@article {pmid42143599,
year = {2026},
author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S},
title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70140},
pmid = {42143599},
issn = {1943-3670},
support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jusélius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; },
abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.

METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.

RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).

CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.

PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.},
}

@article {pmid42143831,
year = {2026},
author = {Deng, Y and Yuan, X and Xu, Y and Jiang, H and Xue, J and Jiang, Y and Wang, Y},
title = {Acetoclastic methanogenesis associated with arsenic methylation in a reducing aquifer: Pathway-specific patterns and mechanistic insights.},
journal = {Water research},
volume = {301},
number = {},
pages = {126114},
doi = {10.1016/j.watres.2026.126114},
pmid = {42143831},
issn = {1879-2448},
abstract = {The distribution of methylated arsenic (MeAs) in reducing groundwater systems remains incompletely understood, in part due to uncertainties regarding how specific methanogenic pathways may influence arsenic biomethylation, a critical issue in arsenic biogeochemistry and risk assessment. To explore this question, we integrated hydrogeochemical characterization, carbon isotopic tracing, metagenomic analysis, and pathway-specific enrichment experiments, focusing on MeAs-rich alluvial-lacustrine aquifers in the central Yangtze River Basin. A strong positive correlation between arsM and mcrA abundances (r = 0.84, p < 0.001) points to a co-occurrence of genetic potential for arsenic methylation and methanogenesis in the studied aquifer. Metagenome-assembled genome (MAG) analysis showed a pathway-specific distribution of arsM gene, a higher proportion of acetoclastic methanogen MAGs harbored complete arsM genes (14.29 %), compared to methylotrophic (9.09 %) and hydrogenotrophic (0.00 %) methanogens. In pathway-specific enrichment assays under controlled laboratory conditions, acetoclastic cultures exhibited the highest capacity for stepwise arsenic methylation (MMA and DMA production), with methylation efficiency reaching approximately 10.2 %, whereas methylotrophic cultures produced only transient MMA and hydrogenotrophic cultures showed minimal methylation. These observations provide insights into pathway-dependent differences in methanogen-associated arsenic methylation, highlighting a possible biogeochemical link between methanogenesis and arsenic cycling in the studied aquifer. These findings contribute to understanding potential controls on MeAs occurrence in reducing groundwater and provide a basis for further investigations in comparable hydrogeological settings.},
}

@article {pmid42144568,
year = {2026},
author = {Rui, Z and Wang, X and Yu, C},
title = {Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70924},
pmid = {42144568},
issn = {1526-4998},
support = {QKEZDZX[2024]010//the Guizhou Provincial Major Scientific and Technological Program/ ; theNationalNaturalScienceFoundationofChina//32160375/ ; },
abstract = {BACKGROUND: Fusarium oxysporum causes damping-off disease in Pinus massoniana seedlings. While Trichoderma koningiopsis can enhance seedling resistance by regulating rhizosphere plant growth-promoting rhizobacteria (PGPR), the specific bacterial compositions and their role in disease resistance remained undefined. To elucidate this mechanism, we used amplicon and metagenomic sequencing to identify T. koningiopsis-assembled PGPR. Synthetic PGPR communities were constructed from isolated strains to validate their effects on disease suppression and growth promotion.

RESULTS: Microbial community analysis indicated that T. koningiopsis reshaped the bacterial community: Actinospica, Dyella, and Streptomyces decreased in presence, and Bacillus and Arthrobacter increased. A total of 153 PGPR strains were isolated from the T. koningiopsis-inoculated treatment. Of these, eight strains demonstrated significant inhibitory effects against F. oxysporum, ranging from 33.81% to 59.52%. Four synthetic communities (SynComs) (C1, C2, HT, and 2K) were further constructed, exhibiting superior inhibitory effects against F. oxysporum compared to individual strains. Compared to the control, the C2 and HT SynComs increased seedling height by 10.18% and 9.44%, and reduced disease incidence by 50% and 36.67%, respectively. These treatments also enhanced protective enzyme activity and alleviated membrane damage. At the molecular level, the C2 and HT SynComs boost plant resistance by modulating the plant hormone and mitogen-activated protein kinase (MAPK) signaling pathways, thereby activating the expression of crucial resistance genes such as PR1, FLS2, and CAT1.

CONCLUSION: Trichoderma koningiopsis alters the composition of rhizosphere PGPR community. The synthetic PGPR community assembled under the influence of T. koningiopsis effectively enhances damping-off resistance and promotes the growth of Masson pine seedlings. © 2026 Society of Chemical Industry.},
}

@article {pmid42145141,
year = {2026},
author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R},
title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {15353141261449964},
doi = {10.1177/15353141261449964},
pmid = {42145141},
issn = {1556-7125},
abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.},
}

@article {pmid42145647,
year = {2026},
author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H},
title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.06.26352545},
pmid = {42145647},
abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.},
}

@article {pmid42146067,
year = {2026},
author = {Cooper, G and Ayotte, SH and Du, ML and Wood, JD and Opp, B and Bothner, B and Peyton, BM},
title = {Arsenic detoxification within thermo-alkaline biofilms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783099},
pmid = {42146067},
issn = {1664-302X},
abstract = {INTRODUCTION: The fundamental principles driving community composition and dynamics of microbial mats in thermoalkaline springs are largely uncharacterized. High in not only temperature but also arsenic (As), the microbial populations of Yellowstone National Parks (YNP), USA thermal springs require unique detoxification mechanisms to survive and carry out basic biological functions.

METHODS: While many studies have focused on which microorganisms are present, few studies have integrated the use of metagenome sequencing, imaging techniques, and mass spectrometry to gain insight into how structure and function of the mat dwelling organisms might be impacted by the high arsenical species in the ecosystem.

RESULTS: Here, we demonstrate via metagenome sequencing that community composition, including microbial genera Roseiflexus, Thermus, and Synechococcus, and as detoxification abilities change with mat depth and distance from the springs. Arsenical speciation confirmed the generation of bioarsenicals by mat-dwelling microorganisms. Microscopy revealed stratification of microorganisms in the mat, potentially reflecting their arsenic redox capabilities.

DISCUSSION: These data demonstrate how microbial mats are modular, stratified systems that shape and are shaped by environmental and geochemical gradients. Together, these findings characterize novel complexity and associations between geochemical cycles of metals and metabolic adaptations necessary for microorganisms to inhabit thermal springs. In conclusion, these findings demonstrate physiochemical heterogeneity of microbial mats in YNP.},
}

@article {pmid42146533,
year = {2026},
author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV},
title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721144},
pmid = {42146533},
issn = {2692-8205},
abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.},
}

@article {pmid42146661,
year = {2026},
author = {Miller, CJ and Pope, CE and Lavitt, MH and Caverly, LJ and LiPuma, JJ and Penewit, K and Lewis, JD and Salipante, SJ and Hoffman, LR},
title = {The Unified Human Virome Database: A toolkit for expanded human virome analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.01.722327},
pmid = {42146661},
issn = {2692-8205},
abstract = {Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes from human gastrointestinal, airway, skin, and urogenital sample metagenomes. We developed an associated toolkit that uses UHVDB to characterize viruses and their potential activity from metagenomes, then applied this toolkit to 1,983 airway sample metagenomes from people with cystic fibrosis. Over half of detected viruses lacked evidence of potential activity and were detected transiently. UHVDB is nearly three times larger than prior viral databases and its ability to identify likely active viruses enables rigorous analysis of viruses from diverse human sample types, expanding the capacity to define virus contributions to health and disease.},
}

@article {pmid42146906,
year = {2026},
author = {Orletskaia, VA and Olekhnovich, EI},
title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0065},
pmid = {42146906},
issn = {2001-0370},
abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.},
}

@article {pmid42147179,
year = {2026},
author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S},
title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9092464/v1},
pmid = {42147179},
issn = {2693-5015},
abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.},
}

@article {pmid42148043,
year = {2026},
author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS},
title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.},
journal = {Environmental health perspectives},
volume = {134},
number = {1},
pages = {75-90},
doi = {10.1021/EHP.6c00064},
pmid = {42148043},
issn = {1552-9924},
mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics & numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; },
abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.},
}

Humans
Uganda
Female
*Gastrointestinal Microbiome
*Air Pollution, Indoor/statistics & numerical data/adverse effects
Adult
*Virome
Middle Aged

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0411725},
doi = {10.1128/spectrum.04117-25},
pmid = {42148573},
issn = {2165-0497},
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0377525},
doi = {10.1128/spectrum.03775-25},
pmid = {42148581},
issn = {2165-0497},
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

@article {pmid42148582,
year = {2026},
author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L},
title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0346925},
doi = {10.1128/spectrum.03469-25},
pmid = {42148582},
issn = {2165-0497},
abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.},
}

@article {pmid42148731,
year = {2026},
author = {Qiu, H and Zhang, Z and Qian, H},
title = {Evolutionary plasticity of cyanobacteria under persistent anoxia: mechanistic insights from marine blue holes and global ecological implications.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0025126},
doi = {10.1128/aem.00251-26},
pmid = {42148731},
issn = {1098-5336},
abstract = {Cyanobacteria are generally viewed as obligate oxic photoautotrophs. However, this paradigm was challenged by Z. Li, H. Zhang, T. Wei, L. He, and Y. Wang in Applied and Environmental Microbiology (92:e02576-25, 2026, https://doi.org/10.1128/aem.02576-25); this group identified transcriptionally active Synechococcus in the dark, permanently anoxic Yongle Blue Hole using integrated metagenomic and transcriptomic analyses. This finding suggests adaptive streamlining under long-term oxygen limitation, expands the recognized ecological range of phototrophic microorganisms, and highlights the potential relevance of microbial adaptation to future ocean deoxygenation.},
}

@article {pmid42148775,
year = {2026},
author = {Shi, W and Liu, L and Wu, L and Wang, X and Peng, Y and Liu, X and Li, C and Xu, J and Wu, Z and Dong, X and Zheng, Q},
title = {Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0035426},
doi = {10.1128/msystems.00354-26},
pmid = {42148775},
issn = {2379-5077},
abstract = {UNLABELLED: Salinity gradients drive microbial diversity and evolution in estuarine-coastal ecosystems, yet viral adaptation remains less well understood. We used metagenomics to study viral adaptation and functions in three representative estuarine-coastal regions in China. Our results reveal salinity-associated adaptations in DNA viruses, with viruses enriched in medium- to high-salinity environments exhibiting higher frequencies of acidic isoelectric points and charged amino acids compared to those enriched in low-salinity environments. Viral genomes encode diverse genes related to ion transporters and organic osmolyte metabolism, suggesting potential roles in osmotic stress responses. Viral microdiversity also varied systematically along the salinity gradient, indicating reduced genetic variation and stronger purifying selection under more saline conditions. Furthermore, we identified diverse AMGs linked to nutrient cycles, with salinity-driven enrichment revealing viral roles in host metabolism. Overall, our findings highlight salinity as a key driver of viral evolution and functional potential in estuarine-coastal ecosystems, providing new insights into how viruses adapt to environmental gradients.

IMPORTANCE: Salinity is a defining environmental gradient in estuarine-coastal systems, yet its role in shaping viral molecular evolution remains poorly understood. By integrating metagenomes, viromes, and metatranscriptomes across three estuaries, this study demonstrates that salinity exerts a strong and consistent imprint on DNA viruses. Increasing salinity selects for viral genomes encoding ion-transport and osmolyte-related proteins and drives systematic shifts in viral proteome composition toward osmoadaptive physicochemical properties. At the population level, higher salinity is associated with reduced viral microdiversity and stronger purifying selection, indicating constrained evolutionary space under osmotic stress. Viral auxiliary metabolic gene repertoires are structured along salinity gradients, with functional differentiation in carbon, nutrient, and nucleotide metabolism. Together, these findings identify salinity as a key evolutionary filter linking viral physiological adaptation, evolutionary dynamics, and functional potential in estuarine and coastal ecosystems.},
}

@article {pmid42148776,
year = {2026},
author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y},
title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0029226},
doi = {10.1128/msystems.00292-26},
pmid = {42148776},
issn = {2379-5077},
abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.

IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.},
}

@article {pmid42149293,
year = {2026},
author = {Fulke, AB and Ratanpal, S},
title = {Integrated pragmatic approach of bioinformatics and cheminformatics for tracking the fecal pollution in an urban marine environment.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {6},
pages = {},
pmid = {42149293},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Feces/microbiology/chemistry ; *Computational Biology ; *Water Pollution/statistics & numerical data/analysis ; *Cheminformatics ; Cities ; *Water Pollutants, Chemical/analysis ; Humans ; },
abstract = {Fecal contamination in urban marine environments poses an alarming global threat to public health, ecosystems, and economies. Traditional fecal indicator bacteria (FIB) methods, while accessible, suffer from delayed results and inability to differentiate pollution sources. To overcome this, microbial source tracking (MST) employs molecular techniques like qPCR to rapidly identify specific origins (human, animal) using genetic markers. Complementary chemical source tracking utilizes distinct chemical signatures (e.g., sterols and pharmaceuticals) for detection, offering low limits and temporal stability. The burgeoning fields of bioinformatics and cheminformatics are crucial for processing the complex, high-volume data generated by these advanced methods. Bioinformatics tools analyze metagenomic data for microbial community profiling and source attribution, while cheminformatics automates the acquisition of chemical-specific data for environmental exposure modeling, enhancing efficiency and transparency. An integrated pragmatic approach leverages these capabilities with Geographic Information Systems (GIS) and remote sensing. GIS serves as a unifying platform, integrating diverse spatial, temporal, sensor, and analytical data to enable comprehensive spatial analysis, real-time monitoring, and predictive modeling of fecal plumes. Hence, this review is aimed toward this holistic framework, which is essential for effective, targeted management strategies to safeguard water quality.},
}

*Environmental Monitoring/methods
*Feces/microbiology/chemistry
*Computational Biology
*Water Pollution/statistics & numerical data/analysis
*Cheminformatics
Cities
*Water Pollutants, Chemical/analysis
Humans

@article {pmid42149451,
year = {2026},
author = {Edelkamp, J and Lousada, MB},
title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3031},
number = {},
pages = {233-242},
pmid = {42149451},
issn = {1940-6029},
mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; },
abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.},
}

*Hair Follicle/microbiology
*Laser Capture Microdissection/methods
*Microbiota/genetics
Humans
*Scalp/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods

@article {pmid42149452,
year = {2026},
author = {Edelkamp, J and Lousada, MB},
title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3031},
number = {},
pages = {243-259},
pmid = {42149452},
issn = {1940-6029},
mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs & derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; },
abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.},
}

Humans
*Hair Follicle/microbiology
*Microbiota/genetics
*Scalp/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
In Situ Hybridization, Fluorescence/methods
Propidium/analogs & derivatives/chemistry
Azides/chemistry
Microbial Viability
Real-Time Polymerase Chain Reaction/methods

@article {pmid42149940,
year = {2026},
author = {Sandi, JD and Brock-Fisher, TM and Kallon, TMPS and Paye, MF and Fofanah, IU and Nosamiefan, D and Kamara, MS and Teh, AJ and Turay, A and Wilkason, C and Baudi, I and Tomkins-Tinch, C and I'Anson, C and Stachler, E and Pekar, JE and Ozonoff, A and Park, D and Happi, C and Sabeti, PC and Grant, DS},
title = {Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {5},
pages = {e0014354},
doi = {10.1371/journal.pntd.0014354},
pmid = {42149940},
issn = {1935-2735},
abstract = {Yellow fever virus (YFV), a mosquito-borne orthoflavivirus that causes severe hemorrhagic disease, is endemic in parts of South America and Africa, yet genomic data from Sierra Leone is lacking despite ongoing case-based surveillance. Using hybrid-capture metagenomic sequencing, we generated a complete 10,611 nt YFV genome (98% coverage) from an adult male patient who reported to the Kailahun Government Hospital with fever and muscle pain. Phylogenetic analysis assigned the genome to the West African II genotype via the YFV Nextstrain build. The Sierra Leone genome showed 57 substitutions, three of which were non-synonymous (NS2B: N79S, NS3: V515I, and NS5 (RdRp domain): A643V), relative to its most recent common ancestor with other genomes from Senegal and the Netherlands. Bayesian phylogenetics estimated the time to the most recent common ancestor with these genomes as January 14, 2001 (95% HPD: December 17, 1987 - April 28, 2009), potentially indicative of long-standing transmission within West Africa that has not been genomically characterized, rather than specific localization to Sierra Leone. Together, these findings underscore the need for expanded genomic surveillance to monitor YFV spread and evolution.},
}

@article {pmid42150467,
year = {2026},
author = {Wang, X and Zhang, Y and Yu, J and Yang, S and Zhang, T and Song, J and Sun, Z},
title = {Metagenomic insights into nitrate- and sulfate-enhanced anoxic biodegradation of PAHs in subsurface soil.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120281},
doi = {10.1016/j.ecoenv.2026.120281},
pmid = {42150467},
issn = {1090-2414},
abstract = {Anoxic biodegradation is pivotal for remediating PAH-contaminated subsurface soils, yet its mechanisms remain poorly understood. In this study, nitrate and sulfate were used as electron acceptors to stimulate the anoxic biodegradation of PAHs in soil by indigenous bacteria. A 180-day anoxic incubation experiment was conducted, coupled with high-throughput sequencing for bacterial community composition, quantitative PCR for microbial abundance, metagenomic sequencing for functional gene profiling, and gas chromatography-mass spectrometry for PAH quantification, to characterize microbial community properties, key functional genes, and their contributions to PAH degradation. After 180 days of incubation, the addition of electron acceptors significantly increased the abundances of total and potential PAH-degrading bacteria (which increased by 0.11-0.24 and 0.09-0.46 orders of magnitude per gram of soil, respectively) and promoted the removal of 3- and 4-ring PAHs (59-64% and 26-33%, respectively). Notably, the degradation efficiency followed the order of NO3[-] > mixed electron acceptors > SO4[2-], revealing a clear preference for nitrate. Nitrate amendment selectively enriched key PAH-degrading taxa like Bacillus. Metagenomic analysis revealed the underlying microbial mechanisms: the functional pathway ko00624 (PAH degradation) was enriched, and the abundances of 15 key genes (e.g., pcaH, ligB, and pht5) involved in upstream and downstream metabolic steps were positively correlated with degradation efficiency. Comparative analysis showed that differences across treatments stemmed primarily from ‌elevated expression of shared core genes (e.g., pht4, phdG, nidB), with nitrate (SN) treatment showing the greatest enrichment. These findings elucidate electron acceptor-driven anoxic PAH transformation, highlighting nitrate's dual role as a nutrient and favorable electron acceptor, and provide a basis for targeted subsurface bioremediation.},
}

@article {pmid42150504,
year = {2026},
author = {Pan, Z and Wang, W and Torabi, E and Zhang, M and Su, Z and Xu, X and Yin, Y and Xu, W and Duan, Y and Chen, J and Maróti, G and Huang, Q},
title = {Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142406},
doi = {10.1016/j.jhazmat.2026.142406},
pmid = {42150504},
issn = {1873-3336},
abstract = {The spatial heterogeneity of multi-metal contamination and its ecological consequences for soil microbial communities remain poorly characterized on a national scale, particularly within paddy ecosystems. This study investigated microbial ecological and genomic responses to heavy metal stress across 48 paddy soils from major rice-growing regions in China, categorized into low (LMS), moderate (MMS), and high (HMS) contamination levels. Our results indicate that multi-metal contamination triggered a significant restructuring of microbial communities, which was accompanied by increased alpha diversity and the enrichment of metal-tolerant taxa (e.g., Planctomycetes and Cyanobacteria). Conversely, microbial co-occurrence networks exhibited systematic simplification as contamination levels increased, characterized by reduced connectivity and a significant loss of keystone taxa. This suggests a transition from functionally redundant communities to modularized, survival-oriented network configurations. Metagenomic analysis revealed positive correlations between metal contamination and the abundance of nitrogen, phosphorus, and sulfur-cycling genes, while carbon-cycling genes remained relatively stable. Furthermore, genome-resolved metagenomics demonstrated widespread co-localization of metal resistance genes (MRGs) and nutrient cycling genes within metagenome-assembled genomes, particularly among key taxa (e.g., Burkholderiaceae, MBNT15). Collectively, these findings elucidate the mechanistic basis of microbial adaptation to multi-metal stress in paddy soils, providing critical insights for optimizing soil health management, developing targeted bioremediation strategies, and enhancing environmental risk assessment frameworks for contaminated agricultural ecosystems.},
}

@article {pmid42150526,
year = {2026},
author = {Thompson, LR},
title = {Microbial ecology: Rise of the planet of the microbes.},
journal = {Current biology : CB},
volume = {36},
number = {10},
pages = {R432-R434},
doi = {10.1016/j.cub.2026.03.072},
pmid = {42150526},
issn = {1879-0445},
mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; },
abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.},
}

*Microbiota/genetics
Metagenomics
Ecosystem
*Bacteria/genetics
*Metagenome

@article {pmid42150690,
year = {2026},
author = {Kruger, F and den Haan, R},
title = {Adaptive laboratory evolution and rational engineering enabled xylose utilisation and xylan conversion in natural isolates of Saccharomyces cerevisiae.},
journal = {Journal of biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiotec.2026.05.007},
pmid = {42150690},
issn = {1873-4863},
abstract = {Second-generation biofuels produced from renewable lignocellulosic biomass (LCB) are attractive alternatives to environmentally damaging, non-renewable fossil fuels. A key challenge in converting LCB to bioethanol is the incomplete utilisation of all available sugars. To address this, the hemicellulose fraction, consisting mainly of xylan, should be converted to the desired product alongside cellulose. This study aimed to develop natural isolate strains of Saccharomyces cerevisiae capable of xylose utilisation and xylan degradation. Strains YI13, YI59 and FIN1 were selected for potential industrial applications due to their high fermentation performance levels under environmental stress and enhanced ethanol production compared to laboratory strains. Xylose utilisation was achieved in these strains by introducing heterologous xylose isomerase (XI) and xylulokinase (XKS) gene cassettes and a xylose transporter (XTR), followed by adaptive laboratory evolution (ALE) in minimal xylose media. The evolved strains were further engineered for cell-associated xylosidase and secreted xylanase activities, yielding variants with strong enzyme activities, optimized xylose metabolism, and high ethanol production from both xylose and xylan. The final engineered version of YI13 showed the best xylose and xylan conversion, with maximum ethanol titres of ~7.1g/L from 20g/L xylose and ~4.7g/L from 40g/L xylan, among the highest ethanol titres from polymeric xylan by direct microbial conversion reported to date. The development of these S. cerevisiae strains provides a useful platform for future development of robust xylan-converting S. cerevisiae strains for large-scale ethanol production, although validation on real-world lignocellulosic feedstocks is still required.},
}

@article {pmid42141292,
year = {2026},
author = {Ghori, R and Ramadoss, D and Ramsland, PA and Blanch, EW and Ammanabrolu, BS},
title = {Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.},
journal = {Extremophiles : life under extreme conditions},
volume = {30},
number = {1},
pages = {},
pmid = {42141292},
issn = {1433-4909},
mesh = {*Microbiota ; India ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Salinity ; *Metagenome ; },
abstract = {Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.},
}

*Microbiota
India
*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Salinity
*Metagenome

@article {pmid42141512,
year = {2026},
author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L},
title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04146},
pmid = {42141512},
issn = {1520-5851},
abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.},
}

@article {pmid42141881,
year = {2026},
author = {Nagy, A and Erdélyi, K and Molnár, Z and Lőrincz, RB and Nagy, O and Koroknai, A and Csonka, N and Kerényi, K and Forgách, P and Horváth, E and Soltész, Z and Nagy, G and Takács, M and Barcsay, E and Szomor, K and Tóth, GE and Cadar, D},
title = {Hungary as a source of West Nile virus diversity and spread in Europe: insights from the 2024 transmission season.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {31},
number = {16},
pages = {},
pmid = {42141881},
issn = {1560-7917},
mesh = {Humans ; Hungary/epidemiology ; *West Nile virus/genetics/isolation & purification/classification ; *West Nile Fever/epidemiology/transmission/virology ; Animals ; Phylogeny ; Phylogeography ; *Culex/virology ; Seasons ; Birds/virology ; Europe/epidemiology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Bayes Theorem ; Incidence ; Male ; Mosquito Vectors/virology ; Middle Aged ; },
abstract = {BACKGROUNDWest Nile virus (WNV) has become established across Europe, with Hungary serving as a key transmission hub since 2004. Following reduced activity during 2020-22, the 2024 season marked a resurgence with the largest geographical distribution ever recorded in Europe.AIMTo analyse the 2024 WNV transmission season in Hungary using a One Health approach and characterise circulating strains within the European phylogeographic context using comprehensive genomic surveillance.METHODSComplete and near-complete genome sequencing was performed on 55 specimens from 38 humans, 15 birds and two Culex pipiens mosquito pools using amplicon-based next-generation sequencing. Phylogeographic analysis incorporated 637 European WNV genome sequences (2004-24) with time-scaled Bayesian phylogenetic reconstruction and continuous spatial diffusion modelling.RESULTSHungary reported 113 human WNV cases in 2024 (n = 111 autochthonous, 2 imported), a 3.7-fold increase from 2023 (incidence: 1.16 vs 0.31 per 100,000 population). Neuroinvasive disease predominated (92%, n = 104) with a 7.9% case fatality rate. All 55 sequenced strains belonged to WNV lineage 2. Phylogeographic analysis revealed Hungary's central role in European WNV dissemination since 2004, with multiple introductions and local diversification across distinct clades. Continuous spatial modelling identified Hungary as a persistent transmission hub with bidirectional viral flow to neighbouring countries, contributing to northward expansion.CONCLUSIONHungary remains a critical WNV transmission hub in Central Europe with established endemicity of multiple lineage 2 clades. The analysis highlights Hungary's role as both a recipient and major source of European WNV diversity, emphasising the need for coordinated surveillance and climate-adapted preparedness strategies.},
}

Humans
Hungary/epidemiology
*West Nile virus/genetics/isolation & purification/classification
*West Nile Fever/epidemiology/transmission/virology
Animals
Phylogeny
Phylogeography
*Culex/virology
Seasons
Birds/virology
Europe/epidemiology
High-Throughput Nucleotide Sequencing
Genome, Viral
Bayes Theorem
Incidence
Male
Mosquito Vectors/virology
Middle Aged

@article {pmid42142571,
year = {2026},
author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Seasonal Shifts in the Belgrade Airborne Resistome and Virulome: A Metagenomic Perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124700},
doi = {10.1016/j.envres.2026.124700},
pmid = {42142571},
issn = {1096-0953},
abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.},
}

@article {pmid42142769,
year = {2026},
author = {Zhang, Z and Hu, Y and Zu, G and Dang, Q and Sun, X and Wu, Y},
title = {Molecular mechanisms of dissolved organic matter transformation and microbial interactions in composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134880},
doi = {10.1016/j.biortech.2026.134880},
pmid = {42142769},
issn = {1873-2976},
abstract = {Industrial composting of food waste digestate (FW) and chicken manure (CM) involves distinct dissolved organic matter (DOM) transformation pathways and different microbial interaction mechanisms. This study used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and shotgun metagenomics (for microbial community profiling) to compare interactions between DOM and microbial communities in the two composting processes. Results show that FW is dominated by labile organic matter (OM). This dominance increases the degree of DOM oxidation and the relative abundance of CHO. This labile carbon environment selected for a simplified microbial community dominated by key genera, yet facilitated active potential molecular transformations (PMTs) of DOM. These PMTs were characterized by an increase in thermodynamically limited processes (TLPs), indicating a carbon source-oriented pathway. In contrast, PMTs of DOM in CM favor thermodynamically favorable processes (TFPs), exhibiting higher aromaticity and CHOS abundance. The microbial community remains highly diverse, strongly connected, and functionally complementary, forming a synergistic network that supports coupled nitrogen-sulfur transformations. Environmental factors differentially regulate the two systems. This study indicates that the initial chemical properties of the composting feedstock fundamentally shape the PMTs of DOM pathways and the microbial communities they drive, providing an important theoretical basis for optimizing organic solid waste resource recovery processes.},
}

@article {pmid42142806,
year = {2026},
author = {Samuelsen, Ø and López-Causapé, C and Aarestrup, FM and Bortolaia, V and Brouwer, MSM and Cantón, R and Egli, A and Grad, YH and Hamprecht, A and Haussler, S and Holt, KE and Hopkins, KL and Howden, BP and Jeannot, K and Kahlmeter, G and Köser, CU and Mathers, AJ and Naas, T and Pournaras, S and Ruppé, E and Schön, T and Stoesser, N and Turnidge, J and Werner, G and Wright, GD and Giske, CG and Oliver, A},
title = {The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the EUCAST Subcommittee.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.05.012},
pmid = {42142806},
issn = {1469-0691},
abstract = {SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of Whole Genome Sequencing (WGS) in Antimicrobial Susceptibility Testing (AST) concluded that WGS antimicrobial susceptibility prediction (WGS-ASP) was not a sufficiently robust alternative to AST to guide clinical decision making at that stage and that more evidence was required [1]. Since then, the use of WGS, bioinformatic tools, machine learning (ML)/artificial intelligence (AI), databases, and prediction approaches has greatly expanded, along with an increased knowledge of resistance mechanisms and their contribution to antimicrobial susceptibility. In response, a new EUCAST ad hoc subcommittee was established in 2024 to review the literature, with the aim of assessing the current potential and limitations of WGS-ASP.

METHODS: As in the previous report, the subcommittee reviewed the literature on a 'by organism' basis but expanded the list to also include enterococci, Haemophilus influenzae and Bacteroides fragilis in addition to those already included in the first version: Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, and Mycobacterium tuberculosis. Additional sections were included to cover advances in metagenomics, other omics technologies and ML/AI. The full report was compiled and reviewed by all subcommittee members before public consultation in November 2025.

Significant progress has been achieved in WGS-ASP, with growing evidence supporting its ability to distinguish wild-type from non-wild-type isolates and, consequently, susceptible from resistant strains, particularly for M. tuberculosis and when clinical breakpoints align with the ECOFF. Despite these advances, important challenges remain before WGS-ASP can be adopted as a clinical decision-making tool. Addressing these gaps will require integrated phenotypic and genotypic surveillance to strengthen the evidence base for complex resistance mechanisms and newer antimicrobial agents, alongside comparative assessments that consider both ECOFF and clinical breakpoints. The analyses will require reference method phenotypic AST and high-quality genomic data. It is critical to ensure that datasets reflect the target populations and encompass the full spectrum of antimicrobial susceptibility, while developing unified interpretation frameworks and harmonized bioinformatics tools to standardize outputs. Robust external quality assessment schemes will be essential for clinical validation, and emerging technologies such as AI and ML offer promising avenues to enhance predictive accuracy. Finally, improvements in cost and turnaround time, coupled with evaluations of setting-specific cost-effectiveness, will be key to enabling practical implementation of WGS-ASP.},
}

@article {pmid42143007,
year = {2026},
author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW},
title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2026.05.002},
pmid = {42143007},
issn = {1424-3911},
abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.

METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.

RESULTS: Significant differences in both α-diversity and β-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.

CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.},
}

@article {pmid42143215,
year = {2026},
author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ},
title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05149-7},
pmid = {42143215},
issn = {1471-2180},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.

RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.

CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.},
}

@article {pmid42143222,
year = {2026},
author = {Yao, Y and Li, Z and Luo, L and Lu, X and Wang, H},
title = {Central nervous system infection associated with Human herpesvirus 7 presenting with predominant persecutory delusions as initial psychiatric manifestations after allogeneic stem cell transplantation: a rare case report with diagnostic and therapeutic implications.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13040-z},
pmid = {42143222},
issn = {1471-2334},
support = {82300248//National Natural Science Foundation of China/ ; 82100143//National Key Research and Development Program of China grant 2022YFC2304600/ ; },
abstract = {BACKGROUND: Human Herpesvirus 7 (HHV-7)-associated central nervous system (CNS) infection is an extremely rare complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT), with no prior reports of initial presentation dominated by psychiatric symptoms.

CASE PRESENTATION: We report a unique case of a 14-year-old female with high-risk acute lymphoblastic leukemia (ALL) who developed acute persecutory delusions and auditory hallucinations as the sole initial manifestations 54 days post-allo-HSCT. Brain magnetic resonance imaging (MRI) revealed multifocal lesions in the right frontal lobe and bilateral parieto-occipital regions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) confirmed the presence of HHV-7, establishing the diagnosis of HHV-7-associated CNS infection. The patient achieved complete clinical and radiological remission following a comprehensive treatment regimen combining antiviral therapy, glucocorticoids, intravenous immunoglobulin (IVIG), and antipsychotic medication.

CONCLUSIONS: This is the first documented case of HHV-7-associated CNS infection post-allo-HSCT presenting with persecutory delusions as the initial symptom, expanding the clinical spectrum of HHV-7-related CNS complications in immunocompromised hosts. Our findings emphasize the importance of considering atypical viral encephalitis in the differential diagnosis of acute psychiatric symptoms post-allo-HSCT and highlight the value of early neuroimaging and CSF mNGS for timely diagnosis and targeted intervention.},
}

@article {pmid42143235,
year = {2026},
author = {Zhong, M and Zhang, H and Yan, H and Li, Y and Zhu, D and Hu, S and Tan, L and Peng, L and Xie, X and Lan, G},
title = {Clinical characteristics, diagnosis and prognosis of Talaromyces marneffei pneumonia in kidney transplant recipients: a retrospective study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13557-3},
pmid = {42143235},
issn = {1471-2334},
support = {2025JJ70074//Natural Science Foundation of Hunan Province/ ; 2024JJ2088//Natural Science Foundation of Hunan Province/ ; 2023JJ30755//Natural Science Foundation of Hunan Province/ ; 82370760//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic dimorphic fungus that increasingly affects immunocompromised individuals, including kidney transplant recipients. However, data on the clinical features, diagnosis, treatment, and prognosis of Talaromyces marneffei pneumonia (TMP) in this population remain limited.

METHODS: This retrospective study included 8 HIV-negative kidney transplant recipients diagnosed with TMP at the Second Xiangya Hospital of Central South University between January 2015 and January 2025. Clinical data, including demographic characteristics, clinical manifestations, imaging findings, microbiological results, treatment regimens and outcomes, were collected and analyzed.

RESULTS: The cohort consisted of 7 males and 1 female with a mean age of 45.12 ± 9.03 years. The median time from transplantation to TMP onset was 356.5 days (IQR, 302.75-771.75). All patients presented with fever, and chest CT showed diverse pulmonary lesions, including nodules and patchy opacities. Metagenomic next-generation sequencing (mNGS) was the primary diagnostic tool, identifying TM in 7 cases (87.5%), with a mean diagnostic time of 5 ± 2.56 days, while conventional culture was positive in only 3 cases. All patients received antifungal therapy, mainly amphotericin B for induction followed by oral azoles for maintenance. Immunosuppressive regimens were adjusted during treatment. All patients achieved clinical cure without severe adverse events, and graft function remained stable.

CONCLUSIONS: TMP is a rare but serious infection in kidney transplant recipients receiving long-term immunosuppression. Early diagnosis using mNGS combined with conventional culture can improve detection efficiency. Timely antifungal therapy with amphotericin B followed by azole maintenance, along with careful adjustment of immunosuppressants, is associated with favorable prognosis.},
}

@article {pmid42143297,
year = {2026},
author = {Feng, J and Wang, Y and Han, J and Li, J and Xu, W and Hu, X},
title = {Gestational psittacosis: a systematic review of clinical manifestations and outcomes.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13575-1},
pmid = {42143297},
issn = {1471-2334},
support = {2025359//Scientific Research Project of Chengdu Municipal Health Commission/ ; 2025GZX002//Primary Health Care Research Project of Ganzi County People's Hospital/ ; 2024-YF09-00021-SN//Key Research and Development Support Program of Chengdu Science and Technology Bureau/ ; SCKFKY20250217//2025 Scientific Research Project of Sichuan Rehabilitation Medical Association/ ; },
abstract = {BACKGROUND: Gestational psittacosis is a rare but severe zoonotic infection caused by Chlamydia psittaci. This systematic review aims to evaluate the clinical characteristics, diagnostic challenges, therapeutic interventions, and maternal-fetal outcomes of this condition.

METHODS: A systematic search was conducted in PubMed, Embase, Web of Science, CNKI, and Wanfang Data from inception to October 31, 2025. Two investigators independently performed study selection and data extraction encompassing maternal demographics, clinical manifestations, laboratory findings, diagnostic modalities, antimicrobial regimens, and maternal-fetal outcomes.

RESULTS: A total of 32 cases from 30 publications were included. The median maternal age was 29 years (IQR: 26-32), and the median gestational age at diagnosis was 26.5 weeks (IQR: 21-30). All patients presented with fever (32/32, 100%), and common symptoms included headache (17/32, 53%), cough (15/32, 47%), and dyspnea (15/32, 47%). Severe disease was frequent: 66% (21/32) required intensive care unit (ICU) admission, 34% (11/32) required endotracheal intubation, and maternal mortality was 13% (4/32). Thrombocytopenia (26/32, 81%), hepatic dysfunction (27/32, 84%), renal impairment (18/32, 56%), and disseminated intravascular coagulation (DIC) (15/32, 47%) were the most prominent laboratory abnormalities. Diagnostic approaches evolved from serology to molecular methods. Recent studies have demonstrated the potential value of metagenomic next-generation sequencing (mNGS) in diagnosis, but further research is needed to confirm its clinical utility. The overall fetal and neonatal mortality was 68% (21/31 with available data), primarily due to stillbirth, spontaneous abortion, or therapeutic induction. These estimates reflect outcomes among reported cases and may overestimate true population-level risk.

CONCLUSION: Gestational psittacosis is a rare but life-threatening infection associated with substantial maternal morbidity and a high risk of fetal loss, although these outcomes may be influenced by publication bias. mNGS has facilitated earlier diagnosis in recent case reports; however, comparative performance data for gestational psittacosis remain limited.

TRIAL REGISTRATION: PROSPERO, CRD420251275911 (Registered 30 December 2025).

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42143373,
year = {2026},
author = {Huntington, CA and Bonavita, CM and Wells, HL and Tiemann, JD and Navarrete-Macias, I and Johnson, RF and Hensley, LE and Anthony, SJ},
title = {Optimization of environmental air sampling for viral metagenomics in a cave-roosting bat assemblage.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-026-00218-3},
pmid = {42143373},
issn = {2524-4655},
support = {#2412522//NSF/ ; },
abstract = {BACKGROUND: Environmental air sampling holds significant potential as a tool for viral surveillance. Its use in agricultural and indoor settings has demonstrated its feasibility and effectiveness but despite this, it has rarely been used in wildlife settings.

METHODS: To enable future applications, we optimized key parameters in air sampling methodology using a cave-roosting bat assemblage as a model system. We systematically investigated the impact of sampling conditions (flow rate, sampling duration, and sampling location/deployment time) and post-sampling treatments (DNA/RNA Shield ratios and secondary filtration) on three viral metrics - total mammalian virus abundance, mammalian RNA virus abundance, and Shannon diversity index - generated from next-generation sequencing data.

RESULTS: We first showed that air sampling can recover broad viral diversity, including alphacoronaviruses and betacoronaviruses. The sampling conditions for maximizing viral metrics were larger air sample volumes (≥24,000 liters) and sampling inside the cave while the bats were roosting, as opposed to at the cave entrance during emergence. Post-sampling treatments had limited impact on viral metrics, but their application may vary depending on the objectives of the study.

CONCLUSION: This work provides a proof-of-concept for applying air sampling for wildlife viral surveillance in a cave-roosting bat assemblage and identifies key sampling parameters.},
}

@article {pmid42143423,
year = {2026},
author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Cupples, AM},
title = {Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities.},
journal = {Journal of environmental management},
volume = {408},
number = {},
pages = {129957},
doi = {10.1016/j.jenvman.2026.129957},
pmid = {42143423},
issn = {1095-8630},
abstract = {Aerobic cometabolism offers a viable strategy for the remediation of chlorinated solvent plumes at oxic sites where anaerobic approaches are limited. Here, propane-enriched mixed cultures (derived from agricultural soils and an impacted site sediment) which previously degraded 1,4-dioxane, were evaluated for their capacity to also degrade trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), and 1,1-dichloroethene (1,1-DCE) over successive transfers. Sustained biodegradation of TCE and cDCE was observed across multiple enrichments and cultures enriched on one compound generally degraded the other. In contrast, 1,1-DCE biodegradation was restricted to a subset of cultures and removal times increased over transfers. Further, 1,1-DCE removal was absent at elevated concentrations, both trends consistent with inhibitory or toxic effects. Whole genome sequencing analyses revealed pronounced substrate-dependent selection of microbial communities, with cDCE-degrading cultures being dominated by Mycobacterium and Mycolicibacterium, whereas TCE-degrading cultures were dominated by Rhodococcus. Rhodococcus metagenome-assembled genomes (MAGs) in the TCE degrading cultures classified as R. opacus or R. wratislaviensis. 1,1-DCE degrading cultures were dominated by Pseudonocardia, although the associated MAGs contained a truncated propane monooxygenase alpha subunit, suggesting other enzymes were responsible for 1,1-DCE transformation. Functional gene analysis identified both group 5 (prmABCD) and putative group 6 propane monooxygenases (although their expression was not examined). Together, these results demonstrate that substrate-specific pressures govern propanotrophic community structure and function, and highlight distinct roles of key actinobacterial genera in chlorinated ethene cometabolism. These findings support the development of propane-based bioaugmentation strategies for the treatment of mixed chlorinated solvent contamination under aerobic conditions.},
}

@article {pmid42143455,
year = {2026},
author = {Jia, W and Li, J and Wang, K and Cheng, L and Jin, N and Yang, Q and Zhang, D and Xia, X and Xu, N and Wang, M and Meng, J and Zhu, Y and Ding, A},
title = {Convergent shifts in microbial communities: Petroleum hydrocarbon contamination suppresses matrix heterogeneity.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142349},
doi = {10.1016/j.jhazmat.2026.142349},
pmid = {42143455},
issn = {1873-3336},
abstract = {Accurate characterization of microbial communities in aquifers is essential for understanding groundwater ecosystem responses to petroleum hydrocarbon contamination. However, existing studies have focused primarily on groundwater, largely overlooking the coupled interactions between groundwater and aquifer sediments, which may bias aquifer-scale evaluations of microbial functional potential. In this study, contaminated groundwater and corresponding aquifer sediment samples were collected from a petroleum hydrocarbon impacted site, together with uncontaminated groundwater and sediment samples outside the contaminant plume as controls. Petroleum hydrocarbon concentrations and principal component analysis (PCA) revealed comparable contamination levels in groundwater and aquifer sediments. Integrating 16S rRNA gene sequencing analysis and metagenomic sequencing analysis, we found that microbial communities in contaminated groundwater exhibited broader niche breadth, higher niche overlap, and increased representation of low-molecular-weight carbon (LMW-C) metabolism, particularly pathways associated with ribose and amino sugar utilization. In contrast, aquifer sediment communities showed higher abundances of multidrug efflux pump genes and functional pathways involved in naphthalene and benzene degradation (PAH-C and MAH-C). Further correlation and community assembly analyses indicated that petroleum hydrocarbon contamination was the primary driver shaping microbial communities in both matrices, overriding intrinsic physicochemical differences. Meanwhile, sediment-specific properties, such as stronger sorption capacity for organic matter and differences in microbial lifestyles contributed to the observed divergence between groundwater and sediment communities. Overall, this study demonstrates that contamination induced selection dominates microbial community assembly in aquifers, and provides a mechanistic basis for improving the evaluation of natural attenuation potential and informing remediation strategies in contaminated aquifer systems.},
}

@article {pmid42143457,
year = {2026},
author = {Zhang, Z and Lv, M and Wang, R and Wang, B and Du, R and Lou, Y and Wang, C and Jiang, X and Hou, H and Li, Z and Chen, F},
title = {Micro-nano biochar interfaces promote adsorption-reduction coupling to accelerate bioelectrodechlorination in groundwater.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142393},
doi = {10.1016/j.jhazmat.2026.142393},
pmid = {42143457},
issn = {1873-3336},
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as trichloroethylene (TCE), are frequently detected high-toxicity contaminants in groundwater. Bioelectrodechlorination provides a sustainable alternative for CAHs remediation, but its practical application is hindered by limited interfacial reactivity due to low CAHs bioavailability and inefficient electron supply. Herein, we propose the construction of biochar-based functional electrodes featuring micro-nano interfacial architectures with hierarchical porosity, excellent biocompatibility, and enhanced interfacial extracellular electron transfer (EET) relative to carbon felt, which strengthened the coupling among local contaminant enrichment, cathode-associated biofilm development, and interfacial electron transfer, thereby accelerating TCE reductive dechlorination. The biochar-modified electrode increased the TCE dechlorination rate by 3.67-fold and reduced the interfacial charge-transfer resistance by 1.79-fold. Cathodic polarization at -0.5 V (vs. SCE) achieved the optimal balance between performance and energy efficiency, delivering 98.7% removal within 48 h at a low energy consumption of 4.1 Wh kg[-1] TCE, whereas less negative or more negative potentials decreased dechlorination efficiency by 4.3-11.0%. Under optimized conditions, TCE was efficiently removed and predominantly converted to cis-1,2-DCE. Biochar functionalization promoted biofilm development and selectively enriched electroactive and dechlorinating populations. Metagenomic analysis revealed marked upregulation of reductive dehalogenase genes (tceA, rdhA) and EET-related genes (cytc-c, e-pilin, and riboflavin). Environmental-economic benchmarking further demonstrated that biochar-based bioelectrodechlorination outperforms organic carbon-driven bioreduction and conventional electroreduction in removal efficiency, electron utilization, process controllability, and material sustainability.},
}

@article {pmid42143575,
year = {2026},
author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J},
title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag126},
pmid = {42143575},
issn = {1751-7370},
abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.},
}

@article {pmid42141123,
year = {2026},
author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X},
title = {Decoding the human gut bacterial plasmids in colorectal cancer.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10278-w},
pmid = {42141123},
issn = {2399-3642},
abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.},
}

@article {pmid42141277,
year = {2026},
author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G},
title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {42141277},
issn = {2662-1355},
abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.},
}

@article {pmid42135082,
year = {2026},
author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P},
title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].},
journal = {Life sciences},
volume = {},
number = {},
pages = {124457},
doi = {10.1016/j.lfs.2026.124457},
pmid = {42135082},
issn = {1879-0631},
}

@article {pmid42135536,
year = {2026},
author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO},
title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42135536},
issn = {1614-7499},
abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.},
}

@article {pmid42135633,
year = {2026},
author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X},
title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05137-x},
pmid = {42135633},
issn = {1471-2180},
support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; },
abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.

RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.

CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.},
}

@article {pmid42136553,
year = {2026},
author = {Yang, L and Chen, X and Jia, A and Liu, Q and Chu, J},
title = {Atypical Streptococcus sinensis infective endocarditis complicated by bacterial meningitis: A case report and literature review.},
journal = {The Journal of international medical research},
volume = {54},
number = {5},
pages = {3000605261447124},
doi = {10.1177/03000605261447124},
pmid = {42136553},
issn = {1473-2300},
mesh = {Humans ; Male ; *Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Streptococcus/isolation & purification/genetics ; *Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis ; *Streptococcal Infections/microbiology/drug therapy/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Vancomycin/therapeutic use ; *Endocarditis/microbiology/complications/drug therapy ; Mitral Valve/microbiology ; Ceftriaxone/therapeutic use ; Echocardiography ; },
abstract = {Infective endocarditis caused by Streptococcus sinensis complicated by bacterial meningitis is exceedingly rare. We report a case of a middle-aged man who initially presented with ischemic symptoms in both lower limbs. Echocardiography revealed mitral valvular vegetations, and blood cultures confirmed S. sinensis. During antibiotic therapy, the patient developed somnolence, dysarthria, and left-sided weakness. Metagenomic next-generation sequencing of cerebrospinal fluid detected S. sinensis, thereby confirming infective endocarditis complicated by bacterial meningitis. Given the high surgical risk, combination antimicrobial therapy with vancomycin and ceftriaxone was administered. The patient's consciousness recovered, and inflammatory and cerebrospinal fluid parameters gradually normalized. This case demonstrates that S. sinensis-associated infective endocarditis can occur in patients with immunocompetent status and often involves the mitral valve, with potential intracranial complications. Early identification by blood culture, metagenomic next-generation sequencing, and 16S rRNA sequencing enables precise pathogen diagnosis. Standardized antibiotic therapy and individualized surgical assessment are crucial to optimize outcomes. For patients with neurological complications, multidisciplinary management is essential to improve survival and long-term prognosis.},
}

Humans
Male
*Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Streptococcus/isolation & purification/genetics
*Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis
*Streptococcal Infections/microbiology/drug therapy/complications/diagnosis
RNA, Ribosomal, 16S/genetics
Vancomycin/therapeutic use
*Endocarditis/microbiology/complications/drug therapy
Mitral Valve/microbiology
Ceftriaxone/therapeutic use
Echocardiography

@article {pmid42136736,
year = {2026},
author = {Takahashi, Y and Sada, RM and Matsuo, H and Yamamoto, S and Matsuzaki, S and Okada, A and Sunada, A and Takao, M and Yamamoto, G and Chuang, CK and Liu, CH and Kutsuna, S},
title = {Diagnostic challenges in postoperative pelvic infections associated with Metamycoplasma hominis: a two-case analysis using metagenomic sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1823299},
pmid = {42136736},
issn = {2235-2988},
mesh = {Humans ; Female ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoplasma hominis/genetics/isolation & purification ; Middle Aged ; *Pelvic Infection/diagnosis/microbiology ; *Postoperative Complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Adult ; *Mycoplasma Infections/diagnosis/microbiology ; },
abstract = {Postoperative gynecological infections may present diagnostic challenges, particularly in the presence of fastidious genital mollicutes and inherently mixed microbial DNA, both of which limit the diagnostic performance of microbiological methods, including Gram staining, conventional culture, 16S rRNA gene PCR followed by Sanger sequencing. This study aimed to illustrate the limitations of conventional microbiological methods in the diagnosis of gynecologic pelvic infections and highlight key considerations for the clinical use of metagenomic next-generation sequencing (mNGS), based on two contrasting cases of postoperative pelvic infections associated with Metamycoplasma hominis (M. hominis). In both cases, neither conventional culture nor 16S rRNA gene PCR/Sanger sequencing identified the causative organism, and shotgun mNGS was subsequently performed. Although the mNGS findings differed markedly between the two cases, M. hominis was considered the most plausible pathogen. These two cases show that the clinical relevance of organisms detected by mNGS should not be judged by read counts alone, particularly in non-sterile specimens or after antibiotic exposure. Even low-abundance reads may represent clinically meaningful pathogens when interpreted within the clinical context. They also highlighted the value of mNGS as a complementary diagnostic tool for gynecological pelvic infections when conventional diagnostic methods are intrinsically limited.},
}

Humans
Female
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
*Mycoplasma hominis/genetics/isolation & purification
Middle Aged
*Pelvic Infection/diagnosis/microbiology
*Postoperative Complications/diagnosis/microbiology
DNA, Bacterial/genetics
Adult
*Mycoplasma Infections/diagnosis/microbiology

@article {pmid42136790,
year = {2026},
author = {Ariyasiri, A and Altaf, A and Mirza, H and Rehman, M},
title = {Genomics for precision surgical source control in anti-microbial resistant infections: A global review with focus on resource-limited settings.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {411AASC},
pages = {S151-S156},
pmid = {42136790},
issn = {1682-024X},
abstract = {BACKGROUND & OBJECTIVE: Antimicrobial resistance (AMR) critically threatens surgical safety, impairing perioperative prophylaxis and complicating infection management. Timely surgical source control is essential but relies on accurate microbiological diagnosis. Conventional culture-based methods are slow and insensitive, often leading to empirical broad-spectrum therapy. This review evaluates the role of advanced genomic diagnostics in enhancing surgical source control for AMR infections, with a focus on challenges and opportunities in low- and middle-income countries (LMICs) like Pakistan.

METHODOLOGY: A narrative review was conducted via a structured search of PubMed, Google Scholar, and ScienceDirect (January 2015-October 2025). Studies involving genomic tools in the management of AMR-related surgical infections were included. Evidence was synthesized thematically, covering genomic platforms, clinical applications, implementation barriers, and LMIC specific perspectives.

RESULTS: Genomic tools, particularly metagenomic next-generation sequencing (mNGS) and rapid multiplex PCR, demonstrate superior sensitivity (80.6-95.45%) and faster turnaround times (e.g., roughly 27 hours for mNGS) compared to culture. They improve pathogen detection in complex infections (e.g., prosthetic joints, necrotizing soft tissue), guide targeted antibiotic therapy, and can reduce broad-spectrum use. However, major implementation barriers exist, including high costs, need for specialized infrastructure and expertise, bioinformatic challenges, and ethical data concerns, which are especially pronounced in LMICs.

CONCLUSION: Genomic diagnostics offer a powerful approach to accelerate and refine surgical source control in the era of AMR. Strategic investments in local capacity, affordable platforms, and integration with antimicrobial stewardship are needed to realize their potential for improving surgical outcomes, particularly in resource-limited settings.},
}

@article {pmid42136862,
year = {2026},
author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M},
title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805596},
pmid = {42136862},
issn = {2296-858X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.},
}

@article {pmid42136870,
year = {2026},
author = {Zhou, Y and Chen, L and Wang, L and Zhao, Z and Tu, J and Chen, H and Wang, S},
title = {Cavitary nodule caused by Emergomyces orientalis in a diabetic patient: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1829356},
pmid = {42136870},
issn = {2296-858X},
abstract = {Emergomyces orientalis is a rare thermally dimorphic fungus belonging to the family Ajellomycetaceae. It exists in the environment as a mold producing conidia, which are inhaled and transform into yeast-like cells at body temperature to cause disseminated infections. While primarily associated with immunocompromised individuals, especially those with HIV. Diagnosis remains challenging due to its morphological similarity to Blastomyces dermatitidis and the frequent failure of routine cultures. Thus, molecular methods such as metagenomic next-generation sequencing (mNGS) have become crucial for early identification. This case report describes a 51-year-old man with type 2 diabetes mellitus presented (T2DM) with a 10-day history of back pain, pharyngeal discomfort, and scant sputum. Chest CT showed multiple bilateral pulmonary nodules, one of which had cavitated. mNGS of a percutaneous lung biopsy confirmed Emergomyces orientalis. Histopathology also supported the diagnosis. The patient was discharged on oral itraconazole after partial symptomatic improvement, with outpatient follow-up arranged. Two months of antifungal therapy resulted in mild reduction of cavitary lesions on follow-up CT.},
}

@article {pmid42137133,
year = {2025},
author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K},
title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {85-96},
pmid = {42137133},
issn = {2008-2258},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.},
}

@article {pmid42137225,
year = {2026},
author = {Meknas, A and Bessonov, K and Eagle, SHC and Peterson, CL and Robertson, J and Ricker, N and Signorelli, T and Nash, J and Reimer, A},
title = {Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.},
journal = {Access microbiology},
volume = {8},
number = {5},
pages = {},
pmid = {42137225},
issn = {2516-8290},
abstract = {This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.},
}

@article {pmid42137573,
year = {2026},
author = {Sun, J and Gao, W and Tan, H},
title = {The role of targeted next-generation sequencing and ultrasound in diagnosing fetal cytomegalovirus infection: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1734139},
pmid = {42137573},
issn = {2296-2360},
abstract = {BACKGROUND: Cytomegalovirus (CMV) infection is a leading cause of congenital infection and neonatal morbidity. Conventional diagnostic methods, such as polymerase chain reaction (PCR) and amniocentesis, remain important in the diagnosis of congenital CMV infection, although each method has its own limitations in clinical practice.

CASE PRESENTATION: A 31-year-old woman, gravida 3 para 1, presented for routine prenatal evaluation. At 18 weeks of gestation, ultrasound revealed echogenic bowel and fetal ascites. Amniocentesis at 19 weeks showed normal chromosomal results, but targeted next-generation sequencing (tNGS) detected CMV DNA with a high viral load, confirming intrauterine infection.

RESULTS: Despite counseling regarding poor fetal prognosis, the patient chose to continue the pregnancy under close ultrasound surveillance. Progressive hydrops fetalis was observed at 23 weeks, and the pregnancy was terminated at 24 weeks.

CONCLUSION: This case suggests that combining tNGS with ultrasound may provide complementary diagnostic information in selected cases of suspected fetal infection. In this patient, tNGS supported the identification of CMV in amniotic fluid when conventional genetic testing was unremarkable. However, as this is a single-case report, the broader diagnostic performance and clinical utility of tNGS require further validation in larger studies.},
}

@article {pmid42137610,
year = {2026},
author = {Oguzie, JU and Cummings, DB and Groves, JT and Hagan, AG and Rodriguez, J and Hernandez-Vidal, G and Moreno-Degollado, G and Shittu, I and Marushchak, LV and Nguyen-Tien, T and Trujillo-Vargas, CM and Silva, DB and Li, F and Richeson, JT and Schneider, NE and Gray, GC},
title = {Detection and Genomic Characterization of Novel Respiratory Viruses in US and Mexican Cattle Farms.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {3247802},
pmid = {42137610},
issn = {1865-1682},
mesh = {Animals ; Cattle ; United States/epidemiology ; *Cattle Diseases/virology/epidemiology ; Mexico/epidemiology ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Farms ; Humans ; Genome, Viral ; *Viruses/isolation & purification/genetics/classification ; *Virus Diseases/veterinary/epidemiology/virology ; },
abstract = {Respiratory virus infections in cattle cause an estimated more than $1 billion in production losses and can threaten human health. During February 2024 to May 2025, we employed a One Health approach to surveil for respiratory viruses among cattle, farm workers, and environmental samples from 11 US and Mexican beef or dairy cattle farms. We studied nasal and ocular swabs from cattle, nasal swabs from cattle workers, bioaerosol samples, and other environmental farm samples using molecular and virological techniques. Among 26 distinct viruses identified in cattle, we detected bovine nidovirus 1, influenza D virus (D/OK-like and D/660-like), bovine coronavirus, bovine rhinitis A and B viruses, bovine respirovirus 3 and bovine respiratory syncytial virus (BRSV); 11 of the 26 detected viruses were non-bovine-associated. Two bovine rhinitis A virus was markedly divergent (provisionally designated BRAV-4). Environmental metagenomics additionally identified influenza D virus, bovine coronavirus, and bovine rhinitis B virus. One human nasal swab tested positive for SARS-CoV-2 (cladeLF.7.3). Our findings reveal the presence of emerging, co-circulating, and environmentally linked pathogens at the human-animal-environment interface, underscoring the constant need for One Health surveillance to safeguard livestock and mitigate zoonotic risk.},
}

Animals
Cattle
United States/epidemiology
*Cattle Diseases/virology/epidemiology
Mexico/epidemiology
*Respiratory Tract Infections/veterinary/virology/epidemiology
Farms
Humans
Genome, Viral
*Viruses/isolation & purification/genetics/classification
*Virus Diseases/veterinary/epidemiology/virology

@article {pmid42137790,
year = {2026},
author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D},
title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1788826},
pmid = {42137790},
issn = {1664-302X},
abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.},
}

@article {pmid42137793,
year = {2026},
author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM},
title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1641069},
pmid = {42137793},
issn = {1664-302X},
abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.},
}

@article {pmid42137803,
year = {2026},
author = {Liu, Y and Chen, C and Gao, J},
title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818141},
pmid = {42137803},
issn = {1664-302X},
abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.},
}

@article {pmid42137806,
year = {2026},
author = {Doughan, GE and Walthart, BK and Schau, CE and Skoland, KJ and Mou, KTY and Brown, JT and Bonnema, JL and Plummer, PJ and Zhang, D and Li, G and Karriker, LA},
title = {Presence of antimicrobial resistance genes in biofilms from swine drinking water pipes before and after treatment with peracetic acid.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1770950},
pmid = {42137806},
issn = {1664-302X},
abstract = {Biofilms can be problematic to swine drinking water systems as they can harbor pathogens, decrease water quality, and may contribute to antimicrobial treatment failure. Water-administered antimicrobials are used for disease treatment in swine populations, yet, little is known about water line ecology and the impact it can have on antimicrobial resistance and stewardship. Water line cleaning and disinfection may aid in removal of water line biofilms, improve swine health, and antimicrobial stewardship. Water line samples were collected pre-treatment (0), 24 h post-treatment with 0.78% CID 2000 Pro (peracetic acid) (1), and 3, 5, 7, 14, 21, 42, 56, and 77-days post-treatment from six wean-to-finish swine farms in Iowa, USA. Biofilm was aseptically extracted from the interior of the water line pipe (n = 119) and submitted for metagenomic analysis to detect antimicrobial resistance genes (ARGs). This study demonstrates high prevalence of ARGs in swine water line biofilms that could confer resistance to both medically important antimicrobials to humans and animals such as aminoglycosides, beta-lactams, fluoroquinolones, colistin, and fosfomycin. From 115 samples, a frequency of 3,904 ARGs were reported, with 184 unique ARGs defined. Four samples contained no ARGs. One hundred and fifty-one integron genes representing three classes were found in 115 of 119 samples, indicating mechanisms of potential spread of multiple drug resistance. ARGs and integron genes combined were significantly lower on average by 10 unique ARGs/ integron genes 24-h post-treatment (1) when compared to pre-treatment (0) counts (p-value = 0.01). The number of unique ARG and integron genes quickly rebounded and were not statistically significant compared to pre-treatment counts on post-treatment dates 3, 5, and 7 (adjusted p-value ≥ 0.05), and by post-treatment date 14, unique ARG and integron genes were significantly higher than pre-treatment (adjusted p-value = 0.012). This study demonstrates that swine water line biofilms can harbor antimicrobial resistance genes which could have potential clinical impacts on pig health and treatment response.},
}

@article {pmid42137815,
year = {2026},
author = {Geng, S and Shi, X and Zhang, Q and Yang, J and Yang, C and Yang, L},
title = {Organic fertilizer enhances microbial functional genes related to nitrogen and phosphorus cycling in rubber tree (Hevea brasiliensis) rhizosphere.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1833968},
pmid = {42137815},
issn = {1664-302X},
abstract = {INTRODUCTION: Nitrogen (N) and phosphorus (P) are the essential nutrient for rubber growth. However, the effect of organic fertilizer application on soil microbial communities and functional genes related to N and P cycling in rubber plantation are unclear.

METHODS: A field trial was established in a rubber plantation with two treatments: organic fertilizer (OF) and an unfertilized control (CK). In this study, we used metagenomics analysis to examine the structural and functional alterations in the microbial community within the rhizospheric soil of rubber when organic fertilizers were applied.

RESULTS: Results showed that compared with the CK treatments, the OF treatment significantly increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP) contents. Taxonomic analysis revealed that OF treatment significantly enriched the phyla Pseudomonadota and Myxococcota, and the genera Pseudolabrys and Gaiella. At the functional level, organic fertilization significantly up-regulated key genes associated with N cycling, including organic N metabolism (gltB), N transport (nrtA, nrtB, nrtC), denitrification (norB, nosZ), nitrification (nxrB), and dissimilatory nitrate reduction (napA, napC). Regarding the P cycle, organic fertilization leads to the downregulation of the high-affinity phosphate transporter gene pstS and the concurrent upregulation of genes governing organic P mineralization (phnA, phoN), regulation (phoB), polyphosphate synthesis (ppk1), and polyphosphate degradation (spoT, relA). The variation partitioning analysis (VPA) results indicated that pH, SOM, and nitrogen nutrients (comprising TN and AN) explained 71.52% of the variation in the abundance of nitrogen-cycling functional genes, while pH, SOM, and phosphorus nutrients (comprising TP and AP) explained 64.95% of the variation in the abundance of phosphorus-cycling functional genes.

CONCLUSION: In summary, the application of organic fertilizer reshapes soil microbial communities and enhances the functional potential for nitrogen (N) and phosphorus (P) cycling. Our study provides a mechanistic basis for developing sustainable nutrient management strategies to optimize N and P bioavailability in tropical rubber agroecosystems.},
}

@article {pmid42137872,
year = {2026},
author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC},
title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783141},
pmid = {42137872},
issn = {2296-861X},
abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.

METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120 days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.

RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p = 0.001) and d56 (p = 0.03) but did not result in significant change in WAZ (p = 0.69) or weight gain (p = 0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.

DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.},
}

@article {pmid42137970,
year = {2026},
author = {Feser, M and Arend, D and Beier, S and Bolger, M and Lübke, NC and Meister, M and Steilen, L and Usadel, B and Scholz, U},
title = {Evolving bioinformatics services - the journey of KPI metrics with Scorpion.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {42137970},
issn = {1613-4516},
abstract = {Key Performance Indicators (KPIs) are essential for evaluating project success and establishing control mechanisms to monitor development, performance, and user acceptance of services in joint projects. However, the absence of standardized frameworks and effective monitoring tools, combined with service providers' reluctance due to fears of comparability, has limited their adoption in scientific contexts. To address this gap, we developed Scorpion, a flexible tool for KPI monitoring in project management. Scorpion enables service providers to retain control over their metrics while supporting centralized reporting. It offers both web-based and programmatic access, with features for KPI submission, visualization, and user and service management. Initially created for bioinformatics and biodiversity projects, Scorpion is applicable across diverse domains. It is particularly valuable for initiatives like the German National Research Data Infrastructure (NFDI), where funding agencies require KPI reporting for evaluation. We present the Scorpion framework, highlighting its design principles, features, and potential to improve project management practices. Use cases illustrate how Scorpion enhances KPI monitoring efficiency and accuracy, contributing to better impact evaluation, quality assurance, and informed decision-making in project and service management.},
}

@article {pmid42138445,
year = {2026},
author = {Ndhlovu, K and Salawu-Rotimi, A and Bopape, FL and Mtsweni, PN and Babalola, OO and Hassen, AI},
title = {Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70360},
doi = {10.1111/1758-2229.70360},
pmid = {42138445},
issn = {1758-2229},
support = {135456//National Research Foundation (NRF), South Africa/ ; },
mesh = {South Africa ; *Glycine max/growth & development/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Bradyrhizobium/genetics/isolation & purification/classification ; Metagenomics ; Nitrogen Fixation ; Phylogeny ; *Biodiversity ; Farms ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Prior to the introduction of the exotic inoculant strain of Bradyrhizobium, South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.},
}

South Africa
*Glycine max/growth & development/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Bradyrhizobium/genetics/isolation & purification/classification
Metagenomics
Nitrogen Fixation
Phylogeny
*Biodiversity
Farms
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid42138618,
year = {2026},
author = {Ran, L and Mao, Y and He, B and Pan, H and Ma, H},
title = {Wildfire-Altered Soil Water-Extractable Organic Matter Drives Divergent Greenhouse Gas Emissions in Anaerobic Subsurface Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04642},
pmid = {42138618},
issn = {1520-5851},
abstract = {Intensifying global climate change has increased wildfire frequency. Wildfire-altered soil water-extractable organic matter (burned-WEOM) is hydrologically transported to unburned areas, profoundly affecting cross-ecosystem carbon-nitrogen cycling and greenhouse gas (GHG) emissions. Taking soils from unburned subtropical forests as the research object, this study combined anaerobic incubation with high-resolution mass spectrometry and metagenomic sequencing to elucidate the regulatory mechanisms of burned-WEOM on soil GHG emissions under anaerobic conditions. The results showed that burned-WEOM increased CO2 emissions by 17.0%, induced a 164.6% surge in N2O emissions, and simultaneously inhibited CH4 emissions by 52.9%. With unique properties of high unsaturation and strong electron exchange capacity, burned-WEOM not only reshapes soil organic matter composition but also drives differential GHG emissions by enhancing complete carbon fixation pathways and recalcitrant carbon decomposition, increasing the abundance of anaerobic methane oxidation (AMO) genes and methanotrophs, enriching denitrifying microorganisms (especially fungi), and boosting N2O-generating gene activity without altering the reduction pathway. Moreover, WEOM molecular characteristics drive differences in GHG emissions: CH4 is mainly fueled by reduced, unsaturated lipid-like compounds, N2O is associated with nitrogen-rich, complex aromatic compounds, and CO2 has a broader range of source substrates. This study provides insights that may improve mechanistic understanding of postfire GHG dynamics and inform process representations in climate models.},
}

@article {pmid42138754,
year = {2026},
author = {Guimarães, LO and Couto, RDS and Reginato, SL and Mucci, LF and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, E},
title = {Wyeomyia confusa Lispivirus (WcLispV-SP): a novel neotropical mosquito virus in the Lispiviridae family.},
journal = {Archives of virology},
volume = {171},
number = {6},
pages = {},
pmid = {42138754},
issn = {1432-8798},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Culicidae/virology ; Open Reading Frames ; Brazil ; Viral Proteins/genetics ; RNA, Viral/genetics ; *Mononegavirales/genetics/classification/isolation & purification ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {Metatranscriptomic analysis of Wyeomyia confusa mosquitoes collected in the Atlantic Forest (Pindamonhangaba, São Paulo, Brazil) led to the identification of a previously uncharacterized virus, designated Wyeomyia confusa Lispivirus (WcLispV-SP), classified within the family Lispiviridae, genus Canmovirus. The viral genome consists of a negative-sense single-stranded RNA (ssRNA-) of 12,698 nucleotides, encoding six open reading frames (ORFs): nucleoprotein (N), two hypothetical proteins (HP/1 and HP/2), glycoprotein (G), ORFan protein, and RNA-dependent RNA polymerase (RdRp-L). Phylogenetic analysis supports the classification of WcLispV-SP as a distinct species within the genus Canmovirus. Structural analysis of the RdRp revealed conserved domains and catalytic motifs characteristic of members of the order Mononegavirales, supporting its functional integrity. These findings expand the known diversity of the Lispiviridae family and highlight the utility of metagenomic approaches for the discovery and characterization of RNA viruses associated with Neotropical sylvatic mosquitoes.},
}

Animals
Phylogeny
Genome, Viral
*Culicidae/virology
Open Reading Frames
Brazil
Viral Proteins/genetics
RNA, Viral/genetics
*Mononegavirales/genetics/classification/isolation & purification
RNA-Dependent RNA Polymerase/genetics

@article {pmid42138983,
year = {2026},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001705},
pmid = {42138983},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.},
}

*Plasmids/genetics
*Soil Microbiology
*Metals, Heavy/pharmacology
Soil/chemistry
*Bacteria/genetics/drug effects/classification/isolation & purification
Gene Transfer, Horizontal
Metagenome
Microbiota/genetics
Cities
Humans
*Drug Resistance, Bacterial/genetics

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag125},
pmid = {42139081},
issn = {1751-7370},
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

@article {pmid42139090,
year = {2026},
author = {Parienti, JJ and Yang, SS and Grinspoon, S},
title = {Selected Industry Highlights From IDWeek 2025.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {82},
number = {Supplement_4},
pages = {S85-S86},
doi = {10.1093/cid/ciag206},
pmid = {42139090},
issn = {1537-6591},
mesh = {Humans ; *HIV Infections/complications/drug therapy ; High-Throughput Nucleotide Sequencing ; },
abstract = {This supplement presents scientific reports from industry-sponsored IDWeek 2025 symposia, highlighting selected advances in infectious diseases and HIV care through clinical case scenarios. One article explores therapeutic approaches to metabolic complications in people with HIV, emphasizing treatment strategies and the clinical reasoning that supports individualized management of excess adiposity. The second examines the clinical integration of metagenomic next-generation sequencing for diagnosing central nervous system infections, outlining both its opportunities and limitations within current diagnostic pathways.},
}

Humans
*HIV Infections/complications/drug therapy
High-Throughput Nucleotide Sequencing

@article {pmid42139092,
year = {2026},
author = {Waldrop, G and Reddy, SP},
title = {Metagenomic Next-generation Sequencing in Central Nervous System Infections: Clinical Strategies, Evidence, and Best Practices.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {82},
number = {Supplement_4},
pages = {S92-S99},
doi = {10.1093/cid/ciag120},
pmid = {42139092},
issn = {1537-6591},
support = {//Delve Bio/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Immunocompromised Host ; Female ; Middle Aged ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections are diagnostically challenging due to their nonspecific clinical presentations and wide array of potential pathogens. The rising population of immunocompromised patients further complicates this landscape, increasing the prevalence of atypical and opportunistic infections that are often missed by conventional testing.

OBJECTIVE: This article provides guidance on the use and clinical interpretation of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in suspected CNS infections.

DISCUSSION: We highlight the paradigm shift from targeted molecular testing to agnostic mNGS, emphasizing key factors that impact diagnostic utility, including specimen handling, neuroanatomical factors, host inflammatory response, and pathogen kinetics. Using illustrative cases, we demonstrate how these biological and technical variables influence test sensitivity and result adjudication. We further discuss the impact of mNGS on clinical decision-making and current limitations regarding cost and turnaround time.

CONCLUSIONS: Cerebrospinal fluid mNGS is a transformative diagnostic tool, particularly for unusual presentations and in immunocompromised hosts. However, it does not replace clinical judgment and requires careful multidisciplinary interpretation. When integrated thoughtfully with clinical and laboratory data, mNGS can meaningfully reduce the diagnostic gap in CNS infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology
Immunocompromised Host
Female
Middle Aged

@article {pmid42139793,
year = {2026},
author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG},
title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.},
journal = {Veterinary microbiology},
volume = {319},
number = {},
pages = {111070},
doi = {10.1016/j.vetmic.2026.111070},
pmid = {42139793},
issn = {1873-2542},
abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.

METHODS: Stool samples from Danish diary calves (n = 32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon α-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3 +). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.

RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.

CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.},
}

@article {pmid42139982,
year = {2026},
author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R},
title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128553},
doi = {10.1016/j.micres.2026.128553},
pmid = {42139982},
issn = {1618-0623},
abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.},
}

@article {pmid42140024,
year = {2026},
author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L},
title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.},
journal = {International journal of food microbiology},
volume = {457},
number = {},
pages = {111847},
doi = {10.1016/j.ijfoodmicro.2026.111847},
pmid = {42140024},
issn = {1879-3460},
abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.},
}

@article {pmid42140051,
year = {2026},
author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M},
title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.},
journal = {Marine pollution bulletin},
volume = {230},
number = {},
pages = {119879},
doi = {10.1016/j.marpolbul.2026.119879},
pmid = {42140051},
issn = {1879-3363},
abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.},
}

@article {pmid42140215,
year = {2026},
author = {Hughes, N and Sathiananthamoorthy, S and Sergaki, C},
title = {Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101400},
doi = {10.1016/j.lanmic.2026.101400},
pmid = {42140215},
issn = {2666-5247},
abstract = {Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.},
}

@article {pmid42140378,
year = {2026},
author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA},
title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121086},
doi = {10.1016/j.cca.2026.121086},
pmid = {42140378},
issn = {1873-3492},
abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.},
}

@article {pmid42140478,
year = {2026},
author = {Mehne, ZS and Honarjou, E and Kahdouee, MK},
title = {Chronic Infections of the Spine: A Systematic Review of Microbial Etiologies, Diagnostic Approaches, and Treatment Outcomes.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108769},
doi = {10.1016/j.ijid.2026.108769},
pmid = {42140478},
issn = {1878-3511},
abstract = {BACKGROUND: Chronic spinal infections are uncommon but potentially devastating conditions, frequently associated with delayed diagnosis, heterogeneous microbiology, and complex management. Existing evidence remains fragmented, and a comprehensive synthesis of microbial etiologies, diagnostic approaches, and treatment outcomes is needed.

METHODS: A systematic review was conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between October 2015 and September 2025 involving adult patients with chronic spinal infections. Data were extracted on causative pathogens, diagnostic modalities, medical and surgical interventions, and clinical outcomes. Risk of bias was assessed using standardized methodological criteria.

RESULTS: Fifty-five studies comprising 3,036 patients were included. Mycobacterium tuberculosis was the most frequently identified pathogen, followed by Brucella species and pyogenic bacteria. Metagenomic next-generation sequencing (mNGS) demonstrated the highest diagnostic yield, with reported sensitivities ranging from 82% to 92%, and showed particular utility in detecting mixed or atypical infections. Biomarker-based and RNA-derived assays demonstrated promising performance in differentiating tuberculous spondylitis from other spinal conditions. Surgical interventions, including minimally invasive and combined approaches, were associated with high fusion and neurological recovery rates.

CONCLUSIONS: Chronic spinal infections show marked microbiological heterogeneity. Integrating molecular diagnostics with tailored surgical and antimicrobial strategies may improve diagnostic accuracy and clinical outcomes.},
}

@article {pmid42140665,
year = {2026},
author = {Vollmers, J and Correa Cassal, M and Kaster, AK},
title = {Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280099.124},
pmid = {42140665},
issn = {1549-5469},
abstract = {Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single-cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole genome amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions with sufficient DNA amounts, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, coassemblies become highly optimized for coabundance variation based binning approaches. "Midi-metagenomics" enables accurate metagenome-assembled genome (MAG) reconstruction from individual sorted samples with higher quality than coassembly and binning of multiple distinct samples and therefore improves analyses of the so-called "microbial dark matter".},
}

@article {pmid42140743,
year = {2026},
author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC},
title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {5},
pages = {},
doi = {10.1136/jitc-2025-014702},
pmid = {42140743},
issn = {2051-1426},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.

METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1×10[11] or 4×10[11] colony forming unit (CFU)/day) plus pembrolizumab (200 mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.

RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-naïve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-naïve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95% CI 5.6 to not reached) and 1.8 months (95% CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.

CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-naïve metastatic NSCLC with PD-L1 >50%.

TRIAL REGISTRATION NUMBER: NCT05877430.},
}

Humans
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Female
Male
Middle Aged
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology
Aged
*Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology
*Melanoma/drug therapy/pathology
*Lung Neoplasms/drug therapy/pathology
Mice
*Head and Neck Neoplasms/drug therapy/pathology
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
Animals
Adult

@article {pmid42140896,
year = {2026},
author = {Blázquez-Sánchez, P and Gunkel, J and Useini, A and Zlobin, A and Zakary, JD and Schöler, A and Graefe, N and Engelberger, F and Cantanhede, F and Frank, R and Zhao, Z and Zarei, A and Butenschön, E and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C and Künze, G},
title = {Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42140896},
issn = {2041-1723},
support = {887913//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ScaDS.AI//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {*Polyethylene Terephthalates/metabolism/chemistry ; Biocatalysis ; *Protein Engineering/methods ; *Hydrolases/metabolism/genetics/chemistry ; Recycling ; Enzyme Stability ; Biodegradation, Environmental ; Molecular Dynamics Simulation ; Metagenome ; *Bacterial Proteins/metabolism/genetics/chemistry ; },
abstract = {Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.},
}

*Polyethylene Terephthalates/metabolism/chemistry
Biocatalysis
*Protein Engineering/methods
*Hydrolases/metabolism/genetics/chemistry
Recycling
Enzyme Stability
Biodegradation, Environmental
Molecular Dynamics Simulation
Metagenome
*Bacterial Proteins/metabolism/genetics/chemistry

@article {pmid42140961,
year = {2026},
author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM},
title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73076-2},
pmid = {42140961},
issn = {2041-1723},
support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.},
}

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41915167},
issn = {1432-184X},
abstract = {UNLABELLED: Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02730-5.},
}

@article {pmid41917256,
year = {2026},
author = {Shen, Z and Liu, Y and Liu, Y and Zhang, P and Li, Y and Li, Z and Qi, H},
title = {Clinical characteristics and mixed infection patterns of ocular surface infection with Epstein-Barr virus.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {16},
number = {1},
pages = {},
pmid = {41917256},
issn = {1869-5760},
abstract = {PURPOSE: To analyze the clinical features of ocular surface diseases caused by Epstein-Barr virus (EBV) infection.

METHODS: A retrospective case series study was conducted. Data from 48 patients (54 eyes) with EBV infection who visited Peking University Third Hospital between January 2023 and October 2025 were collected. Patient demographics and baseline information were recorded. Ophthalmic slit-lamp examination, ocular surface (conjunctiva/cornea) scrapings, bacterial culture of ocular secretions, real-time fluorescence quantitative PCR detection, EBV-specific antibody testing, and metagenomic next-generation sequencing (mNGS) were performed.

RESULTS: Among patients infected with EBV on the ocular surface, the majority were middle-aged individuals in the 31–40 age group. The primary risk factors for onset were keeping pets (10/48), followed by colds (6/48); among those keeping pets, parrots were the most common (5/9). The main clinical manifestations were foreign body sensation (37/54) and yellow discharge (34/54). Common signs included mixed conjunctival hyperemia (31/54), follicles on the lower eyelid conjunctiva (17/54), papillae on the upper eyelid conjunctiva (8/54), and punctate epithelial defects on the cornea (17/54). In most ocular surface scrapings, small round lymphocytes were observed alongside a small number of reactive lymphocytes (44/54), which could simultaneously present with a large number of neutrophils (36/54). There was a significant difference between the presence of yellow discharge and the type of conjunctival hyperemia [Formula: see text]. However, no statistically significant correlation was found between the presence of yellow discharge and the presence of neutrophils in the scraping results [Formula: see text]. Significant differences were found in EBV viral loads among different groups of combined symptoms [Formula: see text] and among different follicle groups [Formula: see text]. No statistically significant correlation was found between the lymphocyte count in the scraping and the EBV viral load in the affected eye [Formula: see text].

CONCLUSION: EBV infection of the ocular surface is prone to concurrent infections; therefore, a detailed medical history inquiry is crucial. Ocular surface tissue scraping examination can rapidly identify viral infection-related inflammatory characteristics and rule out bacterial/fungal infections, providing effective supportive auxiliary diagnostic evidence for viral ocular surface infection, and precise diagnosis of EBV infection needs to be achieved in combination with molecular biological and serological tests.},
}

@article {pmid42014454,
year = {2026},
author = {Muller, E and Bamberger, T and Borenstein, E},
title = {Navigating multi-omic integration methods for human microbiome research.},
journal = {Nature microbiology},
volume = {11},
number = {5},
pages = {1153-1167},
pmid = {42014454},
issn = {2058-5276},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2266/25//Israel Science Foundation (ISF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Host Microbial Interactions ; *Metagenomics/methods ; Multiomics ; },
abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
Host Microbial Interactions
*Metagenomics/methods
Multiomics

@article {pmid42128850,
year = {2026},
author = {Fujii, N and Nakajima, M and Narihiro, T and Kuroda, K and Kindaichi, T},
title = {Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25084},
pmid = {42128850},
issn = {1347-4405},
mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Phylogeny ; Ecosystem ; Genome, Bacterial ; },
abstract = {The phylum Minisyncoccota (formerly known as "Candidatus Patescibacteria"/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.},
}

*Bacteria/classification/genetics/isolation & purification/metabolism
Phylogeny
Ecosystem
Genome, Bacterial

@article {pmid42129189,
year = {2026},
author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E},
title = {Network topology of the gut microbiome associates with metabolic health in obesity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42129189},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; },
abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Male
Female
*Obesity/microbiology/metabolism
Middle Aged
Cross-Sectional Studies
Adult
Feces/microbiology
Metagenomics
*Obesity, Metabolically Benign/microbiology/metabolism
Dysbiosis/microbiology
Phenotype

@article {pmid42129350,
year = {2026},
author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D},
title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01626-2},
pmid = {42129350},
issn = {2730-664X},
abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.

OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.

DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.

RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p = 0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.

CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.

TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.},
}

@article {pmid42129659,
year = {2026},
author = {Chen, J and Li, X and Deng, Z and Ying, Y and Lu, M},
title = {Clinical characteristics of sporadic acute Q fever diagnosed by metagenomic next-generation sequencing: a retrospective analysis and literature review in China.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13477-2},
pmid = {42129659},
issn = {1471-2334},
support = {MISP-102684//MSD Investigator Initiated Studies Program Review Committee/ ; 2022YFC2303203-01//National Key Research and Development Program of China/ ; Z-2017-24-2202//Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; },
abstract = {BACKGROUND: Acute Q fever manifests sporadically in mainland China, where its clinical spectrum and optimal diagnostic strategies remain under-recognized. This study aimed to delineate the clinical phenotype and antimicrobial prescribing patterns of sporadic acute Q fever diagnosed via metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective, single-center cohort study of adult patients with sporadic acute Q fever. A comprehensive literature review of all published sporadic cases across China was subsequently performed to delineate the national clinical spectrum of sporadic Q fever.

RESULTS: The cohort comprised 22 male patients (mean age 36.7±13.5 years). All patients presented with high-grade pyrexia (>39°C) accompanied by a characteristic symptom constellation of headache, fatigue, myalgia, and hepatic involvement (100%, mean ALT 122.2±56.9 U/L). Pneumonia was observed in 2 patients (2/22, 9.1%). A distinct dissociation was observed between markedly elevated C-reactive protein (mean 67.4 ± 33.6 mg/L) and normal leukocyte counts. A pooled analysis of 94 published cases and 22 consecutive patients from our center yielded 116 confirmed Q fever cases (male-to-female ratio 11.9:1, the proportion of hepatitis and pneumonia:87.9% and 24.1%) The median interval from symptom onset to pathogen confirmation was 7.8 ± 2.8 days. mNGS yielded a diagnosis in 77.5 % of 116 patients, the remaining 22.5 % were identified by PCR and antibody testing.

CONCLUSION: Acute Q fever in China predominantly affects young males, presenting as a systemic febrile illness with a distinctive hepatic phenotype (elevated liver enzymes) rather than prominent pneumonia. The clinical triad of high fever, influenza-like symptoms (headache/myalgia), and "WBC-CRP dissociation" (normal white cell count with elevated CRP) serves as a potential clinical indicator. Empiric doxycycline should be initiated promptly in suspected cases. mNGS is a valuable tool for definitive diagnosis, particularly when empiric therapy fails or in severe/complicated cases.},
}

@article {pmid42129710,
year = {2026},
author = {Wang, Z and Tang, J and Yang, K and Cui, Z and Li, Z},
title = {Diagnostic challenges and lessons learned of Guillain-Barré syndrome mimicking central nervous system infection - a case report.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04942-1},
pmid = {42129710},
issn = {1471-2377},
abstract = {BACKGROUND: Guillain-Barré syndrome (GBS) is an immune-mediated disorder affecting the peripheral nervous system, often triggered by infections, vaccinations, trauma, or surgery. Typically, it presents as progressive, symmetric limb weakness with hyporeflexia. However, some GBS subtypes can present atypically with symptoms like headache, facial palsy, and confusion. These symptoms overlap significantly with central nervous system (CNS) infections, often causing diagnostic delays.

CASE PRESENTATION: A 57-year-old man was admitted with cough, sputum, and shortness of breath, having received a rabies vaccination a month earlier. He developed headache, dysphagia, progressive muscle weakness, and impaired consciousness, requiring Intensive Care Unit (ICU) transfer, endotracheal intubation, and mechanical ventilation. The initial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa (sequence count: 6094), combined with fever and a series of clinical symptoms before transfer to the ICU, CNS infection was considered. Treatment with piperacillin-tazobactam, meropenem, and ciprofloxacin yielded no improvement. Albumino-cytological dissociation in the CSF led to a neurology consultation for suspected GBS, and intravenous immunoglobulin (IVIg) therapy began. Negative CSF bacterial cultures and mNGS, along with positive anti-GT1a IgM ganglioside antibodies and electromyogram(EMG) result indicating nerve damage, confirmed the GBS diagnosis. After five days of IVIg, the patient was weaned from mechanical ventilation and showed significant neurological recovery.

CONCLUSION: The significant clinical overlap between GBS and CNS infections poses a major diagnostic and therapeutic challenge. This case highlights the importance of thorough history-taking, comprehensive neurological assessment, careful interpretation of lab results, and early neurologist involvement to minimize diagnostic delays in GBS and prevent subsequent treatment delays.},
}

@article {pmid42129938,
year = {2026},
author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z},
title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02426-5},
pmid = {42129938},
issn = {2049-2618},
support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.},
}

@article {pmid42130304,
year = {2026},
author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z},
title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70324},
pmid = {42130304},
issn = {1462-2920},
support = {LP160101508//Australian Research Council/ ; },
mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Islands ; Coral Reefs ; },
abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.},
}

*Anthozoa/microbiology/growth & development
Animals
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota
*Seawater/microbiology
Islands
Coral Reefs

@article {pmid42130363,
year = {2026},
author = {DU, WQ and Liu, LJ and Zhang, L and Tang, YF and Liu, LQ and Li, XF and Xiao, YY},
title = {[A case of Bartonella henselae meningitis characterized by bone marrow hemophagocytosis].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {28},
number = {5},
pages = {618-623},
pmid = {42130363},
issn = {1008-8830},
mesh = {Humans ; Male ; Adolescent ; *Bartonella henselae ; *Cat-Scratch Disease/complications ; *Lymphohistiocytosis, Hemophagocytic/etiology ; *Bone Marrow/pathology ; *Meningitis, Bacterial ; },
abstract = {A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.},
}

Humans
Male
Adolescent
*Bartonella henselae
*Cat-Scratch Disease/complications
*Lymphohistiocytosis, Hemophagocytic/etiology
*Bone Marrow/pathology
*Meningitis, Bacterial

@article {pmid42130962,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {7},
number = {1},
pages = {9-20},
pmid = {42130962},
issn = {2641-6549},
abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.

MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.

RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).

CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.},
}

@article {pmid42131203,
year = {2026},
author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A},
title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758563},
pmid = {42131203},
issn = {1664-302X},
abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.

METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.

RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.

DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.},
}

@article {pmid42131208,
year = {2026},
author = {Hembram, DB and Panda, SP and Das, BK and Soren, D and Singh, NR},
title = {Microbial elicitors to metabolic reprogramming: an integrative model of plant-microbe interactions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1816468},
pmid = {42131208},
issn = {1664-302X},
abstract = {Plant growth, soil health, and crop productivity with nutritional quality can be significantly enhanced by employing microbial consortia that incorporate diverse microorganisms with complementary functions. Plants produce various types of secondary metabolites such as terpenoids, alkaloids, phenolics, essential oils, and other metabolites through various cellular mechanisms, which are often stimulated by microbial interactions. These metabolites exert beneficial effects on plants and perform multiple roles in agriculture, contributing significantly to growth and economy. This review summarizes microbial consortia-mediated enhancement of plant health and their intricate interactions with host plants. Beneficial microbes of a consortium trigger complex signaling cascades leading to a dynamic regulatory strategy through which plants enhance their secondary metabolite synthesis. Secondary messengers and hormonal cross-talk further integrate the signal to transcription factors, which play a central role in activating or repressing the key genes of the metabolic pathways. Thus, the interplay of microbial signal, secondary messengers, hormonal cross-talk, and key metabolite genes forms the basis of plant secondary metabolite biosynthesis. In addition, recent advances in systems microbiology, including metagenomics, metatranscriptomics, and metabolomics, have enabled a holistic understanding of microbial community dynamics and their collective role in regulating secondary metabolism.},
}

@article {pmid42131214,
year = {2026},
author = {Sudianto, E and Shlafstein, MD and Durieu, B and Harmel, M and Cornet, L and Saw, JH},
title = {Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824103},
pmid = {42131214},
issn = {1664-302X},
abstract = {INTRODUCTION: Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy.

METHODS: Analysis of 46 steam vent associated samples from Hawai'i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes.

RESULTS: This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material.

CONCLUSION: These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.},
}

@article {pmid42131265,
year = {2026},
author = {Cheng, J and Ni, J and Zhao, Y and Jiang, L and Huang, Y and Zhang, Y and Yan, P and Long, Z and Fu, H and Jiang, X},
title = {The clinical utility of metagenomic next-generation sequencing in the management of fever in patients with hematological disorders.},
journal = {Nagoya journal of medical science},
volume = {88},
number = {1},
pages = {84-98},
pmid = {42131265},
issn = {2186-3326},
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Adult ; *Metagenomics/methods ; Aged ; *Hematologic Neoplasms/complications/microbiology ; *Fever/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Patients with hematological malignancies frequently present with severe and intricate infections that pose life-threatening risks. Conventional pathogen detection methods offer limited clinical insights and therapeutic guidance. This retrospective study evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in hematologic patients who remained febrile despite prolonged antibiotic therapy, which means unresponsive to antibiotic therapy. This retrospective analysis included 204 patients with hematologic malignancies, undergoing conventional pathogen detection and peripheral blood mNGS. The cohort was stratified into neutropenia and non-neutropenia groups to compare the diagnostic and therapeutic implications of mNGS versus conventional microbiological tests (CMT). Among the 204 patients with mNGS, the overall positive detection rate was significantly higher than that of CMT (68.1% vs 30.9%, P<0.001). In both the neutropenia and non-neutropenia group, mNGS demonstrated a higher positivity rate for bacteria than for CMT (bacteria, 36.4% vs 15.6%, P<0.01). mNGS proved notably advantageous for bloodstream infections with clinically relevant drug-resistant strains, particularly in the neutropenia cohort (26.4% vs 12.5%, P<0.001). Using a composite reference standard, mNGS manifested sensitivity and specificity rates of 78.4% and 61.9%, respectively. Patients in the neutropenia group derived superior clinical benefit from mNGS, including higher diagnostic accuracy and treatment efficacy (diagnosis, 56.4% vs 40.6%, P=0.036; treatment, 49.3% vs 31.3%, P = 0.016). Additionally, the 30-days mortality rate was notably higher among mNGS-positive patients who tested compared to those who tested negative (17.3% vs 1.5%, P<0.001). mNGS demonstrated clinical relevance in patients with hematologic malignancy who received prolonged antibiotic treatment and holds promise in predicting patient survival prognosis.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Adult
*Metagenomics/methods
Aged
*Hematologic Neoplasms/complications/microbiology
*Fever/microbiology/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use

@article {pmid42131305,
year = {2026},
author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F},
title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1769892},
pmid = {42131305},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; },
abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.

METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.

RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.

DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.},
}

Humans
*Colitis, Ulcerative/microbiology/immunology
*Mycobiome
*Gastrointestinal Microbiome
Adult
Child
Male
Female
*Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Middle Aged
Young Adult
Adolescent
Dysbiosis/microbiology
Metagenome
Child, Preschool
Age Factors
Aged
Feces/microbiology

@article {pmid42131468,
year = {2026},
author = {Mazibuko, X and Mtimka, S and Ngobese, LM and Mafuna, T and Simelane, MB and Yakobi, SH and Gumede, X and Pooe, OJ},
title = {Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation.},
journal = {Bioinformatics and biology insights},
volume = {20},
number = {},
pages = {11779322251413418},
pmid = {42131468},
issn = {1177-9322},
abstract = {Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria, Acidobacteria, and Bacteroidetes, and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity's role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.},
}

@article {pmid42131611,
year = {2026},
author = {Zhai, X and Pan, H and Zheng, J},
title = {Spinal infection caused by Coxiella burnetii and surgical treatments: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1785109},
pmid = {42131611},
issn = {2296-858X},
abstract = {Q fever is a rare global zoonosis caused by Coxiella burnetii, with bone and joint involvement being an uncommon manifestation that poses significant diagnostic challenges. This article reports a case of persistent focal spinal infection caused by C. burnetii in an elderly female without a clear epidemiological exposure history, who was initially misdiagnosed with vertebral compression fractures. The diagnosis was confirmed by third-generation nanopore-based metagenomic next-generation sequencing (mNGS), which detected 12,170 reads of C. burnetii with a relative abundance of 98.27%. The patient was initially treated with oral doxycycline (0.1 g q12h) and rifampin capsules (0.45 g daily) for 4 weeks, resulting in decreased inflammatory markers and reduced paravertebral abscess size. After clinical stabilization, surgical intervention (posterior approach T12-L1 vertebral lesion resection, intervertebral bone graft fusion, and pedicle screw rod fixation) was performed under general anaesthesia. Postoperative follow-up for 3 months showed a significant improvement in the patient's low back pain [visual analogue scale (VAS) score from 6 preoperatively to 1 at 3 months] and functional status [Oswestry Disability Index (ODI) from 65% preoperatively to 10% at 3 months], with normalized inflammatory markers and a reduced C. burnetii IgG antibody titre (from 1:256 to 1:128). Serological follow-up revealed persistent negative IgM antibodies throughout the treatment course. This case highlights the diagnostic value of third-generation mNGS for rare spinal infections caused by C. burnetii and the efficacy of a multimodal treatment approach combining targeted antimicrobial therapy and surgical intervention. The rationale for antibiotic selection and surgical management is discussed, along with the limitations of the present case and clinical insights for managing similar cases.},
}

@article {pmid42132311,
year = {2026},
author = {Tulloch, RL and Rojahn, J and Neaves, LE and Trujillo-González, A and Holleley, CE and Hahn, EE},
title = {Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70153},
doi = {10.1111/1755-0998.70153},
pmid = {42132311},
issn = {1755-0998},
support = {//Centre for Biodiversity Analysis/ ; },
mesh = {*DNA/isolation & purification/genetics ; *Specimen Handling/methods ; Animals ; Metagenomics/methods ; DNA Barcoding, Taxonomic/methods ; Museums ; *Preservation, Biological/methods ; },
abstract = {Advancements in historical genomics increasingly leverage museum collections to study past ecosystems, species interactions and biodiversity. Formalin-fixed, ethanol-preserved specimens, once thought inaccessible to molecular analyses due to DNA degradation, are emerging as valuable genomic resources. If recoverable and reliably attributable, DNA within preservation media could provide a non-destructive alternative to conventional tissue sampling, with the potential to expand molecular access to valuable or irreplaceable specimens. We tested whether preservation media contains recoverable DNA suitable for taxonomic inference. We coupled passive adsorption and active filtration of specimen media with hot alkaline lysis DNA extraction followed by metabarcoding and shotgun metagenomics. DNA was recoverable across samples, including 41 of 61 (~67%) targets in a composite sample. However, detections were dominated by non-target taxa, indicating that preservation media retain a layered mixture of specimen-derived DNA and broader collection-level background. Detection success tracked with preservation chemistry (near-neutral pH and low residual formaldehyde) rather than specimen age. Method choice influenced detections: active filtration increased target detections but admitted more background; passive capture was sparser but more selective; shotgun sequencing retrieved broader vertebrate signals, including reptiles, but was heavily enriched for non-targets. Because both target and non-target taxa were often abundant, read-abundance cut-offs were unreliable for attribution. Spirit-media DNA is therefore best interpreted as a collection-level signal and a screening tool to identify jars with molecular potential (e.g., taxa of conservation or biosecurity interest), rather than as a definitive non-destructive proxy for specimen identity. Prioritising chemically favourable jars and implementing rigorous contamination controls should improve signal interpretability and help unlock the value of preservation media for historical genomics.},
}

*DNA/isolation & purification/genetics
*Specimen Handling/methods
Animals
Metagenomics/methods
DNA Barcoding, Taxonomic/methods
Museums
*Preservation, Biological/methods