopenias or new/worsening radiologic abnormalities should prompt early bone marrow evaluation and comprehensive microbiologic work-up. Metagenomic next-generation sequencing (mNGS) may offer useful adjunctive evidence in diagnostically challenging infections, particularly when invasive sampling is not feasible, but results should be interpreted in conjunction with clinical and radiologic context within a multidisciplinary framework.},
}

Humans
Male
Middle Aged
*Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use
*Carcinoma, Non-Small-Cell Lung/drug therapy/complications
*Lung Neoplasms/drug therapy/complications
*Invasive Pulmonary Aspergillosis/etiology/diagnosis
*Anemia, Aplastic/chemically induced/diagnosis/etiology
Fatal Outcome
*Immune Checkpoint Inhibitors/adverse effects
*Antineoplastic Agents, Immunological/adverse effects

@article {pmid42112463,
year = {2026},
author = {Guo, L and Luo, X and Luo, M and Zhang, M and Wang, B and Fu, Y and Wu, X and Yu, Y and Bai, L and Xu, Z},
title = {Diagnosis and treatment of a patient with mediastinal infection caused by Emergomyces orientalis and Mycobacterium fortuitum.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1778930},
pmid = {42112463},
issn = {2235-2988},
mesh = {Humans ; Female ; Young Adult ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *Coinfection/diagnosis/microbiology/drug therapy ; *Mycobacterium fortuitum/isolation & purification/genetics ; Antifungal Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; *Mediastinum/microbiology/pathology/diagnostic imaging ; Amphotericin B/therapeutic use ; China ; Treatment Outcome ; *Eurotiales/isolation & purification ; },
abstract = {BACKGROUND: Emergomycosis, an emerging dimorphic fungal infection caused by Emergomyces species, primarily affects immunocompromised individuals. Emergomyces orientalis has been reported in China, including rare cases in immunocompetent individuals. Diagnosis remains challenging due to the lack of typical clinical manifestations and radiological features. Co-infection with other pathogens further complicates management, with no prior global reports of concurrent E. orientalis and non-tuberculous mycobacterial (NTM) infections.

CASE PRESENTATION: A 21-year-old immunocompetent woman with occupational exposure to soil presented with cough, fever, and a mediastinal mass on chest CT. The initial biopsy specimens revealed granulomatous inflammation and yeast-like fungi. Metagenomic next-generation sequencing (mNGS) of endobronchial ultrasound (EBUS)-guided specimens confirmed E. orientalis (40 reads). Liposomal amphotericin B induction therapy initially relieved the symptoms. However, recurrence prompted repeat mNGS, which revealed elevated Mycobacterium fortuitum loads (791 reads). Combined with the patient's history of soil exposure, a diagnosis of mediastinal E. orientalis with M. fortuitum co-infection was established based on the clinical presentation, the chest CT findings, histopathological observations of yeast-like fungi, the mNGS results, and the therapeutic response. Following confirmation of the co-infection, tailored adjustments to the antimicrobial regimen led to successful clinical management.

CONCLUSION: To the best of our knowledge, this is the first study in which E. orientalis and M. fortuitum were documented to coexist in the mediastinum. The dual pathogens were identified through a combination of EBUS-guided biopsy and mNGS. Accurate pathogen identification followed by tailored, pathogen-directed therapy is essential for the effective management of an E. orientalis and M. fortuitum mixed infection.},
}

Humans
Female
Young Adult
*Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology
*Coinfection/diagnosis/microbiology/drug therapy
*Mycobacterium fortuitum/isolation & purification/genetics
Antifungal Agents/therapeutic use
High-Throughput Nucleotide Sequencing
Tomography, X-Ray Computed
*Mediastinum/microbiology/pathology/diagnostic imaging
Amphotericin B/therapeutic use
China
Treatment Outcome
*Eurotiales/isolation & purification

@article {pmid42112573,
year = {2026},
author = {Liborio, MP and Peri, AM and Harris, PNA},
title = {Evaluating emerging molecular diagnostics for severe infections in neutropenic patients with hematological malignancies.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2026.2667917},
pmid = {42112573},
issn = {1744-8352},
abstract = {INTRODUCTION: Neutropenia significantly increases infection risk in hematologic malignancies patients, when clinical signs are often subtle and fever may be the only indicator. Molecular diagnostic methods promise faster, more sensitive pathogen detection compared to conventional methods, aiming to improve timely and appropriate therapy.

AREAS COVERED: This review summarizes emerging molecular diagnostics for severe infections in neutropenic hematological malignancies patients, focusing on microbiological performance and, where available, clinical impact. We conducted a search in PubMed and Embase using subject headings: 'molecular diagnosis,' 'neutropenic,' 'infections,' 'hematological malignancies,' supplemented by information from manufacturers of commercial assays. The technologies reviewed include multiplex polymerase chain reaction, microarray-based assays, metagenomic and targeted next-generation sequencing, host transcriptomics, and methods for diagnosing invasive fungal infections. For each, we describe key characteristics, diagnostic performance, and clinical utility when reported.

EXPERT OPINION: Emerging molecular diagnostics shorten time to pathogen and resistance identification and broaden detection of organisms in febrile neutropenic patients with hematological malignancies. These methods are best integrated as complements to culture-based methods within centers with antimicrobial stewardship programs, where they inform earlier targeted therapy and rational de-escalation of antimicrobials. Priority actions include prospective trials powered for measuring clinical outcomes and economic endpoints, with standardized workflows, reporting, and quality assurance to enable clinical implementation.},
}

@article {pmid42112737,
year = {2026},
author = {Ji, G and Duan, J},
title = {Pharmacist-driven optimization of presumptive psittacosis management: a case report of rapid clinical resolution.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {4},
pages = {596-600},
doi = {10.3855/jidc.22259},
pmid = {42112737},
issn = {1972-2680},
mesh = {Humans ; Female ; Middle Aged ; *Psittacosis/drug therapy/diagnosis ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Chlamydophila psittaci/isolation & purification ; Community-Acquired Infections/drug therapy/diagnosis/microbiology ; Animals ; },
abstract = {INTRODUCTION: Chlamydia psittaci has a high incidence of pneumonia after infection, but clinical diagnosis still faces challenges due to the lack of specific clinical manifestations and low positive rates in routine testing.

CASE PRESENTATION: A 60-year-old female patient with community-acquired pneumonia (CAP) failed to respond to initial intravenous antimicrobial therapy with cefmetazole/ciprofloxacin followed by piperacillin-tazobactam/levofloxacin, exhibiting persistent fever and worsening symptoms. Serial laboratory testing revealed progressive elevation of inflammatory markers, with C-reactive protein (CRP) rising from 110.2 to 120.9 mg/L and procalcitonin (PCT) from 1.37 to 2.15 ng/mL. Essential bronchoscopic examination and metagenomic next-generation sequencing (mNGS) could not be performed due to patient refusal, creating a diagnostic deadlock. The clinical pharmacist identified avian exposure during medication rounds, enabling presumptive diagnosis of psittacosis. Immediate pharmacist-initiated interventions included discontinuation of levofloxacin and commencement of targeted oral minocycline therapy. Clinical resolution occurred within 48 hours with defervescence and symptomatic improvement. Subsequent minocycline-induced nausea and diarrhea were effectively managed through pharmacist-instructed co-administration with food. Continuous clinical improvement facilitated discharge on oral minocycline, with follow-up imaging confirming complete resolution of pulmonary infiltrates.

CONCLUSIONS: This case underscores the value of pharmacist-led pharmaceutical assessment in uncovering atypical infection etiologies and guiding targeted antimicrobial therapy.},
}

Humans
Female
Middle Aged
*Psittacosis/drug therapy/diagnosis
*Anti-Bacterial Agents/therapeutic use/administration & dosage
Chlamydophila psittaci/isolation & purification
Community-Acquired Infections/drug therapy/diagnosis/microbiology
Animals

@article {pmid42112819,
year = {2026},
author = {Wei, X and Song, W and Li, S},
title = {Seasonal variations drive microbial community structure and nitrogen cycling in sediments of tributary pumping station forebays.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0304725},
doi = {10.1128/spectrum.03047-25},
pmid = {42112819},
issn = {2165-0497},
abstract = {Discharge from tributary pumping stations often impacts mainstream water quality, yet microbial communities and nitrogen metabolism in pumping station forebays remain poorly understood. Therefore, this study investigated the microbial community structure and nitrogen cycling mechanisms in sediments of tributary pumping station forebays within the Qinhuai River Basin using 16S rRNA and metagenomic sequencing. Results showed significant seasonal variations in the diversity and structure of sediment microbial communities, with higher diversity in spring than in winter. Genes associated with denitrification (e.g., narG, nirS, and nosZ) showed the highest abundance, suggesting that denitrification may be a key nitrogen transformation pathway. Co-occurrence network analysis revealed tighter associations between microbial taxa and nitrogen-cycling genes in spring, indicating more complex potential interactions during this season. The shift of network hubs across seasons suggested a seasonal succession of potential core functions related to nitrogen cycling. Redundancy analysis revealed that nitrate nitrogen (NO3[-]-N), water temperature (WT), and ammonium nitrogen (NH4[+]-N) were the factors most strongly associated with microbial community variation, with WT showing the strongest association with functional gene distribution. Partial least squares path modeling revealed that seasonal variation had a significant positive association with denitrification gene abundance and a significant negative association with genes related to assimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. These findings improve our understanding of microbially mediated nitrogen cycling in pumping station forebays and provide a scientific basis for water quality management in river networks influenced by pumping station drainage.IMPORTANCEThis study is important because it reveals that pumping stations, which are key infrastructure in managed river systems, are not just hydraulic structures but dynamic bioreactors where microbial communities actively transform nitrogen. By demonstrating seasonal variations in microbial diversity and revealing a high denitrification potential, the research provides a mechanistic understanding of how nitrogen pollution is naturally mitigated in these engineered environments. Crucially, it pinpoints temperature as a primary regulator of these microbial functions. These insights allow water managers to proactively optimize pumping operations and design interventions that harness microbial activity, ultimately protecting downstream water quality from nutrient pollution in a changing climate.},
}

@article {pmid42112890,
year = {2026},
author = {Sorokin, DY and Khot, V and Merkel, AY and Mosier, D and Bale, NJ and Koenen, M and Strous, M},
title = {Physiology, functional genomics, and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., the first isolated haloalkaliphile within Verrucomicrobiota, representing a new family, Verruconatronumaceae fam. nov.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0047526},
doi = {10.1128/aem.00475-26},
pmid = {42112890},
issn = {1098-5336},
abstract = {Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1[T] (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch, and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose, and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1[T] features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1[T] (JCM 35393[T]=UQM 41574[T]) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.IMPORTANCEAlkaline soda lakes and soils are extreme habitats dominated by obligate haloalkaliphic prokaryotes, some of which can produce alkali- and salt-stable polysaccharide-degrading exoenzymes useful for industrial and domestic applications. However, so far, little was known about the microbial potential for mineralization of acidic polysaccharides, such as alginate, in these habitats. The described isolates are the first representatives of a new family within the phylum Verrucomicrobiota specializing in the degradation of alginate and related polysaccharides. We present the key enzymatic machinery for alginate breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example, in washing powders and biomass waste recycling. Furthermore, the new family is one of the most abundant taxa in alkaline environments, and these environments are not known to harbor signature alginate producing biota, such as brown algae. This way, our study opens a new window on polysaccharide turnover in alkaline environments.},
}

@article {pmid42112913,
year = {2026},
author = {Krupovic, M and Koonin, EV},
title = {Organization and evolution of the virosphere and the replicator space.},
journal = {Comptes rendus biologies},
volume = {349},
number = {},
pages = {35-75},
doi = {10.5802/crbiol.193},
pmid = {42112913},
issn = {1768-3238},
mesh = {*Viruses/genetics ; *Biological Evolution ; Animals ; Virus Replication ; Humans ; Virion/genetics ; Genome, Viral ; },
abstract = {Viruses are obligate symbionts of cellular life forms that can replicate only within host cells and typically form virions (virus particles) to spread among host organisms. Virions numerically dominate the biosphere, exceeding the number of cells several-fold, and also comprise the main reservoir of genetic diversity on earth. Nearly all organisms host multiple, diverse viruses. Unlike cellular organisms, viruses have genomes (genetic information carriers incorporated into virions) that consist of all forms of RNA and DNA, suggesting an evolutionary connection between extant viruses and the primordial replicator pool. Lately, extensive mining of metagenomes and metatranscriptomes has dramatically expanded the world of viruses (virosphere), revealing an unsuspected and unprecedented diversity. Viruses share no universal genes and have multiple origins. However, about 15 viral hallmark genes each bring together multiple, diverse groups of viruses, and many other genes are shared within such groups. Evolution of viruses is inextricably intertwined with the evolution of their hosts. A key aspect of virus-host coevolution is the arms race resulting in accelerated evolution on both sides, especially of host defenses and viral counter-defenses. A complementary, prominent feature of this coevolution is exaptation, whereby viral genes are coopted by the hosts for antiviral defense and other roles, and conversely, viruses capture host genes for diverse functions in virus replication, virion morphogenesis and virus-host interaction. In this review, we attempt a synthesis of the current understanding of the global organization of the virosphere, the major trends and events in the evolution of viruses, and the high-level taxonomy of viruses.},
}

*Viruses/genetics
*Biological Evolution
Animals
Virus Replication
Humans
Virion/genetics
Genome, Viral

@article {pmid42113294,
year = {2026},
author = {Cortez-Cervantes, J and Carrillo-Reyes, J and Cervantes-Avilés, P and Moreno-Andrade, I},
title = {A statistical framework for identifying microbial indicators of ammonia-induced process instability in food waste anaerobic digestion.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {42113294},
issn = {1615-7605},
support = {IN104825//DGAPA-UNAM PAPIIT/ ; IN105025//DGAPA-UNAM PAPIIT/ ; 2022 Core Lab Genomics Tec-BASE Seed Fund//Instituto Tecnológico y de Estudios Superiores de Monterrey/ ; },
abstract = {Ammonia is an essential nutrient for anaerobic digestion (AD) but becomes inhibitory at elevated concentrations, leading to process instability. Although numerous microbial taxa and functional genes have been proposed as indicators of ammonia stress, most lack systematic validation across defined inhibitory thresholds. In this study, batch anaerobic digestion assays were conducted under increasing total ammonia nitrogen concentrations to experimentally characterize ammonia-induced inhibition. Methane yields obtained from batch tests were fitted using a Hill model to define non-inhibitory, inhibitory, and minimum inhibitory ammonia levels. Shotgun metagenomic sequencing was applied to samples representative of each inhibition level, and a statistical framework integrating differential abundance analysis, network topology, redundancy analysis, and metabolic relevance was used to identify robust microbial indicators. Key taxa, including Anaerolinea, Methanomassiliicoccus, and Syntrophobacter, along with functional genes involved in acetate and propionate metabolism (e.g., acs and fhs), showed consistent and threshold-dependent responses to ammonia stress. These microbial indicators provide mechanistic insight into ammonia-induced AD instability and offer a promising basis for early-warning monitoring and microbial management strategies to improve the operational stability of anaerobic digesters treating food waste.},
}

@article {pmid42113401,
year = {2026},
author = {Bhattacharjee, A and Singh, AK},
title = {Ecological and genomic insights into Bacillus altitudinis as a potential indicator of resistance genes in soil antimicrobial resistance pools.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42113401},
issn = {1614-7499},
support = {OLP-2035//CSIR/ ; OLP-2081//CSIR/ ; OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; },
abstract = {Soil associated with intensive poultry farming serves as a seminal reservoir of antimicrobial resistance genes. This study employed an integrated approach that combined metagenomics, phenotypic analysis, and whole-genome sequencing to investigate the soil resistome of poultry farms in the Jorhat district, Northeast India, and to evaluate Bacillus altitudinis as an environmental potential indicator for antimicrobial resistance. Metagenomic analysis of poultry-affected soil revealed a diverse array of resistance genes, including 753 unique resistance ontologies related to β-lactam, glycopeptide, macrolide, aminoglycoside, chloramphenicol, and colistin resistance. Culture-based testing of soil and fecal isolates (400 isolates) showed high resistance rates to colistin and ciprofloxacin (~60%), as well as notable resistance to erythromycin and kanamycin, indicating strong antibiotic selection pressures in these ecosystems. Among multidrug-resistant strains, B. altitudinis S2 was particularly notable, exhibiting high minimum inhibitory concentrations for last-line antibiotics such as vancomycin (>50 µg/mL), colistin (>50 µg/mL), and fourth-generation cephalosporins. It also demonstrated multidrug β-lactam resistance supported by synergistic inhibitors. Whole-genome sequencing (3.7 Mb) uncovered a complex antimicrobial resistance gene (ARG) profile, including vanZ, mcr-1, catA, mph, aph, and oxa-type β-lactamase genes, alongside multiple SMR, MATE, and RND efflux mechanisms. Many of these genes were located within genomic islands, prophage traces, and mobile genetic elements, strongly indicating horizontal gene transfer from various bacteria, including gut-associated enterococci. The genome also contained genes for resistance to heavy metals and oxidative stress, suggesting co-selection processes that sustain ARGs in soil. The study tries to show B. altitudinis as a crucial environmental indicator for ARGs, serving a genetic bridge between poultry gut microbiota and soil antimicrobial resistance pools, highlighting its significance for One Health antimicrobial resistance surveillance.},
}

@article {pmid42113811,
year = {2026},
author = {Mussa, AJ and Ruboha, JO and Kabota, SA and Martin, MJ and Mwatawala, MW},
title = {Elevation and land use shape soil entomopathogenic fungal communities in the Uluguru mountains, Tanzania: Insights from metagenomic and culture-based approaches.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348781},
doi = {10.1371/journal.pone.0348781},
pmid = {42113811},
issn = {1932-6203},
mesh = {Tanzania ; *Soil Microbiology ; Animals ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Biodiversity ; Soil/chemistry ; Metagenomics/methods ; *Mycobiome ; },
abstract = {BACKGROUND: Soil-borne entomopathogenic fungi (EPFs) support ecological regulation of pests, yet their distribution across tropical mountain agroecosystems is poorly characterized. The study conducted between April and December 2024, evaluated diversity and distribution of soil EPF along the Uluguru Mountains slopes in Morogoro, Tanzania.

METHODS: Twenty-four soil samples were collected from cultivated and fallow soils at low (518 m), medium (1100 m), and high (1700 m) elevations on the Uluguru slopes (Morogoro, Tanzania). Amplicon sequencing of the ITS region profiled fungal communities, and selective isolation with ITS barcoding confirmed cultivable taxa. Diversity indices, Bray-Curtis dissimilarity, Principal Coordinate Analysis (PCoA), and PERMANOVA evaluated patterns across elevation and land use.

RESULTS: Fourteen EPF species in 12 genera were detected, dominated by Ophiocordycipitaceae (56.1%) and Clavicipitaceae (37.8%). Purpureocillium lilacinum, Metarhizium anisopliae, Clonostachys rosea, and Pochonia chlamydosporia were widespread. Cultivated soils at medium- and high elevations showed greater richness and diversity (1.37 and 1.57) than fallows (0.64 and 0.48) respectively, while high-altitude fallows were strongly dominated by Metapochonia suchlasporia. Community composition clustered by land use, with elevation as a secondary driver (PERMANOVA p = 0.06). Selected P. lilacinum and C. rosea species caused 10-50% mortality of Spodoptera frugiperda larvae in preliminary laboratory assays.

CONCLUSIONS: Elevation and land use jointly structure EPF communities in the Uluguru Mountains. Some taxa showed preliminary pathogenicity in laboratory assays, indicating potential for future evaluation as biological control agents in smallholder farming systems. Public deposition of sequencing reads will facilitate reuse and benchmarking.},
}

Tanzania
*Soil Microbiology
Animals
*Fungi/genetics/classification/isolation & purification
*Altitude
Biodiversity
Soil/chemistry
Metagenomics/methods
*Mycobiome

@article {pmid42113832,
year = {2026},
author = {Cai, Y and Wei, Y and Du, G and Zhang, X and Wang, Z and Wang, Z and Han, Z and Zhang, Y and Xu, Y and Han, X and Li, J and Li, Q},
title = {Identification and genetic characterization of a distinct genotype of Puumala orthohantavirus in Hebei Province, China.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {5},
pages = {e0014250},
doi = {10.1371/journal.pntd.0014250},
pmid = {42113832},
issn = {1935-2735},
abstract = {Orthohantavirus infections pose a significant threat to human health, while numerous orthohantaviruses have been identified, suspected viral infections remain undiagnosed in the world, which highlights the need for further identification and characterization of viruses circulating in humans and host animals. In this study, viral metagenomics was utilized to investigate orthohantaviruses present in tissue samples collected from rodents trapped at the Bashang Grassland of Hebei Province, China. A total of 145 wild rodents belonging to six species were captured in the study area, and 725 tissue samples (lung, liver, kidney, spleen, gut) were collected in 2024. A Puumala orthohantavirus (PUUV), named Guyuan strain, was identified in Myodes rufocanus, with a positive rate of 0.69%. The complete genomic sequences of the L, M, and S segments were obtained and confirmed by Sanger sequencing. Phylogenetic analysis of these genomic sequences with those of other orthohantavirus species showed that the L, M, and S segments clustered with PUUV genomic sequences, while sharing a nucleotide sequence similarity of 81.2%, 80.2%, and 84.3% with previously characterized reference viral strains Kitahiyama128L, Tobetsu_04, and Baltic/205 Cg, respectively. Amino acid homology analysis demonstrated that the sequences exhibited the highest identity to PUUV Hokkaido strain at a level of 95.4%, 94.6%, and 97.0% respectively. Viral particles were observed in lung and kidney tissues using transmission electron microscopy, and viral protein antigen was detected in viral RNA-positive lung, liver, and kidney tissues through immunofluorescence assay with antibodies against the PUUV nucleocapsid protein, thereby confirming the virus's multiorgan tropism. The results demonstrated that a distinct genotype of PUUV was circulating in rodents in the study areas, which may have implications for zoonotic transmission surveillance and public health management in Hebei Province.},
}

@article {pmid42114216,
year = {2026},
author = {Que, H and Jiang, X and Wu, X and Li, S},
title = {Construction of a "three-stage and four-level" evaluation system for cerebrospinal fluid pathogens based on mNGS: insights from a case of co-detection of Cryptococcus and Epstein-barr virus.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117457},
doi = {10.1016/j.diagmicrobio.2026.117457},
pmid = {42114216},
issn = {1879-0070},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) has brought about a revolutionary change in the diagnosis of central nervous system (CNS) infections. Nevertheless, the interpretation of results with multiple detected pathogens still poses a substantial clinical challenge.

AIM: A preliminary exploration of the application value of the developed "Three-Stage, Four-Level" assessment system in interpreting mNGS cerebrospinal fluid test reports.

METHODS: Based on a systematic review of relevant domestic and international literature, combined with practical experience in the field, a multi-dimensional "Three-Stage, Four-Level" evaluation system centered on a clinical-microbiological evidence chain was constructed. This study explores the application value of the system through a case of mNGS detection for co-preservation of Cryptococcus and Epstein-Barr virus (EBV) in cerebrospinal fluid (CSF).

RESULTS: The system effectively integrated multi-source information, facilitating a precise and stratified interpretation of CSF mNGS results. It successfully differentiated Cryptococcus as the pathogenic agent and EBV as a latent pathogen. Consequently, early antifungal therapy was initiated, resulting in a gradual improvement of symptoms and a favorable prognosis.

CONCLUSION: This case initially demonstrates that the "Three-Stage,Four-Level "evaluation system provides a standardized and operational framework for interpreting mNGS cerebrospinal fluid multiplex pathogen detection results, showing preliminary value in precisely distinguishing pathogen types; however, further validation with larger sample sizes is warranted.},
}