@article {pmid42789300,
year = {2026},
author = {Li, M and Mao, J and Liu, S and Yu, H and Qin, H and Liu, X and Tu, R and Chen, S and Liu, Z and Zhang, S and Mao, J},
title = {Ethanol exposure is associated with spatial and taxon-specific gut microbiota remodeling characterized by ecological adaptation rather than broad activation of microbial ethanol metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734657},
doi = {10.1080/19490976.2026.2734657},
pmid = {42789300},
issn = {1949-0984},
mesh = {Animals ; *Ethanol/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; Acetaldehyde/metabolism ; Metagenomics ; },
abstract = {Alcohol-associated diseases are linked to gut microbiota disruption, but how ethanol intake is associated with microbial functional remodeling remains unclear. Here, using male C57BL/6J mice, we integrated spatiotemporal quantification of ethanol and acetaldehyde across the gastrointestinal tract with 16S rRNA sequencing, metagenomics, metaproteomics, and metabolomics. Our results showed that small-intestinal communities were enriched in taxa and functions related to bile acid tolerance/utilization, whereas cecal communities exhibited pronounced remodeling of multiple core functions associated with ecological adaptation. Although the abundance of several ethanol metabolism-related genes increased, this genetic potential was not broadly translated into detectable protein-level activation. Ethanol metabolism-related proteins were mainly derived from Lachnospiraceae, whose metabolic activity was suppressed. In contrast, Muribaculaceae, Desulfovibrionaceae, and Barnesiellaceae gained functional advantages in substrate acquisition, energy metabolism, oxidative stress defense, and proteostasis. These findings provide a region-resolved functional map indicating that ethanol-associated microbiota remodeling is characterized by ecological adaptation, rather than uniform activation of direct microbial ethanol metabolism.},
}

Animals
*Ethanol/metabolism
Male
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
Acetaldehyde/metabolism
Metagenomics

@article {pmid42790038,
year = {2026},
author = {Wang, X and Zhang, Y and Zhang, L and Han, Y and Liu, J and Bi, X and Huang, S and Yang, T},
title = {Aeration change from horizontal brush to fine bubble substantially reduces the emission of inhalable antibiotic resistome from wastewater to air.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143712},
doi = {10.1016/j.jhazmat.2026.143712},
pmid = {42790038},
issn = {1873-3336},
abstract = {Aeration-mediated aerosolization in wastewater treatment plants (WWTPs) poses considerable sanitary menaces. However, the effect of aeration patterns on the emission of inhalable antibiotic resistome in WWTPs remains poorly understood. Herein, we analyzed seasonal metagenomics of fine particulate matter (PM2.5) and wastewater under two aeration patterns, with consistent inflow condition, aeration efficiency, and location background in the same WWTP. PM2.5-borne antibiotic resistance genes (ARGs) exhibited higher occurrence, mobile potential, pathogen involvement, and resistome risks under horizontal brush aeration than under fine bubble aeration. And the airborne resistome risks peaked in winter. Regardless of aeration patterns, mobile ARGs in PM2.5 were mainly carried by integrases and resistant to macrolide-lincosamide-streptogramin. Totally, 6 pathogenic antibiotic resistant bacteria (PARB), including Klebsiella pneumoniae and Pseudomonas aeruginosa, expressed ARG mobility in aeration environments. Horizontal brush aeration drove 74.52% of the ARGs and 75.00% of the PARB from wastewater into the air, which were higher than the 57.53% of ARGs and 50.00% of PARB driven by fine bubble aeration. For aeration-related PM2.5 resistome, aeration patterns were the principal inducement through regulating bacterial community and PM2.5 concentration. These distinguish the aerosolization response of wastewater resistome to aeration patterns that can help process selection and hygiene protection.},
}

@article {pmid42790042,
year = {2026},
author = {Feng, J and Li, SL and Chen, C and Zhang, L and Dai, XY and Chen, X and Wu, H and Smets, BF and Graham, DW and Wu, D and Chen, M},
title = {Potential dissemination of multidrug-resistant pathogens into local watersheds via aircraft wastewater from overseas aviation network.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143695},
doi = {10.1016/j.jhazmat.2026.143695},
pmid = {42790042},
issn = {1873-3336},
abstract = {Cross-border air travel contributes to antimicrobial resistance (AMR) spread, yet evidence linking aircraft wastewater to local environmental contamination remains limited. Metagenomic sequencing revealed that aircraft wastewater harbors approximately 10-fold higher levels of antibiotic resistance genes (ARGs) compared to municipal wastewater treatment plant (WWTP) influents (∼2.5 ARGs/cell) and effluent-receiving water (∼ 0.35 ARGs/cell). Furthermore, distinct resistome signatures and microbial assembly patterns were identified in aircraft wastewater relative to those in domestic wastewater sources. Notably, throughout this continuum, closely related Escherichia coli strains (ST2, with ≤10 core-genome single-nucleotide polymorphism differences) were isolated from WWTP samples receiving aircraft wastewater, whereas no such isolates were found in non-related samples. These strains consistently exhibited polymyxin resistance (carrying the mcr-1 gene) and extended-spectrum β-lactam (multidrug) resistance, a trait maintained under environmental selection (iCAMP, R[2] fit = 0.23), as confirmed by fluorescence-based bacterial tracing assays. Source-tracking further revealed that aircraft wastewater from regions with higher microbial community similarity, rather than geological proximity, contributed more substantially to domestic wastewater-borne multidrug resistant genes composition. Our findings suggest a potential route by which multidrug-resistant bacteria and ARGs associated with last-resort antibiotics may disseminate from the overseas aviation network into domestic WWTPs and effluent-receiving water, supporting integrated oversea-to-local surveillance.},
}

@article {pmid42790581,
year = {2026},
author = {Yin, J and Zhang, Y and Luo, W and Ma, Y and Sun, Y},
title = {Temperature shapes a modular division of labor among soil fungi to facilitate antibiotic dissipation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129241},
doi = {10.1016/j.envpol.2026.129241},
pmid = {42790581},
issn = {1873-6424},
abstract = {The antibiotics used in veterinary medicine accumulate in agricultural soils, where their persistence selects for antibiotic-resistance genes (ARGs). Soil fungi possess diverse metabolic enzyme systems and substantial potential for antibiotic biodegradation, but how temperature shapes fungal community succession and the functional pathways involved in antibiotic removal remains poorly understood. Herein, soils with histories of no fertilizer and organic fertilizer application (UF and OF, respectively) were spiked with 21 tetracyclines, quinolones and sulfonamides at approximately 2 mg kg[-1] per compound and incubated for 18 months at natural (NT; monthly mean of approximately 15 °C, ranging from -5.6 °C to 28.1 °C), constant (CT, 20 °C), and low (LT, 4 °C) temperatures. Dissipation kinetics were combined with fungal community and metagenomic profiling, co-occurrence networks, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-residual correlations. Dissipation was slower in OF (total-antibiotic half-life [DT50] of 22-58 d) than in UF (DT50 of 18-44 d). Temperature exerted a stronger effect, with dissipation fastest at NT (DT50 of 18-22 d) and slowest at LT (DT50 of 44-58 d); ARGs followed the same trend, declining less than the parent compounds and least of all at LT. Temperature restructured the fungal community (PERMANOVA, P ≤ 0.018), chiefly by replacing taxa rather than by nested loss. Fungal-assigned KEGG pathways were inversely correlated with residual antibiotic concentrations (Spearman's ρ = -0.34 to -0.54, P < 0.05) and fell into three candidate functional modules: antibiotic capture and transport, oxidative transformation, and intracellular transformation. Across all temperatures the community retained a capture-and-transport core, for which no significant temperature contrast was detected, whereas oxidative and intracellular transformation were both less abundant at LT. Temperature therefore influences soil antibiotic dissipation by reshaping fungal community structure and redistributing annotated potential among complementary fungal functions. Accounting for this temperature dependence can improve bioremediation strategies for antibiotic-contaminated agricultural soils.},
}

@article {pmid42791078,
year = {2026},
author = {Gottesdiener, LS and DeLaurentis, C and Pereira, MR},
title = {A Case of Disseminated Encephalitozoon cuniculi in a Lung Transplant Recipient: Microsporidiosis in the Era of Molecular Diagnostics.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70325},
doi = {10.1111/tid.70325},
pmid = {42791078},
issn = {1399-3062},
support = {T32 AI007613//National Institute of Allergy and Infectious Diseases/ ; KL2 TR002385/TR/NCATS NIH HHS/United States ; },
}

@article {pmid42791132,
year = {2026},
author = {Bastón-Paz, N and García-Durán, C and Bayraktar, D and Palacios, E and Moreno-Blanco, A and Top, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oliver, A and Oteo-Iglesias, J and Cantón, R and Gil, C and Schürch, AC and Del Campo, R and de Dios Caballero, J},
title = {Functional and Compositional Shifts in Lung and Gut Microbiota after One Year of Treatment with Highly Effective CFTR Modulators in Cystic Fibrosis.},
journal = {Archivos de bronconeumologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arbres.2026.08.007},
pmid = {42791132},
issn = {1579-2129},
abstract = {BACKGROUND: Highly effective CFTR modulator therapy with elexacaftor-tezacaftor-ivacaftor (ETI) has revolutionized clinical outcomes in cystic fibrosis (CF), yet its effects on gut and lung microbiota, especially at the functional level, are poorly understood.

METHODS: In a 12-month prospective study, we enrolled 35 clinically stable CF patients initiating ETI. Paired fecal and sputum samples, collected at baseline and after 12 months, were analyzed using shotgun metagenomics, metaproteomics, and short-chain fatty acid (SCFA) quantification. Multi-omics data were integrated with clinical parameters assessing lung, hepatic, pancreatic, and intestinal function.

RESULTS: ETI drove significant clinical improvements, including increased ppFEV1, higher fecal elastase, and better nutritional status, despite persistent major lung pathogens and minimal changes in liver or intestinal inflammation markers. Microbiota composition showed limited shifts: alpha diversity was stable, and beta diversity changes accounted for only small variance in both compartments. However, butyrate-producing genera enriched in feces, while oropharyngeal taxa increased in sputum. Metaproteomics revealed broad downregulation of host neutrophil-driven inflammatory proteins; sputum additionally showed increased abundance of extracellular matrix-related proteins. Microbial proteins linked to carbohydrate/lipid metabolism, particularly butanoate pathways, increased in feces alongside a trend for higher butyrate. In sputum, formaldehyde dehydrogenase enzymes rose, indicating enhanced oxidative microbial metabolism.

CONCLUSIONS: ETI is associated with minimal compositional but substantial functional reprogramming in CF microbiota. These changes are accompanied by an increase in butyrate-producing taxa, attenuation of host pro-inflammatory pathways, and a shift in lung metabolism toward oxidation. Despite ongoing pathogenic colonization, these changes suggest CFTR modulation is associated with a less inflammatory, more stable host-microbiota ecosystem.},
}

@article {pmid42791821,
year = {2026},
author = {Liu, W and Yang, Y and La, Y and Ma, X and Wu, X and Chu, M and Guo, X and Yan, P and Liang, C},
title = {Effects of Eucommia ulmoides Leaf Extract on Growth Performance, Serum Biochemistry, Rumen Microbiota, and Metabolic Profiles in Yaks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182965},
pmid = {42791821},
issn = {2076-2615},
support = {CARS-37//National Beef Cattle Industrial Technology System/ ; },
abstract = {This study aimed to investigate the effects of adding Eucommia ulmoides leaf extract (ELE) to the diet on the growth performance, serum biochemical parameters, rumen fermentation parameters, rumen microorganisms and metabolites of yaks. Ten male yaks (two years old) were selected and randomly divided into two groups (n = 5). The control group (C, 153.48 ± 7.48 kg) was fed the basal diet, while the experimental group (H, 146.72 ± 1.87 kg) was fed the basal diet supplemented with 1.0 g/kg feed dry matter (DM) of ELE for 75 days. The results showed that the average daily gain, the serum total antioxidant capacity, catalase, and superoxide dismutase were significantly higher in the H group than in the C group (p < 0.01), while the serum total cholesterol, creatinine, alkaline phosphatase, blood urea nitrogen, and malondialdehyde were significantly lower than those of the C group (p < 0.05); in contrast, low-density lipoprotein cholesterol was significantly elevated in the H group (p < 0.01). Furthermore, the concentrations of acetate, butyrate, and hexanoic acid increased significantly compared with the C group (p < 0.05); 2-Hydroxypropanoic acid, butanedioic acid, and pentanedioic acid decreased significantly in the H group compared with the C group (p < 0.05). The metagenomic analysis revealed that ELE not only promoted the growth of cellulose-degrading bacteria but also significantly reduced the abundance of the virulence factors and carbohydrate-active enzymes (p < 0.05). In the experimental and control groups, the dominant microorganisms were Bacillota and Prevotellaceae, respectively. Metabolomics analysis further revealed that the differential metabolites were significantly enriched in pathways including purine metabolism, β-alanine metabolism, glutathione metabolism, and cGMP-PKG. The Pearson correlation analysis revealed that there were interactions among various microorganisms and metabolites, which can promote the growth and health of yaks. In conclusion, ELE can promote the growth and health of yaks by regulating the serum biochemical parameters, rumen fermentation, rumen microbial flora, and metabolism.},
}

@article {pmid42791967,
year = {2026},
author = {Shouqair, D and Verma, S and Alghafri, R and Nassar, R and Mohamed, L and Dhaheri, FA and Everett, D and Shibl, AA and Rodríguez, J and Moradigaravand, D and Khan, M and Goering, R and Senok, A},
title = {Source-Resolved Wastewater Metagenomics Reveals Distinct Resistome and Virulome Landscapes Across an Urban Wastewater Continuum.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090817},
pmid = {42791967},
issn = {2079-6382},
support = {Grant# AJF-NIH-1-MBRU//This work was funded by Grant# AJF-NIH-1-MBRU as part of the UAE-NIH Collaborative Re-search Initiative (UAE-NIH-CRI) which comprises four collaborating UAE institutes: Al Jalila Foundation, Mohammed Bin Rashid University of Medicine and Health Sciences,/ ; },
abstract = {BACKGROUND/OBJECTIVES: Wastewater-based antimicrobial resistance (AMR) surveillance typically relies on treatment plant influent as a single integrated matrix, obscuring source-specific signals. In arid settings where treated effluent is reused, understanding how resistomes and virulomes are structured across wastewater compartments is essential for One Health monitoring.

METHODS: Shotgun metagenomic sequencing was applied to 57 wastewater samples collected in Dubai, United Arab Emirates, between October 2024 and January 2025. Samples represented nine community sewer nodes, two tertiary-care hospital outflows, and influent and effluent from two wastewater treatment plants (WWTP). Datasets were used for taxonomic, resistome, and virulome profiling. Alpha diversity was compared using Wilcoxon rank-sum tests, beta-diversity differences were assessed using permutational multivariate analysis of variance, and source-associated AMR genes were identified using linear discriminant analysis effect size analysis.

RESULTS: A total of 1470 bacterial species, 822 antimicrobial resistance genes (ARGs), and 1554 virulence factor genes were identified. Bacterial diversity was significantly lower in WWTP effluent than in other compartments. Hospital wastewater was enriched for class D β-lactamases, including multiple blaOXA variants, whereas community wastewater and WWTP influent shared dominant macrolide and aminoglycoside resistance genes including msr(E), mph(E), strB and aadA1. Despite marked reductions in bacterial diversity after treatment, no significant difference in ARG diversity was observed between WWTP influent and WWTP effluent (p = 0.558), with resistance genes such as blaVEB, msr(E), mph(E) detected in the latter. Virulome profiles shifted from fimbrial gene dominance in untreated sources toward biofilm- and persistence-associated genes in WWTP effluent. ARG alpha diversity varied over time, whereas taxonomic and virulome diversity remained stable.

CONCLUSIONS: Community and influent wastewater capture population-level AMR carriage, hospital outflows concentrate clinically relevant resistance determinants, and WWTP effluent retains resistance markers despite microbial biomass reduction. Compartment-resolved metagenomic surveillance provides a practical One Health framework for identifying high-value monitoring points.},
}

@article {pmid42791995,
year = {2026},
author = {Mware, B and Kibet-Rono, G and Mwangi, K and Lugano, D and Osiany, S and Kiritu, E and Dobi, PO and Muli, C and Juma, J and Njeru, R and Machuka, EM and Bett, B and Ogwell, A and Abworo, EO and de Oliveira, T and Muloi, DM and Tessema, SK and Oyola, SO},
title = {Wastewater Metagenomic Surveillance Reveals Socioeconomic Patterns of Pathogen Diversity and Antimicrobial Resistance in Nairobi, Kenya.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090845},
pmid = {42791995},
issn = {2079-6382},
support = {BMZ001201//Federal Ministry of Economic Cooperation and Development/ ; HTH 017//Rockefeller Foundation/ ; 101103171//Global Health EDCTP3 Joint Undertaking, its members, and the Bill & Melinda Gates Foundation/ ; TF0B8412//World Bank Group/ ; SAMVAC//South African Medical Research Council/ ; },
abstract = {Background: Wastewater and Environmental Surveillance (WES) has become a useful public health tool as an early-warning system revealing emergence/re-emergence of pathogenic diseases and spread of antimicrobial resistance (AMR). We characterized the taxonomic composition, relative abundance, and antibiotic resistance genes (ARGs) of wastewater-identified bacterial pathogens across socioeconomically and epidemiologically diverse sewerage catchments in Nairobi, Kenya-a key East African urban city representing a low- and middle-income country (LMIC). Results: Metagenomic analysis of Nairobi's wastewater revealed distinct bacterial and antimicrobial resistance (AMR) profiles. Campylobacteraceae (52.5% ± 17.9%) and Bacteroidaceae (19.8% ± 9.9%) dominated the communities. While Arcobacter cryaerophilus was ubiquitous, Bacteroides fragilis and A. suis abundances varied by neighborhood socioeconomic status. We detected critical clinical pathogens-including Escherichia coli, Vibrio cholerae, Mycobacterium tuberculosis, and the ESKAPE species-alongside 207 distinct ARGs conferring resistance to 11 antibiotic classes. Both taxonomic and ARG compositions showed high spatial heterogeneity, with maximum variation in low-income areas. Temporal analysis captured shifting pathogen dynamics, and metagenomic abundances for Vibrio cholerae and Klebsiella pneumoniae were validated via qPCR. Conclusions: Our findings underscore the utility of WES as a scalable, non-invasive public health tool. By capturing community-level pathogen composition and AMR dynamics, WES bypasses the limitations of clinical diagnostic access, providing a vital early-warning system for underserved urban populations. To maximize its public health utility, environmental genomic signals must serve as actionable triggers for coordinated One Health responses, including targeted clinical diagnostics, localized antimicrobial stewardship reviews, proactive risk communication, and prioritized sanitation infrastructure upgrades.},
}

@article {pmid42792000,
year = {2026},
author = {Timoteo, FD and Di Giulio, E and Di Domenico, M and Secondini, B and Marotta, F and Matteucci, G and Zilli, K and Romualdi, T and Palmieri, D and Garofolo, G and Janowicz, A},
title = {Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090850},
pmid = {42792000},
issn = {2079-6382},
support = {SG-2021-12375470//Ministero della Salute/ ; },
abstract = {Background/Objectives: Wastewater-based epidemiology (WBE) has emerged as a valuable One Health approach for monitoring antimicrobial resistance (AMR) at the population level. Although quantitative PCR (qPCR) and shotgun (SG) metagenomics are widely used for wastewater surveillance, studies integrating these complementary approaches remain limited. This study aimed to investigate the occurrence, seasonal dynamics, and diversity of antimicrobial resistance genes (ARGs) in municipal wastewater from Central Italy by combining targeted qPCR and SG metagenomic sequencing. Methods: Influent wastewater samples were collected monthly from eight municipal wastewater treatment plants in Central Italy between April 2025 and March 2026. Clinically relevant antimicrobial resistance genes were quantified by quantitative real-time PCR, while SG metagenomic sequencing was used to characterize resistome composition, resistance gene families, and ARG sequence diversity using bioinformatic pipelines. Results: All investigated ARGs were detected in every sample. Significant seasonal variation was observed for all investigated markers, including qnrS, blaKPC, blaCTX-M and intI1. Metagenomic analysis revealed broadly similar resistome profiles across sampling sites and time points, dominated by resistance genes to macrolide-lincosamide-streptogramin, aminoglycosides, β-lactams, and fluoroquinolones. High sequence diversity was observed within the dominant ARG families, highlighting the complementary value of SG metagenomics for comprehensive resistome characterization. Conclusions: The integration of targeted qPCR and SG metagenomics provided a comprehensive characterization of antimicrobial resistance in municipal wastewater. While qPCR enabled sensitive quantification of clinically relevant ARGs and revealed seasonal trends, metagenomics expanded resistome characterization by identifying dominant resistance classes, gene families, and sequence variants. These findings support the implementation of integrated molecular approaches for routine wastewater-based AMR surveillance within a One Health framework.},
}

@article {pmid42792028,
year = {2026},
author = {Morikwe, UC and Kiki, LC and Ezeanowai, FC and Hall, S and Bhatia, S and Maswanganye, TN and Jeje, O and Hill, MS and Graves, JL and Deng, D and Jeffers-Francis, L},
title = {Building-Scale Wastewater Metagenomics Reveals Temporal Patterns in Resistance and Virulence Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090878},
pmid = {42792028},
issn = {2079-6382},
support = {EEC-2133504//U.S. National Science Foundation/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) and virulence represent co-evolving dimensions of microbial pathogenic potential whose ecological organization in building-scale wastewater systems remains poorly understood. Methods: Using shotgun metagenomic sequencing, we characterized the temporal dynamics and ecological associations of antimicrobial resistance genes (ARGs) and virulence factors (VFs) in 12 wastewater grab samples (2 per semester) collected from a university residence hall designated for COVID-19 quarantine between 2021 and 2023. Results: The wastewater microbiome was anchored by a stable core of gut-associated anaerobic bacteria, with community composition exhibiting significant Spring-versus-Fall structuring and a year × semester interaction that explained 60% of the community variation. A marked shift toward opportunistic taxa, particularly Acinetobacter, during Fall 2023 represented the most pronounced temporal perturbation. Total ARG abundance remained stable across semesters, while resistome composition shifted significantly, indicating that temporal dynamics were driven by compositional turnover rather than changes in overall resistance burden. VF functional categories were broadly conserved across sampling periods, consistent with their structural embedding within the persistent fecal core microbiome. Correlation and network analyses revealed modular ecological coupling between resistance and virulence functional categories, with metal/co-resistance and fosfomycin classes showing the strongest associations with virulence functions. At the community level, a Benjamini-Hochberg-corrected co-occurrence network resolved into taxa-anchored resistance modules and separate virulence-function clusters, with Acinetobacter and fluoroquinolone resistance as the principal connectors. Conclusions: These findings indicate that building-scale wastewater metagenomics can capture ecologically structured functional gene dynamics, highlighting its potential as a surveillance tool for monitoring AMR and virulence in built environments.},
}

@article {pmid42792243,
year = {2026},
author = {Tang, W and Wang, Z and Dong, Y and Cao, J and Chen, Y},
title = {Monochromatic Blue Light Enhances Antioxidant Status and Remodels the Gut Microbiome in Association with Increased Plasma Melatonin in Broiler Chickens.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091204},
pmid = {42792243},
issn = {2076-3921},
support = {32172801//National Natural Science Foundation of China/ ; 32372954//National Natural Science Foundation of China/ ; 32573308//National Natural Science Foundation of China/ ; },
abstract = {The intestinal microbiome of broiler chickens has potential to regulate host health and growth performance. Although previous studies have revealed that the intestinal microbiota composition is affected by different factors including monochromatic light, the underlying mechanisms remain poorly understood, particularly regarding the causal role of light-sensitive hormones such as melatonin. To address this gap, a 2 × 4 factorial design was adopted in the present study, with two surgical treatments (sham-operation or pinealectomy) and four light conditions (white, blue, green, and red light), to investigate whether blue light modulates gut microbiota and antioxidant status through melatonin-dependent pathways. Broilers were reared under different monochromatic light conditions. On day 3 post-hatching, we ablated circulating melatonin production by conducting a pinealectomy or control sham-operation model. Accordingly, the broilers were assigned to eight groups: white light + sham-operation (WL), white light + pinealectomy (WP), blue light + sham-operation (BL), blue light + pinealectomy (BP), green light + sham-operation (GL), green light + pinealectomy (GP), red light + sham-operation (RL), and red light + pinealectomy (RP). On day 35, blue light was found to most effectively elevate plasma melatonin, which activated the Mel 1a/Nrf2/NQO1 pathway to reduce oxidative stress and remodel the jejunal microbiota. Metagenomic analysis identified Akkermansia muciniphila, Bifidobacterium longum and Ligilactobacillus aviarius as key bacteria enriched in blue light. Consequently, classes of microbiota-derived metabolites like stearidonic acid and indole propionic acid triggered the variation of tryptophan, bile acid and lipid metabolism, which contributed to broiler growth promotion. Moreover, pinealectomy accompanied by plasma melatonin deprivation significantly nullified the blue-light-induced effects. These insights confirm blue light is more effective in microbiota modulation by inducing melatonin secretion and providing a new strategy for light management in the broiler industry.},
}

@article {pmid42792532,
year = {2026},
author = {Cupples, AM and Richards, J and Basaldua Del Cid, M},
title = {Data Mining of Groundwater Genomes for Metagenome-Assembled Genomes (MAGs) Containing Monooxygenase Operons Associated with Contaminant Biodegradation.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181586},
pmid = {42792532},
issn = {2079-7737},
support = {2413523//U.S. National Science Foundation/ ; },
abstract = {This study examined freely available whole genome sequencing (WGS) data for genes associated with contaminant biodegradation. Thirteen WGS datasets (>600 individual samples) involving more than 12,000 Gbases from multiple countries were examined. The Department of Energy Systems Biology Knowledgebase (KBase) was used to create metagenome-assembled genomes (MAGs) containing the operons of interest. The arrangement and length of subunits for each operon were compared. Phylogenetic trees were created for common biomarkers (tmoA, pmoA, prmA, mmoX, dmpN). MAGs were uploaded into publicly available KBase narratives. Thirty-four MAGs, within the phyla Actinomycetota, Pseudomonadota and Chloroflexota, were identified with the full propane monooxygenase operon (prmABCD). Twenty-six MAGs, within the classes Gammaproteobacteria and Alphaproteobacteria, contained the full operon for soluble methane monooxygenase (mmoXYBZDC). More than 100 MAGs contained the full operon for ammonia/particulate methane monooxygenase (pmoCAB) and were classified within the Gammaproteobacteria and Alphaproteobacteria groups, as well as other phyla. Fifty-five MAGs, within Burkholderiales (Gammaproteobacteria) and Alphaproteobacteria, contained the full operon for toluene-4-monooxygenase (tmoABCDEF). From the MAGs containing the full operon for toluene monooxygenase, thirty-three also contained the full operon for phenol monooxygenase (dmpKLMNOP). The MAGs generated and their associated functional gene sequences have the potential to improve molecular detection methods for site bioremediation.},
}

@article {pmid42792542,
year = {2026},
author = {Ong, CJN and Cabalbag, JN and Cruz, JTP and Valderama, TT and Roslin, CR and Magtibay, CM and Lonogan, JKK and Libres, AC and Matamis, JG and Mamaat, JER and Mortel, FA and Bacalzo, GD and Cabuhat, KSP and de Leon, CS and Nuevo, JJM and Aguilan, JR and Fortaleza, JAG},
title = {Mapping Bacteriophage-Based Antimicrobial Research in Southeast Asia: A Bibliometric Analysis of Scientific Productivity, Knowledge Structure, and Emerging Research Pathways.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181596},
pmid = {42792542},
issn = {2079-7737},
abstract = {Southeast Asia faces a substantial burden of antimicrobial resistance (AMR), creating increasing interest in bacteriophage-based antimicrobial strategies. However, the regional development, contributors, collaboration patterns, and evolving research priorities of this field remain insufficiently characterized. This study conducted a bibliometric analysis of Scopus-indexed publications on bacteriophage-based antimicrobial research affiliated with Southeast Asian countries from 1981 to 2025. Bibliometrix/Biblioshiny and VOSviewer were used to evaluate scientific production, citation patterns, leading contributors, collaboration networks, and conceptual and thematic development. A total of 862 publications were analyzed, with scientific output accelerating markedly after 2019 and reaching its highest level in 2025. Thailand emerged as the dominant regional contributor, with Vongkamjan (n = 21) and Surachat (n = 20) as the two most prolific authors. Mahidol University (n = 182), Prince of Songkla University (n = 142), and Universiti Putra Malaysia (n = 139) were the leading institutions, demonstrating a concentration of research capacity in Thailand and Malaysia. Scientific Reports was the most productive journal (30 publications), whereas Frontiers in Microbiology recorded the highest citation count among the leading sources (963 citations). Collaboration mapping revealed increasingly interconnected regional and international research networks. Thematic analyses demonstrated a transition from foundational and pathogen-specific investigations toward AMR, bacteriophage therapy, biofilm control, aquaculture, genomic and comparative genomic analysis, wastewater and public-health applications, and One Health-oriented research. Emerging topics included endolysins, quorum sensing, CRISPR-associated approaches, metagenomics, and genome-informed phage characterization. These findings demonstrate the rapid expansion and thematic diversification of bacteriophage-based antimicrobial research in Southeast Asia while highlighting persistent geographic concentration and the need for stronger regional infrastructure, collaboration, and translational capacity.},
}

@article {pmid42792603,
year = {2026},
author = {Yang, X and Yu, J and Wang, Y and Zhao, Y and Wang, K and Lu, X and Zhang, L},
title = {Study on the Risk of Phosphorus Leaching in Dryland from Typical Purple-Soil Regions and Its Control Mechanisms.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181658},
pmid = {42792603},
issn = {2079-7737},
support = {No.2022YFC3204004//the National Key Research and Development Program/ ; },
abstract = {Phosphorus (P) leaching from dryland from purple soils poses a significant risk to water quality, yet effective mitigation strategies and their underlying microbial mechanisms remain poorly understood. This study aimed to evaluate the efficacy of biochar (B), a silicon-based conditioner (Si), and their combination (BSi) in controlling P leaching, hypothesizing that B would immobilize P while Si would mobilize it. The indoor soil column leaching experiments were conducted with four treatments (CK, B, Si, BSi), measuring leachate P fractions and soil P forms, and employed metagenomic sequencing combined with partial least-squares path modeling (PLS-PM) and Bayesian structural equation modeling (BSEM) to explore microbial functional mechanisms. Results showed that B alone reduced cumulative leaching of inorganic P (IP), organic P (OP), and total P (TP) by a range of 5.4-6.3%, while increasing available phosphorus (Olsen-P) by 39.4% in the surface layer. Si and BSi promoted leaching, with BSi reducing available P sharply, despite raising TP. Metagenomic analysis revealed that B suppressed subsurface IP solubilization genes (e.g., gcd, ppx) and optimized OP mineralization, whereas Si inhibited mineralization via reducing key microbial taxa. BSEM further identified water-soluble P (Water-P) and total nitrogen (TN) as direct positive drivers of inorganic P dissolution. Collectively, the key biological mechanisms for leaching reduction involve inhibiting subsurface IP solubilization, optimizing surface OP mineralization, and enhancing P transport/starvation responses. Collectively, biochar applied alone offers the optimal balance between P retention and crop-available P supply in dryland purple soils, and provides mechanistic insights-through functional gene profiling-that can inform the design of more sustainable P fertilization and leaching control practices.},
}

@article {pmid42792653,
year = {2026},
author = {Azamfirei, L and Bica, D and Mihai, MA and Beata, B and Banescu, C},
title = {Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091910},
pmid = {42792653},
issn = {2227-9059},
abstract = {Background: Precision diagnostics are more and more important in intensive care units (ICUs), where rapid identification of infectious agents and antimicrobial resistance determinants is crucial for timely and appropriate treatment. Conventional microbiological methods are frequently limited by long turnaround times and reduced sensitivity, which may delay appropriate treatment. Nanopore sequencing allows rapid, direct, and long-read sequencing of DNA/RNA molecules without the need for amplification, avoiding biases introduced by NGS during amplification and library preparation and generating data in real time. Objectives: This narrative review aims to summarize current knowledge of nanopore technology in the ICU, discuss nanopore principles and current clinical applications in intensive care medicine, highlight its advantages and limitations, and explore future perspectives for integrating nanopore-based diagnostics into precision critical care. Methods: A literature search was performed using PubMed and Web of Science. The literature search was conducted with no lower restriction, covering English-language publications. Results: Nanopore sequencing enables real-time, long-read, single-molecule analysis of native nucleic acid molecules, rapid pathogen identification, antimicrobial resistance profiling, metagenomic analysis, and direct sequencing without amplification. Recent studies have proved the clinical utility of nanopore sequencing in critically ill patients with sepsis, bloodstream infections, hospital-acquired pneumonia, ventilator-associated pneumonia, and fungal and viral infections. Its portability, rapid turnaround time, and potential for point-of-care implementation make it particularly attractive for ICU settings. Conclusions: Nanopore sequencing technology represents a promising molecular diagnostic tool, but wider clinical implementation warrants further larger studies with clinical outcome endpoints, standardized bioinformatic pipelines, and clearer validation pathways.},
}

@article {pmid42792947,
year = {2026},
author = {Du, Q and Xing, L and Zhu, C and Li, P},
title = {Gut Microbiota and Metabolic Pathway Signatures for Inflammatory Bowel Disease Identified via Subject-Stratified Random Forest Based on the Longitudinal HMP2 Cohort.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091053},
pmid = {42792947},
issn = {2073-4425},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Random Forest ; *Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Feces/microbiology ; Female ; Machine Learning ; },
abstract = {Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10[-5] and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini-Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray-Curtis community variance (R[2] = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626-0.705, mean AUC = 0.665), all-significant-pathway model (0.645-0.712, mean AUC = 0.679), strict-pathway model (0.620-0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Random Forest
*Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Feces/microbiology
Female
Machine Learning

@article {pmid42793803,
year = {2026},
author = {Kim, SY and Lee, JE and Lee, DH and Kim, HY and Kim, KH and Jeong, H and Chung, C},
title = {Diagnostic Reassessment of a Pulmonary Mass Initially Suspected to Represent IgG4-Related Lung Disease: The Complementary Role of Tissue Metagenomic Sequencing.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/diagnostics16183018},
pmid = {42793803},
issn = {2075-4418},
support = {no. 2022R1A2C2010148//National Research Foundation of Korea/ ; no. HR20C0025//Korea Health Industry Development Institute/ ; },
abstract = {Background/Objectives: Pulmonary mass-like lesions may mimic malignancy, infection, or inflammatory disease, complicating diagnosis when radiologic, histopathologic, and microbiologic findings overlap. This case illustrates the importance of diagnostic reassessment when the clinical course and treatment response are not fully consistent with the initial diagnosis. Methods: A 69-year-old man with diabetes mellitus and mild emphysema presented with chronic cough, purulent sputum, and a recurrent left upper lobe mass. Computed tomography-guided biopsy revealed dense lymphoplasmacytic infiltration with eosinophils, fibrosis, and increased IgG4-positive plasma cells, leading to a presumptive diagnosis of IgG4-related lung disease. Limited improvement with steroid therapy and recurrent hemoptysis prompted multidisciplinary reassessment, including tissue metagenomic next-generation sequencing (mNGS). Results: Imaging findings were compatible with subacute invasive aspergillosis, although conventional fungal staining, culture, antigen testing, serologic studies, and bronchial washing analyses were negative. Tissue mNGS detected 348 low-abundance Aspergillus-derived reads, accounting for 0.03% of non-host reads. Following initiation of voriconazole, the lesion decreased from 47 mm to 32 mm within six weeks and regressed further thereafter. Symptoms resolved, and hemoptysis did not recur. Conclusions: This case highlights the importance of diagnostic reassessment when findings and treatment response do not fully support the initial diagnosis. Tissue mNGS may provide complementary evidence for probable subacute invasive aspergillosis when interpreted alongside radiologic findings, exclusion of alternative diagnoses, and treatment response.},
}

@article {pmid42794458,
year = {2026},
author = {Carini, F and Sorce, A and Ciuppa, ME and David, S and Giammanco, M and Di Carlo, P and Evola, S and Tomasello, G and Mulè, G and Carollo, C},
title = {Gut, Oral, and Fungal Microbiota in Hypertension: A Multi-Compartment Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188029},
pmid = {42794458},
issn = {1422-0067},
mesh = {Humans ; *Hypertension/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Mycobiome ; *Microbiota ; *Fungi ; },
abstract = {The gut microbiota is an established modulator of blood pressure, but the oral bacteriome and the fungal mycobiome have been examined largely in isolation from it and from each other. No previous synthesis has evaluated all three compartments within one analytical framework, or treated sex and ethnicity as primary analytical axes rather than adjustment covariates. Systematic review reported according to PRISMA 2020 and, for the synthesis, the SWiM guideline. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to 30 June 2026. Observational human studies in adults reporting gut, oral, or fungal microbiota data stratified by blood pressure status were eligible, together with Mendelian randomisation studies and studies with a nested experimental causal component. Two reviewers screened and extracted independently, with a third resolving disagreement. Risk of bias was assessed with the Newcastle-Ottawa Scale and certainty of evidence with GRADE adapted for exposure-outcome questions. Increased abundance of the Ruminococcus gnavus group was the most convergent taxon-level finding, replicated in three independent populations on two continents, including one prospective multi-ethnic cohort with full adjustment and correction for multiple comparisons (OR 1.07, 95% CI 1.01-1.14 for incident hypertension). In the oral compartment, depletion of the nitrate-reducing commensal Neisseria subflava converged across a United States prospective cohort and an Italian case-control study using unrelated methods, and salivary nitric oxide was approximately three-fold lower in hypertensive subjects. Depletion of the short-chain fatty acid producers Faecalibacterium and Roseburia and enrichment of Klebsiella were convergent but geographically restricted. Mycobiome evidence was contradictory: two studies reported fungal dysbiosis, one of them already at the pre-hypertensive stage, while a cross-cohort metagenome-wide study on two independent cohorts from Beijing and Dalian (N = 159 hypertensive patients, 101 healthy controls) identified 61 gut bacterial species with consistent altered abundance across both cohorts while finding no replicable mycobiome signal. Recurring across compartments and kingdoms was the collapse of microbial co-correlation networks in hypertension, alongside a dissociation between null alpha diversity and significant beta diversity. Associations differed by ethnicity within a single multi-ethnic cohort and were generally stronger in women. Certainty of evidence, assessed per individual convergent finding, was very low for every taxon-level finding and low for salivary nitric oxide; these ratings concern the attribution of hypertension to specific organisms, not the existence of a microbiota-hypertension association, which is supported at community level in every compartment examined and by experimental transfer models. That the microbiota differs in hypertension is well supported; which organisms are responsible is not. The most reproducible signal is structural rather than taxonomic, and conventional differential-abundance analysis is not designed to detect it. No individual microbial taxon is currently ready to serve as a marker of hypertension or to inform clinical practice.},
}

Humans
*Hypertension/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Mycobiome
*Microbiota
*Fungi

@article {pmid42794824,
year = {2026},
author = {Kim, M and Song, WH and Ju, HJ and Koh, YK and Kim, SJ and Lee, YB and Lee, M},
title = {Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188397},
pmid = {42794824},
issn = {1422-0067},
mesh = {Humans ; *Scabies/drug therapy/microbiology ; *Skin Microbiome ; *Metagenomics/methods ; Male ; Female ; *Skin/microbiology ; Shotgun Sequencing ; Sarcoptes scabiei ; Metagenome ; Adult ; *Microbiota ; },
abstract = {Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini-Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.},
}

Humans
*Scabies/drug therapy/microbiology
*Skin Microbiome
*Metagenomics/methods
Male
Female
*Skin/microbiology
Shotgun Sequencing
Sarcoptes scabiei
Metagenome
Adult
*Microbiota

@article {pmid42795339,
year = {2026},
author = {Carissimi, C and De Angelis, F and Laudadio, I and Fulci, V and Stronati, L and Manella, S and Alvaro, D and D'Andrea, G and Silecchia, G and Cardinale, V},
title = {Bile Microbiota Profiling in Obese and Non-Obese Patients: A Comparison of Shotgun Metagenomics and 16S rRNA Amplicon Sequencing.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091474},
pmid = {42795339},
issn = {2075-1729},
support = {PNC1221852F49EDDD//Grant Piano Nazionale Complementare Salute/ ; },
abstract = {Recent advances in metagenomics have expanded our ability to detect low-abundance microbial communities. While the gut remains the most densely populated microbial habitat, emerging evidence has proposed that microorganisms might also inhabit anatomical sites once considered sterile, such as the biliary system. We apply next-generation DNA sequencing to characterize the bacterial community of bile in obese and non-obese patients with symptomatic gallstones. Bile samples were collected from 64 patients (32 obese, 32 non-obese) undergoing elective cholecystectomy. We incorporated negative (sterile tubes) and positive (mock microbial community standard) controls to evaluate contamination risks. We applied both 16S rRNA gene amplicon and shotgun metagenomic sequencing. Both sequencing methods detected extremely low bacterial biomass in bile. Specifically, shotgun metagenomic sequencing identified bacterial DNA traces in only eight samples, displaying minimal community similarity. In the positive controls, our measurements confirmed the expected microbial community composition, and in the negative controls, no bacterial DNA was detected. In contrast, 16S rRNA gene sequencing showed bacterial DNA in all bile samples as well as in negative controls, suggesting a higher susceptibility to contamination. Our findings suggest that bile may not be consistently colonized by bacterial communities in uncomplicated gallstone disease.},
}

@article {pmid42795462,
year = {2026},
author = {Szili, K and Dézsi, C and Gulyás-Oldal, V and Sallai, D and Patay, G and Paschali, E and Nagy, S},
title = {Toward AI-Driven Detection of Asymptomatic Chronic Conditions from Stool Metagenomics and Dietary Data: A Multimodal Deep Learning Framework for T1DM, T2DM, MOS/PCOS, Cancer, and Autoimmune Disease.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091880},
pmid = {42795462},
issn = {2076-2607},
abstract = {Chronic non-communicable conditions-type 1 and type 2 diabetes mellitus (T1DM, T2DM), metabolic obesity syndrome (MOS), polycystic ovary syndrome (PCOS), colorectal and extra-intestinal cancers, and systemic autoimmune disease-share a prolonged asymptomatic phase during which conventional screening is invasive, insensitive, or resource-intensive. This review synthesizes the 2021-2026 literature on fecal microbiome-based artificial intelligence (AI) diagnostics across these conditions, extracting reported discrimination, validation strategy, microbial and short-chain fatty acid (SCFA) biomarkers, and cross-cohort reproducibility. Across the primary classifier studies tabulated here, reported areas under the curve (AUCs) span 0.76-0.99 under internal validation but 0.69-0.91 under external or cross-population validation; in the four studies reporting both, the median AUC falls from 0.875 to 0.810. Verified external-validation values include 0.82 for colorectal cancer, 0.79 for T2DM and 0.792 for discrimination of systemic lupus erythematosus from rheumatoid arthritis and controls. Clinical readiness turns on this internal-to-external gap more than on the headline AUC. We propose a multimodal deep learning architecture coupled with explainable AI; no component has been implemented or evaluated on data, and it is presented as a design proposal. Fecal-microbiome-based multimodal AI is technically feasible but clinically unvalidated, pending prospective, harmonized cross-cohort trials.},
}

@article {pmid42795487,
year = {2026},
author = {Che, M and Zhang, J and Kudelaiti, K and Zhang, J and Liusui, Y and Dong, Z},
title = {Effects of Co-Application of γ-Polyglutamic Acid and Chemical Fertilizer on Rhizosphere Microbial Community Structure and Function of Cotton at Different Growth Stages in an Arid Cotton Field.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091905},
pmid = {42795487},
issn = {2076-2607},
support = {2024D01A82//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Long-term excessive nitrogen application in arid cotton fields increases nitrate leaching risk during fallow and disrupts rhizosphere microecology. To clarify the cross-growth-stage regulatory effects of the biostimulant γ-polyglutamic acid (γ-PGA) combined with chemical fertilizer on rhizosphere microbial communities, we compared chemical fertilizer alone (NK) and γ-PGA plus chemical fertilizer (GT) using rhizosphere soils collected at boll-setting (August) and fallow (October), with physicochemical measurements and metagenomic sequencing technology. At boll-setting, GT lowered pH by 0.74 units compared with NK and increased NH4[+]-N, NO3[-]-N, and TN by 339.3%, 491.4%, and 23.0%, respectively. By fallow, GT increased TOC by 70.6% and maintained NH4[+]-N at 18.38 mg/kg, while NK accumulated 66.85 mg/kg NO3[-]-N. GT buffered post-harvest fungal community disturbance (Shannon: GT 4.06 vs. NK 2.80) and shifted bacterial communities toward oligotrophic taxa and archaea toward ammonium-preferring taxa. A metagenomic LEfSe analysis showed that GT was enriched in functional genes related to [Q]: Secondary metabolite biosynthesis, transport and catabolism, [T]: Signal transduction mechanisms, and [V]: Defense mechanisms, indicating a shift from resource acquisition to conservative maintenance. Mantel tests revealed that microbial functional profiles showed the strongest association with NH4[+]-N (r = 0.828 in August, r = 0.883 in October, p < 0.001). Thus, γ-PGA with chemical fertilizer stabilizes fallow rhizosphere microbial communities, reduces nutrient leaching, and promotes carbon-nitrogen co-retention.},
}

@article {pmid42795512,
year = {2026},
author = {Pan, S and Zheng, W and Feng, Z and Ouyang, Z and Ma, M and Huang, L and Wang, L and Wang, X and Quan, C},
title = {A Butyrate-Producing Probiotic, Clostridium butyricum DMZ-SG06, Improves Growth Performance, Immune Function and Gut Microbiota in Largemouth Bass (Micropterus salmoides).},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091931},
pmid = {42795512},
issn = {2076-2607},
support = {2022020332-JH2/1013//Department of Science and Technology of Liaoning Province/ ; },
abstract = {Intensive aquaculture and antibiotic overuse have rendered largemouth bass (Micropterus salmoides) prone to frequent mass mortalities and economic losses. Probiotics are promising antibiotic alternatives for improving intestinal health and immunity. This study evaluated a novel butyrate-producing strain Clostridium butyricum DMZ-SG06 to elucidate its growth-promoting and immunomodulatory mechanisms. Three dietary treatments were used: control (Con, basal diet), T1 (basal diet supplemented with 1 g C. butyricum powder containing 5 × 10[8] CFU per 10 g diet), and T2 (basal diet supplemented with 1 mL C. butyricum suspension containing 5 × 10[8] CFU per 10 g diet). A total of 270 healthy juvenile largemouth bass (5.63 ± 0.03 g) were randomly allocated to three groups (90 fish per group), with each group divided into three replicate tanks (60 × 40 × 34 cm) (30 fish per tank). Fish were fed the corresponding diets to apparent satiation for a 60-day rearing period. Results showed that T2 increased weight gain rate (WGR) by 11.35% compared with control (p < 0.05, 213.90 ± 12.30% vs. 192.10 ± 10.20%) and significantly improved the specific growth rate (SGR, p < 0.05), with T2 performing best. Probiotic treatments markedly improved intestinal morphology, nonspecific immune indices, and antioxidant status (p < 0.05), with T2 exerting the most prominent effects. C. butyricum DMZ-SG06 significantly reduced the levels of pro-inflammatory cytokines. For instance, TNF-α levels in T2 decreased 1.39-fold compared with the control group (128.57 ± 4.97 pg/g vs. 178.67 ± 7.80 pg/g, p < 0.05). Meanwhile, the levels of anti-inflammatory cytokines were upregulated. For example, IL-10 levels in T2 increased 1.32-fold relative to the control group (321.89 ± 15.03 pg/g vs. 244.31 ± 7.57 pg/g, p < 0.05). Metagenomic analysis revealed reduced Acinetobacter abundance, enriched beneficial genera (Lactobacillus, Parabacteroides, p < 0.05), and enhanced microbial functions related to the phosphotransferase system and galactose metabolism (p < 0.05). In conclusion, C. butyricum DMZ-SG06 promotes largemouth bass growth and intestinal health via butyrate metabolism, immune modulation, and microbiota remodeling. Notably, the liquid bacterial suspension formulation exerts a more significant effect on enhancing the fish's growth performance and intestinal health than the powder counterpart, supporting its application as a safe probiotic in antibiotic-free aquaculture.},
}

@article {pmid42795518,
year = {2026},
author = {Yang, J and Wang, Z and Wang, C and Li, Y and Niu, Y and Feng, J and Xie, S and Li, X},
title = {Metagenomic Insights into the Functional Profiles of Carbon, Nitrogen, and Phosphorus Cycles in Yuncheng Salt Lake Under Different Salinity Gradients.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091937},
pmid = {42795518},
issn = {2076-2607},
support = {202204051001035//the Special Fund for Science and Technology Innovation Teams of Shanxi Province/ ; 202303021222246; 202303021212258//the Fundamental Research Program of Shanxi Province/ ; YHYJ-2023003//the "Listed and Commanded" Project from Yuncheng Salt Lake Protection and Utilization Research Institute of Shanxi Province/ ; YQ-2023003//the Doctoral Research Start-up Project/ ; 32300111//the National Natural Science Foundation of China/ ; YCKJ-2024022//the Yuncheng City Science and Technology Program Project/ ; },
abstract = {Salinity is a key driver of microbial community structure and function in salt lake ecosystems, yet how it shapes functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling remains poorly understood. We collected metagenomic samples along a natural salinity gradient in Yuncheng Salt Lake and examined how salinity was associated with microbial taxonomic and functional diversity and with C, N, and P cycling genes. Both diversity metrics decreased significantly with increasing salinity and were positively correlated with each other. The composition and abundance of C, N, and P cycling genes differed significantly among the low-, medium-, and high-salinity groups. In carbon cycling, most carbon fixation genes were more abundant at higher salinity, whereas most carbon degradation genes were less abundant; within carbon fixation, reductive tricarboxylic acid (rTCA) cycle and Calvin cycle gene abundances were higher. In nitrogen cycling, nitrogen mineralization and assimilation genes were significantly more abundant. In phosphorus cycling, transporter and pyrimidine metabolism genes were more abundant, whereas the relative contribution of purine metabolism genes declined. Co-occurrence network analysis revealed dense positive co-occurrence associations among C, N, and P cycling genes, with mer, GLU, and ppk1 as highly connected genes. Mantel tests identified salinity and pH as the primary environmental factors associated with functional gene variation. These results suggest that salinity may regulate C, N, and P cycling genes partly by reshaping microbial community structure in salt lake ecosystems.},
}

@article {pmid42795531,
year = {2026},
author = {Zhang, YX and Wang, LX and Zhang, JG and Li, C and Wu, LF and Jiang, XF and Chun, Y},
title = {Sexual Propagation Enhances Tea Quality Through Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Camellia sinensis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091949},
pmid = {42795531},
issn = {2076-2607},
support = {32460785//National Natural Science Foundation of China，Grant No. 32460785/ ; 20241ZDD02045//Jiangxi Provincial Key Laboratory of Plantation and High-Valued Utilization of Specialty Fruit Trees and Tea/ ; 202301//Open Research Project of Jiangxi Intelligent Agricultural Machinery Equipment Engineering Research Center/ ; 202558-22380//Yingtan Municipal Science and Technology Plan Project/ ; YCTY202508//Integrated Pilot Project for Research, Development, Manufacturing, Promotion, and Application of Agricultural Machinery Equipment in Jiangxi Province/ ; },
abstract = {Tea quality is largely determined by the accumulation of specialized metabolites in fresh leaves, yet the effects of the propagation method on tea quality and its belowground ecological basis remain insufficiently understood. In this study, sexually propagated (SR) and asexually propagated (AR) tea plants were compared by integrating soil physicochemical analysis, leaf quality and physiological measurements, widely targeted metabolomics, and rhizosphere metagenomic profiling. Compared with AR, SR plants exhibited more favorable rhizosphere nutrient conditions, with soil organic matter, total nitrogen, alkali-hydrolyzable nitrogen, and available phosphorus increasing by 23.1%, 18.2%, 27.8%, and 161.5%, respectively, although available potassium decreased by 24.4%. SR leaves also contained higher dry matter, tea polyphenol, and soluble sugar contents, which increased by 11.5%, 58.8%, and 8.6%, respectively. In addition, superoxide dismutase, peroxidase, and indole-3-acetic acid oxidase activities were 30.4%, 92.0%, and 21.7% higher under SR, whereas hydrogen peroxide content remained unchanged. Metabolomic profiling revealed marked differences in leaf metabolic composition between the two propagation types, with differentially accumulated metabolites mainly enriched in flavonoid biosynthesis, phenolic acid metabolism, caffeine metabolism, carotenoid biosynthesis, plant hormone signaling, and α-linolenic acid metabolism. Rhizosphere metagenomic analysis further showed that SR was characterized by higher relative abundances of Actinomycetota, Pseudomonadota, Planctomycetota, Alphaproteobacteria, and Streptomycetales, together with distinct microbial functional profiles related to glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism. Significant correlations were identified between several SR-enriched microbial taxa and quality-related metabolites, particularly flavonoids and phenolic acids. Overall, under the present field conditions, sexual propagation was more favorable than asexual propagation for tea quality formation, as reflected by improved nitrogen and phosphorus availability, greater accumulation of quality-related metabolites, higher antioxidant enzyme activities, and distinct rhizosphere microbial carbon-metabolic potential. These findings provide an integrated soil-microbiome-metabolome perspective for understanding propagation-related differences in tea quality.},
}

@article {pmid42795541,
year = {2026},
author = {Li, Q and Wang, J and Wang, Z and Cheng, C and Bao, S and Chai, S and Dai, D and Wang, X and Song, Q and Chen, Y and Lv, J and Ma, Y and Sonam, T and Qiu, J and Wang, S},
title = {Segment-Specific Gut Microbiome and Bile Acid Profiles in Grazing and Stall-Fed Yaks.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091960},
pmid = {42795541},
issn = {2076-2607},
abstract = {The yak is an iconic ruminant of the Qinghai-Tibet Plateau, yet segment-specific variation in its intestinal microbial functional potential and bile acid profiles under different feeding systems remains insufficiently characterized. Six healthy adult male yaks with similar body weights (320 ± 30 kg) were assigned to grazing (G) or stall-feeding (S) systems, with three animals per group, for a 90-day trial comprising a 10-day adaptation period and an 80-day formal experimental period. The individual yak was considered the experimental unit, and intestinal segments sampled from the same animal were treated as repeated observations. Liver tissue and digesta from the duodenum, ileum, cecum, and colon were analyzed using targeted bile acid metabolomics and shotgun metagenomics. Principal coordinate analysis based on Bray-Curtis dissimilarities showed segment-associated clustering of microbial communities, with PCo1 and PCo2 explaining 65.5% and 18.9% of the total variation, respectively. ANOSIM identified a significant intestinal-segment effect on microbial community composition (R = 0.2208, BH-FDR = 0.0144), whereas the overall feeding-system effect was not significant (R = 0.3747, BH-FDR = 0.1200). No statistically significant feeding-system differences were detected in Shannon, Simpson, Chao1, or ACE indices within individual intestinal segments (BH-FDR ≥ 0.800), and PERMDISP detected no significant differences in within-group dispersion (BH-FDR ≥ 0.1682). Bacillota and Bacteroidota were the dominant phyla. Descriptive functional profiling showed higher mean ileal abundances of GH2 (0.0035 vs. 0.0026), GH3 (0.0029 vs. 0.0024), and GH43 (0.0021 vs. 0.0013) in grazing yaks, whereas the starch-associated GH13 family showed its highest mean abundance in the colon of stall-fed yaks. These metagenomic patterns represent predicted genomic functional potential rather than gene expression, enzyme activity, or metabolic flux. Cecal total bile acid concentration showed a nominal between-group difference (unadjusted Welch's p = 0.0109), but this difference did not remain significant after correction across the five anatomical sites (BH-FDR = 0.0545). In the colon, stall-fed yaks had a lower conjugated-to-unconjugated bile acid ratio and a higher secondary-to-primary bile acid ratio than grazing yaks (BH-FDR < 0.05). Feeding-system-associated descriptive patterns were observed in predicted microbial functional profiles, whereas statistically supported between-group differences were limited mainly to selected colonic bile acid ratios. Given the limited animal-level replication, these findings should be considered exploratory.},
}

@article {pmid42795547,
year = {2026},
author = {Yuan, L and Zhang, C and Li, W and Yi, J and Liu, C and Jin, W and Li, G and Wang, B and Li, S and Wang, H},
title = {Intestinal Microbiota Structure of Xichuan Black-Bone Chickens and Preliminary Evaluation of a Probiotic-Based Fecal Microbiota Substitute.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091966},
pmid = {42795547},
issn = {2076-2607},
support = {2026ZC75//Henan Academy of Agricultural Sciences/ ; 2026BX54//Henan Academy of Agricultural Sciences/ ; 2025XMYG04//Henan Academy of Agricultural Sciences/ ; },
abstract = {In this study, we aimed to explore the intestinal microbiota structure of Xichuan black-bone chickens (XBCs) and evaluate the effect of fecal microbiota substitute transplantation (FMST) by comparing it with traditional fecal microbiota transplantation (FMT). Metagenomic sequencing was used to analyze the microbiota composition and diversity of different intestinal segments (duodenum, jejunum, ileum, cecum, and rectum) of adult XBCs. Probiotic strains were subsequently isolated and screened from the cecal contents under anaerobic conditions to prepare FMST preparations. In total, 90 1-day-old XBCs were randomly divided into the FMT group, FMST group and control group (CK) for the transplantation experiment. The results revealed that the cecum had the highest species richness among all intestinal segments, with a mean species number of 7593.2. Three probiotic strains, namely, Lactobacillus crispatus, Weissella paramesenteroides and Bacillus amyloliquefaciens, were successfully screened and identified. In the transplantation experiment, the FMT group exhibited optimal α diversity of the cecal microbiota, while compared with the FMT group, the FMST group had significantly reduced expression of pro-inflammatory cytokines (IL-6, TNF-α, and IL-1β) and increased expression of intestinal tight junction proteins (claudin-1 and ZO-1). In conclusion, the cecum of XBCs has the most abundant microbial resources. Under the short-term intervention model tested herein, the custom FMST formulation delivers superior intestinal protective effects and shows promising potential as a standardized alternative to conventional FMT, which is highly important for the standardized application of fecal microbiota transplantation in poultry production.},
}

@article {pmid42795557,
year = {2026},
author = {Wu, P and Sang, Z and Zhang, G},
title = {Dual Engines of Adsorption and Biodegradation: Ammonium Nitrogen Removal and Mechanism Analysis by EM-Modified Corn Straw Biochar in Aqueous Solution.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091976},
pmid = {42795557},
issn = {2076-2607},
support = {PL2025D022//The Natural Science Foundation of Heilongjiang Province/ ; },
abstract = {Agricultural ammonium pollution from farmland drainage and low-value crop straw utilization are two critical rural environmental problems that cannot be solved by single remediation approaches. Herein, a novel composite was prepared by immobilizing effective microorganisms (EM) on corn straw biochar to construct a synergistic adsorption-biodegradation system, and its nitrogen removal mechanism was systematically investigated at structural and molecular levels. Metagenomic analysis detected a complete set of heterotrophic nitrification-aerobic denitrification (HN-AD) functional genes (amoA, hao, napA, nirK, norB, nosZ) in the isolated strain Bacillus thuringiensis A1, revealing the genetic potential of this strain for ammonium biodegradation. EM modification optimized biochar pore structure and increased the equilibrium adsorption capacity to 1.215 mg/g, which was 66.4% higher than that of pristine biochar (0.73 mg/g). Sterilization control tests indicated that physicochemical adsorption occupied the dominant position in ammonium removal, while microbial biodegradation acted as an auxiliary removal pathway. Importantly, the synergistic relationship between the two pathways should be interpreted cautiously, since autoclaving may subtly alter biochar physicochemical properties, and direct paired characterization of viable composites before and after sterilization is technically unavailable. Kinetic and thermodynamic results further validated the improved adsorption performance after modification. Overall, EM immobilization promoted ammonium adsorption via pore optimization, while pore-confined microbes achieved sustainable HN-AD biotransformation, jointly realizing synergistic nitrogen removal. This study provides a mechanistic reference for the optimized design and application of biochar-microbe composites in agricultural nitrogen pollution control.},
}

@article {pmid42795569,
year = {2026},
author = {Senok, A and Alghafri, R and Shouqair, D and Verma, S and Mohammed, L and Naji, M and Albastaki, A and Nassar, R and Everett, D and Goering, R and Khan, M},
title = {Aircraft Wastewater as a Sentinel for Transboundary Antimicrobial Resistance: An Integrated Genomic Approach.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091988},
pmid = {42795569},
issn = {2076-2607},
support = {AJF-NIH-1-MBRU//This work was funded by Grant# AJF-NIH-1-MBRU as part of the UAE-NIH Collaborative Re-search Initiative (UAE-NIH-CRI) which comprises four collaborating UAE institutes: Al Jalila Foundation, Mohammed Bin Rashid University of Medicine and Health Sciences,/ ; },
abstract = {Aircraft wastewater (AWW) provides a composite environmental matrix reflecting passengers from diverse geographic origins and may serve as a surveillance tool for AMR monitoring. To characterize microbial community composition, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and genome-resolved features of AWW. Samples (N = 10) were collected from long-haul flights arriving in the UAE between October 2024 and February 2025. Shotgun metagenomic sequencing and high-throughput quantitative PCR (HT-qPCR) were performed. Metagenome-assembled genomes (MAGs) were reconstructed. Shotgun metagenomics identified 752 bacterial species dominated by gut-associated families, including Lachnospiraceae and Ruminococcaceae. A total of 345 ARGs were detected, with tetracycline resistance genes being most abundant. Regional variation in resistome composition was supported by permutational multivariate analysis of variance (PERMANOVA, p = 0.010), and principal coordinate analysis indicated separation by flight-origin region. MAG reconstruction recovered 1012 genomes, with 85.4% resolved to species level. MAG-based annotation identified 280 VFGs corresponding to 116 non-redundant virulence genes. HT-qPCR confirmed the widespread presence of key ARG classes and mobile genetic elements across samples, in keeping with metagenomic findings. AWW contains diverse microbial communities and AMR determinants. Genome-resolved analysis provided organism-level context for resistome and virulome characterization, confirming AWW as an environmental matrix for monitoring transboundary AMR dynamics.},
}

@article {pmid42795596,
year = {2026},
author = {Wang, J and Huangfu, S and Li, R and Li, H and He, H and Chang, B and Ma, H and Ma, H and Zhang, J and Hou, R and Song, H and Yang, X},
title = {Metagenomic Insights into Microbial Functional Potential Associated with Soil Carbon, Nitrogen, and Phosphorus Cycling Along an Elevational Gradient in a Warm-Temperate Forest.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092015},
pmid = {42795596},
issn = {2076-2607},
support = {32301401//National Natural Science Foundation of China/ ; 31670630//National Natural Science Foundation of China/ ; 2026CYJSTX07-15//Modern Agro-industry Technology Research System/ ; 202404021301049//The Special Project for Guiding the Transformation of Scientific and Technological Achievements in Shanxi Province/ ; SXBYKY2022037//Scientific Research projects for doctoral graduates and postdoctoral researchers working in Shanxi Province/ ; },
abstract = {Soil microbial functional potential is crucial to maintaining forest productivity and ecosystem functions. However, how microbially mediated soil nutrient cycling responds to environmental changes, particularly those caused by variations in elevation, remains poorly understood. Using the natural temperature gradient in a temperate mountain forest, this study investigated the differences in functional microbial groups and functional genes involved in soil carbon, nitrogen and phosphorus cycling along the elevation gradient, and analyzed the associations between environmental factors and these differences. The results showed that the low-elevation gradient (LE) had significantly higher abundances of genes involved in carbon degradation (pfkC, pgi1, and LSC1) but significantly lower abundances of those involved in carbon fixation (K18602, K18603, and K18604). Compared with the high-elevation gradient (HE), the LE had a significantly higher abundance of the nitrogen-cycle gene involved in organic degradation and synthesis (nao), but significantly lower abundances of denitrification (norB) and dissimilatory nitrate reduction genes (narG, narI, and napC). The abundances of the key genes involved in phosphorus metabolism (aphA and purO) were significantly higher at HE than at LE, whereas the abundance of the key gene associated with phosphorus transport (phnT) was significantly lower. The composition of the microbial community at the phylum level involved in carbon, nitrogen and phosphorus cycling at different elevations was similar, but the relative abundance of Thermoproteota and Nitrospirota increased significantly at HE. The annual average temperature, pH and carbon acquisition enzymes (β-glucosidase and β-D-cellobiosidase) were significantly associated with microbial community composition and functional genes related to carbon, nitrogen and phosphorus cycles. Additionally, genes involved in the carbon, nitrogen and phosphorus cycles were closely related through synergy and antagonism, especially the metabolic pathways encoded by purO, phnT and nrfA. These results provide metagenomic insights into the response patterns of microbial functional potential associated with soil carbon, nitrogen, and phosphorus cycling along an elevational gradient in a warm-temperate forest.},
}

@article {pmid42795597,
year = {2026},
author = {Chen, H and Xu, B and Xie, Q and Gu, Z and Guo, S and Chen, S},
title = {Seasonal Variations in Microbial Community Structure and Function in the Waters Along the Yangtze-to-Huaihe Water Diversion Project According to Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092016},
pmid = {42795597},
issn = {2076-2607},
support = {2024AH051079//The key project of natural science research of Anhui Provincial Education Department/ ; 2023AH010039//The Anhui Provincial University Innovation Team Project, Digital Agriculture Innovation Team/ ; 2025AHGXZK40116//The Youth Project of Natural Science Research of Anhui Provincial Education Department/ ; X2025xqkc002//The Anqing Normal University Graduate Education Quality Project/ ; },
abstract = {Water diversion projects can alleviate the uneven spatiotemporal distribution of water resources, but they may also impact functions of aquatic ecosystems in the waters along the route. Despite their importance, the temporal and spatial changes in multi-domain microbial community structure and function along the route remain poorly understood. Metagenomics was employed to investigate the community structure and function of bacteria, archaea, and fungi in the aquatic environments along the Yangtze-to-Huaihe water diversion project in winter and summer seasons. The results showed that seasonal variations may drive a trade-off in the species diversity of bacterial and fungal communities. Seasonal variations altered microbial communities (especially for the bacteria), and exerted a greater influence on community structure than spatial factors. Microbial community composition was more sensitive to seasonal fluctuations than functional genes. The species spatial turnover played a dominant role in shaping microbial communities (especially for winter) in both seasons. Archaea, bacteria, fungi and KEGG functional genes all exhibited a positive correlation with some environmental factors in summer but not in winter. PLS-SEM indicated that water quality and microbial composition directly significantly impacted functional genes. This study offers a theoretical basis for maintaining the stability of water ecological microorganisms in water transfer projects.},
}

@article {pmid42795606,
year = {2026},
author = {Méndez-Rodríguez, A and Ledesma, J and López-González, C and Zarza, H and López-Wilchis, R and Labiod, N and Cuesta, I and Casas, I and Echevarría, JE and Vázquez, A and Juste, J},
title = {Virome Diversity in Three Bat Species in Different Environments in Southern Spain.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092025},
pmid = {42795606},
issn = {2076-2607},
support = {PLEC2021-007968//NEXTHREAT/ ; //European Union NextGeneration EU/PRTR funds/ ; },
abstract = {Viruses represent a major component of global biodiversity and are integral to ecological and evolutionary processes shaping host populations and communities. Bats, with high species richness and ecological diversity, provide a system to examine how host traits and environmental context structure viral communities. Here, we characterize viral diversity from three bat species (Pipistrellus kuhlii, Cnephaeus isabellinus, and Nyctalus lasiopterus) using samples across two environments in southern Spain: a well-preserved Mediterranean forest (Sierras de Cazorla, Segura, and Las Villas Natural Park, CSVNP) and a human-modified wetland-agrosystem mosaic (Doñana National Park, DNP). Metagenomics detected 72 eukaryotic virus species, including viruses reported in mammals, insects, arachnids, and plants. Viral richness and composition varied among samples, bat species, and environments. Samples of P. kuhlii exhibited the highest richness, driven by insect-associated viruses. C. isabellinus showed a higher contribution of vertebrate-related viruses, whereas N. lasiopterus exhibited the lowest richness. CSVNP samples showed higher viral richness and more exclusive taxa, whereas DNP samples exhibited lower richness, with a greater contribution of arthropod-associated viruses, potentially reflecting prey communities. Despite this, diversity metrics were similar between environments, indicating structurally comparable communities composed of distinct taxa. Bat viromes appear to be associated with host ecology, trophic behavior, and environmental context.},
}

@article {pmid42795609,
year = {2026},
author = {Cui, Y and Lu, S and Su, D and Huang, Z},
title = {Multiple Phosphonate Degradation Pathways in Amphidinium carterae-Associated Bacteria Potentially Contribute to Host Adaptation to Phosphorus Limitation.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092028},
pmid = {42795609},
issn = {2076-2607},
support = {42306167//National Natural Science Foundation of China/ ; 2023J01896//Fujian Provincial Department of Science and Technology/ ; },
abstract = {Phosphonates in the ocean can serve as an alternative phosphorus (P) source for microorganisms when phosphate is scarce. Dinoflagellates cannot utilize phosphonates, but some associated bacteria can degrade these compounds and release phosphate. However, the community composition of these bacteria and their phosphonate degradation pathways remain poorly understood. In this study, the dinoflagellate Amphidinium carterae was cultured with 2-aminoethylphosphonic acid (2-AEP) as the exclusive P source. Metagenomic and genomic analyses were conducted to identify bacterial taxa and genes related to phosphonate utilization (phn genes). Specific strains were isolated from 2-AEP cultures to characterize phosphonate degradation gene clusters. Ten of the 20 most abundant genera were found to possess the genetic potential for phosphonate utilization, with Labrenzia, Phycocomes, and Pseudosulfitobacter as the dominant genera. The identified phn genes constituted multiple pathways, including the C-P lyase, PhnW-PhnX, and PhnW-PhnY-PhnA pathways, indicating that A. carterae-associated bacteria can utilize phosphonates through diverse mechanisms, with some strains even possessing more than one pathway. Five isolated bacterial strains were confirmed to be capable of degrading 2-AEP. These findings underscore the ecological significance of bacterial diversity and metabolic versatility in helping dinoflagellate hosts adapt to P scarcity, providing novel insights into bacteria-algae interactions and marine P cycling.},
}

@article {pmid42795614,
year = {2026},
author = {Correia, LN and Correia, A and Bessa, LJ},
title = {Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092033},
pmid = {42795614},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) represents one of the foremost global public health threats, undermining the efficacy of antibiotic therapies across all clinical disciplines, including dentistry. The oral cavity, housing one of the most diverse microbial ecosystems in the human body, contains a largely underappreciated reservoir of antibiotic resistance genes (ARGs), collectively defined as the oral resistome. This review synthesises current evidence on the oral resistome across five thematic areas. First, we contextualise the global burden of AMR, highlighting its scale and implications for oral healthcare. Second, we define the oral resistome and characterise its composition, distribution across oral microhabitats, and the principal determinants that govern its structure and dynamics. Third, we critically appraise metagenomic approaches, from early culture-based and PCR-targeted methods to shotgun metagenomics and functional screening, that have expanded the resolution of resistome characterisation. Fourth, we examine multi-omics integration, including genomics, transcriptomics, and metabolomics, and its capacity to reveal the ecological and molecular drivers of resistance within the oral ecosystem. Finally, we explore how resistome profiling can inform precision oral health, enabling individualised antimicrobial stewardship, microbiome-based risk stratification, and patient-tailored preventive and therapeutic strategies in the era of personalised dentistry.},
}

@article {pmid42795646,
year = {2026},
author = {Wu, Y and Feng, Y and Wu, B and Gao, Y and Xu, J},
title = {Effects of Chlorella pyrenoidosa Amendment on Tetracycline-Copper Dissipation, Soil Microbial Communities, and Tetracycline Resistance Genes.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092065},
pmid = {42795646},
issn = {2076-2607},
support = {QNPY202104//Shenyang University of Technology Cultivation Fund/ ; 202563379//Science and Technology Commissioner Project of the Department of Science and Technology of Liaoning Province/ ; },
abstract = {Tetracycline (TC)-copper (Cu) co-contamination can impair soil functioning and intensify selection for antibiotic resistance. In a 49-day microcosm experiment, we evaluated the effects of Chlorella pyrenoidosa supplementation on soils treated with TC (0, 30, or 100 mg·kg[-1]) and Cu (0, 100, or 500 mg·kg[-1]). TC removal, extractable Cu, soil physicochemical properties, enzyme activities, tetracycline resistance genes (TRGs), and microbial community composition were assessed. In unamended contaminated microcosms, TC dissipation ranged from 22.7% to 43.5%, whereas C. pyrenoidosa amendment increased TC dissipation to 49.9-73.5%. The addition also reduced extractable Cu by 35.6-50.6%, partially restored dehydrogenase and catalase activities, and altered bacterial community structure. Metagenomic analysis showed that tetX was the predominant TRG detected and that algal supplementation was associated with lower total TRG signals and reduced relative abundances of several pollution-associated taxa, including Rhodanobacter. Correlation analyses revealed associations among TRGs, microbial taxa, and treatment conditions but did not establish direct host-gene relationships or horizontal gene transfer. Overall, C. pyrenoidosa application enhanced TC removal and Cu immobilization and was associated with reduced enrichment of the tetracycline resistome.},
}

@article {pmid42795661,
year = {2026},
author = {Vacaras, C and Vacaras, V and Nistor, C and Jucan, C and Furdui, IM and Vesa, SC and Strilciuc, S and Ștefănescu, E and Chira, D and Rafila, A and Muresanu, DF},
title = {Longitudinal Stability of the Gut Microbiota in Relapsing-Remitting Multiple Sclerosis: A Prospective Observational Study.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092080},
pmid = {42795661},
issn = {2076-2607},
support = {//Foundation for the Study of Nanoneurosciences and Neuroregeneration and by the Romanian Society of Microbiology./ ; },
abstract = {The gut microbiota plays a key role in immune regulation in multiple sclerosis (MS), yet longitudinal data on microbiome dynamics and their relationships with disability and biomarkers remain limited. This study aimed to identify longitudinal gut microbiome changes in patients with relapsing-remitting multiple sclerosis (RRMS) and their association with disability and specific serum biomarkers, including predicted metabolic pathways. In this prospective longitudinal study, 29 treatment-naïve RRMS patients were evaluated at baseline and after one year of disease-modifying therapy. Clinical assessments included the Expanded Disability Status Scale (EDSS) and disability tests. Serum glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), and S100B protein concentrations were measured at both visits. Gut microbiota composition was characterized by shotgun metagenomic sequencing, including taxonomic composition, diversity measures, functional pathways, gut metabolic modules, and gut-brain modules. In the 29 patients, overall gut microbiota composition and diversity remained stable during follow-up. Although EDSS progression was associated with a trend toward greater microbiome instability, this association did not reach statistical significance. Several bacterial taxa and predicted metabolic pathways showed nominal associations with disability, but were not significant after correction. GFAP levels increased significantly over time, whereas NfL levels decreased and S100B levels remained unchanged. Early RRMS is characterized by a stable gut microbiome during the first year of treatment. Exploratory taxonomic and functional associations did not remain significant after correction for multiple testing, highlighting the need for larger longitudinal cohorts.},
}

@article {pmid42795676,
year = {2026},
author = {Divyashri, G and Hutti, H and Madduri Venkata, LP and Kumar, BP and Yachie, A and Ghosh, S},
title = {Multidimensional Physiological and Gut Microbiome Profiling Identifies Subtle Physiological Patterns in an Apparently Healthy Aging Indian Cohort: A Cross-Sectional Observational Study.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092097},
pmid = {42795676},
issn = {2076-2607},
abstract = {Aging is characterized by gradual shifts in cellular and physiological processes, even in individuals who remain apparently clinically healthy. These changes reflect a coordinated decline in metabolic efficiency, immune regulation, organ function, psychological resilience, and sleep integrity, domains increasingly recognized as interconnected determinants of apparently healthy aging. This study explored age- and sex-associated patterns in multidimensional physiological domains and gut microbiota features among 45 apparently healthy middle-aged and elderly participants across four age-sex groups (middle-aged males, n = 13; middle-aged females, n = 11; elderly males, n = 13; elderly females, n = 8). Comprehensive clinical, metabolic, inflammatory, hepato-renal, psychological, and sleep parameters were standardized into domain-specific Z-scores, which were integrated into a composite multidimensional physiological health index (MPHI), a systems-level physiological index developed as a proxy for physiological processes associated with mitochondrial function and apparently healthy aging rather than a direct measure of mitochondrial biology. Whole-metagenome sequencing and MetaPhlAn-based taxonomic profiling were used to characterize gut microbiota composition and diversity. Despite no statistically significant overall differences among the four age-sex groups in multivariate analysis (MANOVA, p = 0.103) and gut microbial community structure (PERMANOVA, p = 0.651), descriptive variation was observed across several physiological domains, while microbiota-host associations remained exploratory and nominal after FDR correction. Middle-aged males showed comparatively less favorable metabolic and inflammatory profiles, while selected psychosocial and sleep-related measures showed variation across the age-sex groups, particularly among elderly females. Principal component analysis (PCA) of domain scores indicated multidimensional physiological variation influenced by inflammatory, metabolic, and hepato-renal indices, although substantial overlap was observed among the age-sex groups. The MPHI showed descriptive variation across the groups, with elderly males showing the highest composite scores and middle-aged females the lowest. Overall, the apparently healthy cohort showed subtle variation across interconnected physiological domains in the absence of overt differences in gut microbial community structure. These findings support the potential utility of composite physiological indices for exploratory characterization of multidimensional physiological variation during aging, while highlighting the need for validation in larger independent cohorts and against direct mitochondrial biomarkers.},
}

@article {pmid42796680,
year = {2026},
author = {Wu, M and Wang, J and Xie, Z and Xiang, Y and Yao, C and Liu, M and Shang, Y and Li, C and Ma, X and Tuo, W and Du, H and Huang, L and Cai, Q},
title = {Mapping the Evolution of Diagnostic Research on Mycoplasma pneumoniae: A Bibliometric Analysis (1980-2025).},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090912},
pmid = {42796680},
issn = {2076-0817},
support = {2024AFB968//Natural Science Foundation of Hubei Municipal Health Commission/ ; WX21M03//Medical Research Project of Wuhan Municipal Health Commission/ ; },
mesh = {*Mycoplasma pneumoniae/isolation & purification/genetics ; *Pneumonia, Mycoplasma/diagnosis/microbiology/epidemiology ; *Bibliometrics ; Humans ; },
abstract = {Mycoplasma pneumoniae (MP) is a major etiological agent of respiratory tract infections. This study sought to systematically map the current landscape, thematic progression, collaborative networks, and emerging priorities in diagnostic research on MP infections. Data were extracted from the Web of Science Core Collection from 1 January 1980, to 12 May 2025. Bibliometric and visualization analyses across countries/regions, institutions, authors, co-cited references, keywords, and disease-related terms were conducted using CiteSpace, VOSviewer, Pajek, and SCImago Graphica. Analysis of 2093 articles revealed consistent growth in research output related to MP diagnosis. Most publications originated in China (n = 623). The United States Centers for Disease Control and Prevention demonstrated the greatest total link strength in institutional collaboration networks. Key high-frequency keywords reflect the ongoing transition from traditional pathogen confirmation to integrated diagnostic approaches incorporating molecular testing, macrolide-resistance detection, co-infection evaluation, and risk stratification. Current research has increasingly targeted diagnostic optimization and the early identification of refractory or severe Mycoplasma pneumoniae pneumonia. This study provides a structured overview of the knowledge structure, thematic evolution, and technological frontiers in MP diagnostic research. The findings highlight key challenges, thereby offering guidance for interdisciplinary innovation and informing future diagnostic research directions.},
}

*Mycoplasma pneumoniae/isolation & purification/genetics
*Pneumonia, Mycoplasma/diagnosis/microbiology/epidemiology
*Bibliometrics
Humans

@article {pmid42796698,
year = {2026},
author = {Huang, J and Zhao, H and Wang, F and Zeng, B and Ma, Z and Wang, R and Yang, Y and Amier, M and Yilihaer, B and Lu, Y},
title = {Whole-Genome Sequencing and Intestinal Metagenome Sequencing Revealed the Carriage and Transmission of Salmonella enterica in Xinjiang, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090930},
pmid = {42796698},
issn = {2076-0817},
mesh = {*Salmonella enterica/genetics/isolation & purification/classification ; Humans ; China/epidemiology ; Whole Genome Sequencing ; *Salmonella Infections/transmission/microbiology/epidemiology ; *Metagenome ; Phylogeny ; *Gastrointestinal Microbiome ; Feces/microbiology ; Virulence Factors/genetics ; *Carrier State/microbiology/epidemiology ; Metagenomics ; Genome, Bacterial ; },
abstract = {Background:Salmonella enterica, a major foodborne pathogen, poses a severe global public health threat. However, data regarding its carriage characteristics, transmission patterns, and association with intestinal microbiota in healthy populations of Xinjiang, China, remain insufficient, limiting the formulation of targeted salmonellosis prevention and control strategies. Methods: In this study, 31 Salmonella enterica strains isolated from more than 2000 healthy individuals in Urumqi were subjected to whole-genome sequencing to analyze serovars, antimicrobial resistance (AMR) genes, and virulence genes. Meanwhile, metagenomic sequencing was performed on 50 fecal samples (culture negative) from 2000 healthy individuals to investigate intestinal microbiota structure, Salmonella enterica prevalence, and related microbial taxa. Results: The results showed that 60% of samples (30/50) were positive by the read-based criterion (≥1000 Salmonella-specific reads), while the assembly-verified criterion (≥1000 reads and contigs > 1 kb) confirmed Salmonella-specific sequences in 12% (6/50). Among the 31 culture-confirmed isolates, Salmonella Typhimurium and Salmonella Paratyphi B were the dominant serovars, together accounting for 60%. All isolates harbored core virulence genes for Type III secretion system and adhesion factors, with low AMR gene carriage and no multidrug-resistant strains. Phylogenetic analysis showed that Urumqi-derived isolates were distributed across multiple genomic clusters, suggesting active inter-regional circulation of S. enterica within the available dataset. Salmonella enterica carriage did not affect gut microbial α-diversity but altered community composition, with Escherichia coli, Shigella flexneri, and Klebsiella pneumoniae as key associated taxa. Conclusions: This study found that Urumqi-derived isolates are widely distributed across genomic clusters in Xinjiang, with a unique local transmission chain identified, though definitive source attribution requires further geographically balanced sampling. Salmonella enterica carriage exhibited ecological niche synergy with intestinal Enterobacteriaceae, but did not significantly affect gut microbial diversity.},
}

*Salmonella enterica/genetics/isolation & purification/classification
Humans
China/epidemiology
Whole Genome Sequencing
*Salmonella Infections/transmission/microbiology/epidemiology
*Metagenome
Phylogeny
*Gastrointestinal Microbiome
Feces/microbiology
Virulence Factors/genetics
*Carrier State/microbiology/epidemiology
Metagenomics
Genome, Bacterial

@article {pmid42796710,
year = {2026},
author = {Prątnicka, A and Kraberger, S and Varsani, A and Stenzel, T},
title = {New Parvovirus and Other Swab-Associated Viruses Identified in the Eurasian Goshawk (Astur gentilis).},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090942},
pmid = {42796710},
issn = {2076-0817},
support = {//Ministry of Science and Higher Education/ ; },
mesh = {Animals ; *Parvovirus/genetics/isolation & purification/classification ; Phylogeny ; Genome, Viral ; *Parvoviridae Infections/veterinary/virology ; *Bird Diseases/virology ; Open Reading Frames ; Metagenomics ; },
abstract = {Cloacal swabs were collected from 12 Eurasian goshawk chicks during routine veterinary inspections to evaluate the gut-associated virome of goshawks used for falconry. The material was used for metagenomic screening with high-throughput sequencing. Sequences belonging to several viral families (Poxviridae, Circoviridae, Anelloviridae, Retroviridae, Parvoviridae and Astroviridae) were detected and their occurrence differed across samples G1-G12. Most of the identified sequences were highly similar to those of viruses that infect poultry, suggesting a probable alimentary transmission route. Two complete genomes of closely related chicken astroviruses, most likely strains belonging to subgroup Biii, were identified. Their ORF2 proteins shared 98.78% amino acid identity. Another complete genome was identified as that of pigeon circovirus with 98.96% nucleotide identity to a strain previously reported from China. A parvovirus genome sequence, distinct from those of known members of the genus Aveparvovirus genus was also identified. This parvovirus genome sequence represents approximately 86% of the average aveparvovirus genome length (5422 bp) and contains three open reading frames. The sequence lacks the 3' region of the capsid gene is missing and the 3' UTR. The NS1 protein sequence of this virus shares 52.42% amino acid identity with that of its closest relative, the nonstructural protein of silver pheasant parvovirus. These findings suggest that parvovirus infection may occur in birds of prey and that the detected virus may represent a novel member of the genus Aveparvovirus. The infected bird showed no clinical symptoms during sampling; thus, the role of this parvovirus in raptor pathology as well as the possibility that it was of dietary origin remains unknown and requires further investigation.},
}

Animals
*Parvovirus/genetics/isolation & purification/classification
Phylogeny
Genome, Viral
*Parvoviridae Infections/veterinary/virology
*Bird Diseases/virology
Open Reading Frames
Metagenomics

@article {pmid42796718,
year = {2026},
author = {Láng, L and Kemenesi, G and Novák, J and Lanszki, Z and Görföl, T},
title = {Viral Metagenomic Analysis of Bat Fly Pupae.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090950},
pmid = {42796718},
issn = {2076-0817},
support = {FK146793//National Research, Development and Innovation Office/ ; 003_2025_PTE_RK/57//University of Pecs/ ; },
mesh = {Animals ; *Chiroptera/parasitology/virology ; *Metagenomics/methods ; *Pupa/virology ; *Diptera/virology ; *Viruses/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Hungary ; *Metagenome ; Phylogeny ; Genome, Viral ; },
abstract = {Bats are important reservoirs of zoonotic viruses, yet the role of their obligate ectoparasites, particularly bat flies, in viral maintenance and transmission remains poorly understood. Although viral sequences have been detected in adult bat flies, vertical transmission to their offspring has not been investigated. Here, we present the first metagenomic analysis of bat fly pupae to assess transgenerational viral persistence. Eighty pupae associated with a large Miniopterus schreibersii colony in Hungary were analyzed by next-generation sequencing. We generated more than 69 million reads and over 28,000 assembled contigs. Although initial classification suggested the presence of viral sequences, none were confirmed following sequence-level validation. These findings highlight the substantial potential for false-positive viral assignments in metagenomic datasets and the importance of rigorous post-classification validation. While our results provide no evidence that vertical transmission is a major mechanism of viral maintenance in bat-bat fly systems, this conclusion is limited by the relatively small sample size and single sampling occasion. Highly divergent or low-abundance viruses may also have remained undetected. Broader sampling across seasons and locations is therefore needed to assess the generality of these findings. Nevertheless, this study provides a valuable first step toward understanding potential transgenerational viral persistence in bat flies and highlights the need for complementary approaches to clarify their role in viral transmission.},
}

Animals
*Chiroptera/parasitology/virology
*Metagenomics/methods
*Pupa/virology
*Diptera/virology
*Viruses/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Hungary
*Metagenome
Phylogeny
Genome, Viral

@article {pmid42796731,
year = {2026},
author = {Stîngă, RI and Nadăş, GC},
title = {Biofilm Dynamics and Antimicrobial Resistance in Rabbit Odontogenic Infections: A One Health Perspective.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090963},
pmid = {42796731},
issn = {2076-0817},
mesh = {Animals ; *Biofilms/drug effects/growth & development ; Rabbits ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/drug effects ; Humans ; },
abstract = {Rabbit odontogenic abscesses are among the most challenging chronic infections encountered in exotic animal medicine because of their polymicrobial etiology, biofilm-associated persistence, and poor response to conventional antimicrobial therapy. Biofilm formation plays a central role in disease pathogenesis by promoting bacterial adhesion, extracellular polymeric substance (EPS) production, quorum sensing (bacterial cell-to-cell communication), metabolic heterogeneity, and the persister-cell formation (transiently antibiotic-tolerant bacterial subpopulations), collectively reducing antimicrobial susceptibility and contributing to treatment failure and recurrence. In addition to biofilm-mediated tolerance, antimicrobial resistance (AMR) further complicates disease management through mechanisms including horizontal gene transfer, efflux pump activation, enzymatic antibiotic degradation, reduced membrane permeability, and target modification. This review summarizes current knowledge on the microbiology, biofilm dynamics, and resistance mechanisms associated with rabbit odontogenic infections while examining recent advances in molecular diagnostics, including culture-independent sequencing technologies, metagenomics, and advanced imaging approaches. Current and emerging anti-biofilm strategies, such as local antimicrobial delivery systems, enzymatic biofilm disruption, quorum-sensing inhibitors, bacteriophage therapy, antimicrobial peptides, photodynamic therapy, and nanotechnology-based approaches, are critically discussed in the context of their potential application in rabbits. Comparative evidence from human endodontic infections and other veterinary biofilm-associated diseases highlights the translational relevance of rabbit odontogenic abscesses as a naturally occurring model for chronic polymicrobial infections. Finally, key research gaps are identified, emphasizing the need for standardized experimental models, integrated multi-omics analyses, combining genomic, transcriptomic, proteomic, and metabolomic data, longitudinal clinical investigations, and evidence-based antimicrobial stewardship. By integrating microbiology, biofilm biology, antimicrobial resistance, and One Health concepts, this review provides a comprehensive framework to support future research and improve the diagnosis, treatment, and prevention of rabbit odontogenic infections.},
}

Animals
*Biofilms/drug effects/growth & development
Rabbits
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology/therapeutic use
Bacteria/drug effects
Humans

@article {pmid42797815,
year = {2026},
author = {Moreira, G and Silva, E and Mourão, J and Mesquita, JR},
title = {First European Identification of a Partial Tacheng Tick Virus 8-like Underscores the Hidden Burden of Tick-Borne Flavivirus-like Viruses.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18090984},
pmid = {42797815},
issn = {1999-4915},
support = {2025.05151.BD//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Flavivirus/genetics/classification/isolation & purification ; Portugal ; Dermacentor/virology ; *Ticks/virology ; },
abstract = {Tick-associated viruses are an underexplored component of global viromes, and highly divergent RNA viruses often remain undetected due to low abundance and sequence divergence. Tacheng tick virus 8 (TcTV8) is a poorly characterized RNA flavivirus-like virus originally reported from Dermacentor-associated ticks in China, with few subsequent reports and no confirmed detections outside Asia. Here, we report the detection and partial genomic characterization of a TcTV8-like virus in ticks collected from Portugal. Sequence-independent (SISPA) nanopore sequencing of individual ticks recovered three partial fragments (~2.7 kb, ~14% of the reference genome; ~30% of the reference covered at ≥1×), which shared high amino-acid identity with the TcTV8 polyprotein, including a methyltransferase-region domain. Phylogenetic analysis placed the Portuguese sequence within the TcTV8 lineage. Read-level classification and coverage analysis further support the presence of this virus in the positive sample. These findings represent, to our knowledge, the first detection of a TcTV8-like virus in European ticks, extending its known geographic range beyond Asia. The detection of this cryptic viral lineage highlights the need for broader tick virome surveillance to better understand the diversity, evolution, and ecology of flavivirus-like viruses.},
}

Animals
Phylogeny
Genome, Viral
*Flavivirus/genetics/classification/isolation & purification
Portugal
Dermacentor/virology
*Ticks/virology

@article {pmid42797835,
year = {2026},
author = {Yang, Q and Ye, L and Wang, L and Zhang, Y and Zhu, Y and Shen, J},
title = {Clinical Characteristics, Viral Etiology, Management, and Prognosis of Pediatric Fulminant Myocarditis: A 10-Year Single-Center Study.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091004},
pmid = {42797835},
issn = {1999-4915},
support = {L242052//Beijing Natural Science Foundation/ ; None//Nantong Municipal Key Medical Discipline./ ; },
mesh = {Humans ; *Myocarditis/virology/therapy/diagnosis/mortality/etiology ; Female ; Male ; Prognosis ; Retrospective Studies ; Child ; Child, Preschool ; *Virus Diseases/virology/complications/therapy ; Infant ; Prospective Studies ; },
abstract = {Background: Fulminant myocarditis (FM) is a life-threatening inflammatory cardiac disease in children, frequently triggered by viral infections. Although mechanical circulatory support has improved short-term survival, data on viral etiology and long-term outcomes remain limited, particularly in Asian populations. Methods: We conducted a mixed retrospective-prospective analysis of pediatric FM patients at the Children's Hospital of Fudan University from 2015 to 2025. Clinical data from 2015 to 2023 were collected retrospectively, while data from 2024 onward were collected prospectively. Clinical data, microbiological findings (PCR and metagenomic next-generation sequencing), treatment strategies, and outcomes were extracted from electronic medical records. Follow-up data for survivors were collected through December 2025. Results: A total of 53 children with FM were included. Median age was 91.5 months; 43.4% were male, and 56.6% were female. Common presenting symptoms included fever (64.2%) and vomiting (56.6%). Microbiological evidence was identified in 11 patients (20.8%), with rhinovirus (5.7%) and influenza virus (5.7%) being the most frequent, followed by enterovirus (3.8%) in peripheral specimens. During hospitalization, 79.2% required mechanical ventilation, 64.2% received extracorporeal membrane oxygenation (ECMO), and 45.3% underwent continuous renal replacement therapy (CRRT). Intravenous immunoglobulin (IVIG) was administered to 84.9%. In-hospital mortality was 13.2% (7/53), and 17.0% (9/53) of patients were discharged against medical advice (DAMA). Among 35 followed patients (median 12.4 months), most achieved favorable cardiac recovery; however, persistent conduction abnormalities, structural cardiac changes, and neurological sequelae were observed in a minority. Conclusions: Pediatric FM carries substantial in-hospital morbidity and resource utilization, despite favorable recovery rates in most survivors. The low pathogen detection rate in peripheral blood and the lack of endomyocardial tissue sampling preclude definitive conclusions regarding the underlying etiology, whether active viral replication or immune-mediated injury predominates. Endomyocardial biopsy-based investigations are urgently needed to clarify the underlying pathobiology.},
}

Humans
*Myocarditis/virology/therapy/diagnosis/mortality/etiology
Female
Male
Prognosis
Retrospective Studies
Child
Child, Preschool
*Virus Diseases/virology/complications/therapy
Infant
Prospective Studies

@article {pmid42797867,
year = {2026},
author = {Kushugulova, A and Kamzayeva, N and Kozhakhmetov, S and Vinogradova, E and Jarmukhanov, Z and Mukhanbetzhanov, N and Kovenskiy, A and Kossumov, A and Rakhmankulova, A and Ukybassova, T},
title = {Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091036},
pmid = {42797867},
issn = {1999-4915},
support = {BR24992853//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; Female ; *Human Papillomavirus Viruses/genetics/isolation & purification/classification ; *Cervix Uteri/virology/pathology/microbiology ; *Vagina/virology/microbiology ; *Papillomavirus Infections/virology ; *Dysbiosis/virology/microbiology ; *Virome ; Bacteria/classification/genetics ; Bacteriophages/genetics ; Microbiota ; Metagenomics ; Papillomaviridae/genetics ; },
abstract = {The cervicovaginal virome remains poorly characterized in relation to human papillomavirus (HPV) infection and bacterial community structure. We performed shotgun metagenomic sequencing of 311 cervicovaginal specimens from a Kazakhstani cohort spanning seven groups defined by HPV status and cervical cytology. Viral community composition differed according to HPV status, with increasing representation of the oncogenic Alphapapillomavirus 9 clade across more abnormal cytological categories. Predicted phage functional profiles also differed between NILM HPV-positive and NILM HPV-negative women. Integrase, excisionase, transcriptional repressor, anti-repressor Ant, and amidase annotations showed differential prevalence after false-discovery-rate correction. Auxiliary metabolic and host-interaction genes associated with nucleotide metabolism, DNA modification, anti-restriction functions, and toxin-antitoxin systems were also differentially represented. Stratification by bacterial community state type revealed contrasting predicted functional repertoires, with toxin-antitoxin-associated annotations enriched in Lactobacillus crispatus-dominated communities and anti-restriction-associated annotations enriched in Gardnerella vaginalis-dominated communities. These findings identify associations between HPV status, bacterial community structure, and cervicovaginal viral composition and predicted phage functions. Longitudinal and experimental studies are required to determine the directionality and biological activity of these associations.},
}

Humans
Female
*Human Papillomavirus Viruses/genetics/isolation & purification/classification
*Cervix Uteri/virology/pathology/microbiology
*Vagina/virology/microbiology
*Papillomavirus Infections/virology
*Dysbiosis/virology/microbiology
*Virome
Bacteria/classification/genetics
Bacteriophages/genetics
Microbiota
Metagenomics
Papillomaviridae/genetics

@article {pmid42797872,
year = {2026},
author = {Ran, W and He, X and Luo, D},
title = {Viral Metagenomic Sequencing Reveals Viral Codetection Patterns in Children with Respiratory Syncytial Virus Infection.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091041},
pmid = {42797872},
issn = {1999-4915},
support = {2024YFC2311502//National Key R&D Program of China/ ; IVDC-202404//Young Scholar Scientific Research Foundation of IVDC/ ; },
mesh = {Humans ; *Respiratory Syncytial Virus Infections/virology ; *Metagenomics ; *Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification ; *Coinfection/virology ; Child, Preschool ; *Viruses/genetics/classification/isolation & purification ; Infant ; Female ; Male ; Child ; Metagenome ; Genome, Viral ; Genotype ; Phylogeny ; Respiratory Tract Infections/virology ; Nasopharynx/virology ; },
abstract = {Respiratory syncytial virus (RSV) is a leading cause of pediatric respiratory infections, yet the frequency and composition of viral codetections in affected children have not been extensively profiled using unbiased sequencing approaches. Here, we performed viral metagenomic sequencing on nasopharyngeal swabs collected from 42 pediatric patients with confirmed RSV infection to characterize the codetection landscape. RSV was detected and genotyped in all specimens. Beyond RSV, we identified nine additional human respiratory viruses coexisting across the cohort; several of these fall outside the scope of routine diagnostic panels, although their clinical significance remains uncertain. Codetections were the rule rather than the exception: 30 of 42 samples harbored at least three viruses, with up to seven distinct viruses detected in a single case. These findings underscore the taxonomic breadth and polymicrobial complexity of respiratory infections in children. Our results describe the viral codetection landscape in RSV-infected children, revealing a broader spectrum of co-occurring viruses than typically captured by targeted diagnostics, although the clinical significance of most codetections remains uncertain. These findings highlight the polymicrobial complexity of RSV infections and underscore the need for prospective studies to determine which codetections are clinically meaningful.},
}

Humans
*Respiratory Syncytial Virus Infections/virology
*Metagenomics
*Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification
*Coinfection/virology
Child, Preschool
*Viruses/genetics/classification/isolation & purification
Infant
Female
Male
Child
Metagenome
Genome, Viral
Genotype
Phylogeny
Respiratory Tract Infections/virology
Nasopharynx/virology

@article {pmid42797912,
year = {2026},
author = {Morua, E and Criado-Mesas, L and Chumaceiro, G and López Palma, M and Malinverni, R and Sanseverino, W and Aiese Cigliano, R and Cuyas, L and Matías-Hernández, L},
title = {Impact of Combined Botanical Functional Ingredients on the Canine Gut Microbiome.},
journal = {Veterinary sciences},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/vetsci13090877},
pmid = {42797912},
issn = {2306-7381},
support = {EXP00143151/SNEO-201134//Centre for Industrial Technological Development/ ; Torres Quevedo Programme//Ministry of Science and Information/ ; },
abstract = {The canine gut microbiome plays a key role in digestive, immune, and metabolic health and is increasingly recognized as an important indicator of overall animal well-being. Medicinal and Aromatic Plants are emerging as a promising approach to support intestinal balance through modulation of the gut microbiome. This pilot study evaluated the effects of Aloe vera, Artemisia annua, and Curcuma longa on the gut microbiome of healthy dogs. The study included eighteen healthy dogs, divided into an Experimental group (n = 9) and a Control group (n = 9). Dogs in the Experimental group received a daily combination of the three plants for 30 days, while Control dogs received microcrystalline cellulose as a placebo. Fecal samples were collected on Day 30 and analyzed using shotgun metagenomic sequencing. Differential abundance analysis revealed an enrichment of taxa associated with short-chain fatty acid production in the Experimental group, including Megasphaera elsdenii, Blautia, Butyricimonas, Bacteroides, and Phascolarctobacterium, together with a reduction in opportunistic and dysbiosis-associated taxa, such as Enterocloster bolteae, Anaerobiospirillum spp., and Stenotrophomonas maltophilia. Functional profiling showed a reduction in pathways related to virulence-associated mechanisms and iron siderophore systems, alongside an increase in pathways associated with GABA and putrescine metabolism and serine endopeptidase activity. Overall, these findings suggest that supplementation with these functional botanical ingredients may promote a more balanced and functionally beneficial gut microbiome in healthy dogs.},
}

@article {pmid42797975,
year = {2026},
author = {Tsekova, AA and Kantserova, NP and Lysenko, LA and Sukhovskaya, IV},
title = {Core, Resident, and Transient Members of the Trout Gut Microbiome: Dietary, Environmental, Stress and Pathogen/Antibiotic Modulation.},
journal = {Veterinary sciences},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/vetsci13090940},
pmid = {42797975},
issn = {2306-7381},
support = {25-24-01228//Russian Science Foundation/ ; },
abstract = {The gut microbiome of rainbow trout plays a crucial role in fish nutrition, immune function and stress resistance, making it a key factor in aquaculture sustainability. This review systematizes metagenomic data that enable the distinction between resident and transient microbial communities and the identification of a core microbiome. At the phylum level, the core is predominantly composed of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Mycoplasmatota, with additional phyla detected depending on the gut region and methodological approach. Diet-induced changes are often rapid and reversible: insect meal and certain probiotics increase the abundance of beneficial Bacillota and suppress opportunists. Unlike dietary shifts, chronic stressors-particularly elevated temperatures and antibiotic treatment-can override these benefits, causing a persistent alpha diversity reduction, overgrowth of Pseudomonadata, and depletion of key commensals. The autochthonous mucosal microbial community is more resilient to short-term fluctuations but can be irreversibly altered by prolonged stress or antimicrobial therapy, leading to dysbiosis and reduced colonization resistance. A holistic understanding of host-microbe-environment interactions is essential for establishing dynamic reference ranges for a "healthy" microbiome. Such knowledge would enable early detection of dysbiosis and support the rational development of functional feeds and probiotics in commercial trout farming.},
}

@article {pmid42798051,
year = {2026},
author = {Wang, X and Bian, J and Xu, J and Li, Y and Ji, S and Qin, L and Meng, Q},
title = {Lymphocutaneous sporotrichosis: A case report from southeastern China and review of the literature.},
journal = {Medicine},
volume = {105},
number = {39},
pages = {e50812},
doi = {10.1097/MD.0000000000050812},
pmid = {42798051},
issn = {1536-5964},
mesh = {Humans ; *Sporotrichosis/diagnosis/drug therapy/microbiology ; Male ; Middle Aged ; *Sporothrix/isolation & purification/genetics ; Itraconazole/therapeutic use/administration & dosage ; Antifungal Agents/therapeutic use/administration & dosage ; China ; High-Throughput Nucleotide Sequencing ; Debridement ; },
abstract = {RATIONALE: Sporotrichosis is a dermatomycosis caused by the dimorphic fungus Sporothrix schenckii sensu lato. The traditional gold standard for the definitive diagnosis of the disease is fungal culture. Our case describes the patient diagnosed lymphocutaneous sporotrichosis through the metagenomic next-generation sequencing (mNGS) quickly.

PATIENT CONCERNS: A 53-year-old male presented with protracted multiple ulcerated lesions. The pathological analysis of his skin biopsy specimen was inflammatory reaction, routine hematological and biochemistry examinations, the imaging of heart, lung and stomach were normal.

DIAGNOSES: The wounds were received debridement in our ward. Sporothrix schenckii was identified by the culture and the mNGS of the wound pus.

INTERVENTIONS: Following definitive diagnosis, oral itraconazole was administered to the patient; meanwhile, regular clinical follow-up visits and reevaluations were scheduled for continuous monitoring.

OUTCOMES: The patient recovered well, and no signs of recurrence were detected during follow-up.

LESSONS: This case illustrates that mNGS, as an emerging molecular biological diagnostic technique, holds significant diagnostic value for the rapid identification of sporotrichosis. Timely and accurate diagnosis is essential for achieving favorable clinical outcomes.},
}

Humans
*Sporotrichosis/diagnosis/drug therapy/microbiology
Male
Middle Aged
*Sporothrix/isolation & purification/genetics
Itraconazole/therapeutic use/administration & dosage
Antifungal Agents/therapeutic use/administration & dosage
China
High-Throughput Nucleotide Sequencing
Debridement

@article {pmid42798109,
year = {2026},
author = {Wang, R and Li, N and Tian, J and Zeng, X},
title = {Clinical characteristics of Chlamydia psittaci pneumonia diagnosed by next-generation sequencing: An observational study.},
journal = {Medicine},
volume = {105},
number = {39},
pages = {e50850},
doi = {10.1097/MD.0000000000050850},
pmid = {42798109},
issn = {1536-5964},
support = {2025XYLH172//University-Hospital Joint Fund Project of Hunan University of Chinese Medicine/ ; },
mesh = {Humans ; Female ; *Chlamydophila psittaci/genetics/isolation & purification ; Male ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Psittacosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Hyponatremia ; },
abstract = {Chlamydia psittaci pneumonia is often underdiagnosed due to nonspecific presentation and limited diagnostic tools, with scarce data on the comparative utility of metagenomic next-generation sequencing (mNGS) versus targeted next-generation sequencing (tNGS) in this setting. This study aimed to characterize the clinical features of C psittaci pneumonia and provide comparative data on mNGS and tNGS, with emphasis on diagnostic accessibility, while also quantifying underreported features such as hyponatremia. A retrospective analysis was conducted on 10 patients with C Psittaci pneumonia admitted to the Department of Respiratory and Critical Care Medicine at the Second People's Hospital of Hunan Province between January 2022 and February 2025. Clinical data, laboratory tests, imaging findings, treatment regimens, and outcomes were collected and analyzed descriptively. Among the 10 patients (6 male, 4 female; median age 70 years), 9 had underlying comorbidities and 2 had severe pneumonia. A history of avian exposure was reported in 40% of cases. All patients presented with fever (mean temperature: 39.5 ± 0.7°C), accompanied by nonspecific symptoms including cough (n = 4), chills (n = 5), anorexia (n = 5), and myalgia (n = 3). Laboratory findings revealed normal white blood cell counts in 8 cases, while lymphocytopenia, elevated inflammatory markers, abnormal liver enzymes, and hyponatremia were observed in 9 patients. Imaging predominantly showed unilateral lung consolidation (n = 5) or ground-glass opacities (n = 3), with pleural involvement in 9 cases. mNGS and tNGS were performed on bronchoalveolar lavage fluid in 5 cases each; tNGS provides a more cost-saving and rapid alternative. Post-diagnosis, treatment with moxifloxacin, doxycycline, or omadacycline for 10 to 21 days yielded generally favorable outcomes. C psittaci pneumonia is characterized by high fever and systemic symptoms, with imaging typically showing unilateral consolidation, ground-glass opacities, or mass-like lesions with pleural involvement, accompanied by liver injury, elevated inflammatory markers, and hyponatremia. Both tNGS and mNGS are effective diagnostic tools, and tNGS provides a more cost-saving and rapid alternative. Early treatment with fluoroquinolones or tetracyclines confers significant therapeutic benefits.},
}

Humans
Female
*Chlamydophila psittaci/genetics/isolation & purification
Male
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Psittacosis/diagnosis/drug therapy/microbiology
Aged
Middle Aged
Anti-Bacterial Agents/therapeutic use
Hyponatremia

@article {pmid42798262,
year = {2026},
author = {Scionti, K and Václavková, I and Schoissengeier, V and Wagner, KH},
title = {Investigating Overweight and Obesity Risk in Shift Workers Using Omics Technologies.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70233},
doi = {10.1111/obr.70233},
pmid = {42798262},
issn = {1467-789X},
support = {101080788//EU Commission/ ; },
abstract = {Night shift workers are at higher risk of developing overweight and obesity. The disruption of the physiological circadian rhythm leads to metabolic alterations, such as decreased insulin sensitivity, increased adipogenesis, and inflammation, with effects on their health and leading, among other diseases, to obesity. Omics technologies represent novel investigation tools to understand in depth the biological mechanisms behind the circadian disruption and consequent effects on metabolism. The data obtained from the use of omics technologies in the field of transcriptomics, proteomics, metabolomics, and metagenomics reveal the involvement of molecular pathways in the circadian disruption due to shift work and give comprehensive insights into the most crucial molecules, such as clock genes, hormones, or microorganisms responsible for a downstream cascade effect. There is a clear need to further explore obesity risk in night shift workers through omics-based studies, particularly in human field studies. Many of the investigations so far have focused on animal models with simulated circadian disruption. Upcoming omics data can undoubtedly support the advancement toward a personalized approach that could protect the health of night shift workers. This review focuses on studies supported by omics technologies on circadian disruption and metabolic alterations leading to obesity or increasing its risk.},
}

@article {pmid42798402,
year = {2026},
author = {Ahn, J and Kim, M and Min, SH and Bae, HG and Bae, JY and Kwon, J and Yi, H and Park, DH},
title = {Fecal microbiota transplantation from duodenal light stimulation-conditioned donors is associated with improved glucose tolerance and intestinal incretin-related remodeling in diabetic Goto-Kakizaki rats.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900693},
pmid = {42798402},
issn = {2235-2988},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Rats ; *Diabetes Mellitus, Type 2/therapy/metabolism ; *Incretins/metabolism ; *Gastrointestinal Microbiome ; *Duodenum/microbiology ; Male ; Glucose Tolerance Test ; Disease Models, Animal ; Blood Glucose ; Feces/microbiology ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder characterized by impaired glucose homeostasis and β-cell dysfunction. Emerging evidence suggests that the gut microbiota-incretin axis may contribute to metabolic regulation. However, whether microbiota from duodenal light stimulation (DLS)-conditioned donors can influence metabolic phenotypes via fecal microbiota transplantation (FMT) remains unclear.

METHODS: We evaluated whether FMT from DLS-conditioned donors was associated with metabolic and intestinal changes in diabetic GK (Goto-Kakizaki) rats. Recipients received FMT from week -2 to week 0 and were then followed for 7 weeks after the final FMT dose. Metabolic phenotyping, intestinal histology, short-chain fatty acid (SCFA) profiling, and shotgun metagenomic profiling of bacterial and viral communities were performed.

RESULTS: FMT recipients showed within-group improvement in OGTT glucose profiles, without significant changes in fasting glucose levels. Total glucose AUC0-120 was significantly reduced within the FMT group in the within-group (period) comparison; however, the group × period interaction was not significant, indicating no statistically significant longitudinal between-group treatment effect. Early GLP-1 responses showed a modest increasing trend in FMT recipients, whereas total GLP-1 AUC0-120 was not significantly changed. HOMA-β (homeostatic model assessment of β-cell function) increased within the FMT group, and pancreatic insulin-positive area was greater in FMT recipients than in controls at the study endpoint. Intestinal remodeling was evident, including an increased villus:crypt ratio and increased colonic GLP-1-positive cells. FMT was associated with fecal bacteriome differences, including one FDR-significant taxon and several nominally associated taxa, such as Akkermansia muciniphila and Xylanibacter rodentium. No significant global shift in fecal virome composition was observed, although selected viral taxa showed nominal group-associated differences that did not remain significant after FDR correction. Exploratory network analysis suggested group-specific bacteriome-virome association patterns after FMT.

CONCLUSION: FMT from DLS-conditioned donors was associated with improved glucose tolerance, intestinal incretin-related remodeling, increased pancreatic insulin-positive area, and fecal bacteriome differences in diabetic GK rats based on within-group longitudinal changes for the glucose- and β-cell-related outcomes, for which the group × period interactions were not significant, whereas the histological and microbiome differences reflect cross-sectional between-group comparisons at the study endpoint. These findings support a hypothesis-generating link between donor-conditioned FMT, intestinal remodeling, and microbiome-associated metabolic regulation, while further studies are required to define DLS-specific and donor-derived effects.},
}

Animals
*Fecal Microbiota Transplantation/methods
Rats
*Diabetes Mellitus, Type 2/therapy/metabolism
*Incretins/metabolism
*Gastrointestinal Microbiome
*Duodenum/microbiology
Male
Glucose Tolerance Test
Disease Models, Animal
Blood Glucose
Feces/microbiology

@article {pmid42798678,
year = {2026},
author = {Yang, L and Wang, Y and Zhao, K and Ke, Y and Gao, X and Liu, E and Chai, Z},
title = {Metagenomics reveals the effects of potassium fertilizer gradients on soil phosphorus-cycling microbial communities and functional genes, and their relationship with yield.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1918329},
doi = {10.3389/fmicb.2026.1918329},
pmid = {42798678},
issn = {1664-302X},
abstract = {The rational application of potassium (K) is essential for soil nutrient transformation in orchards. Microbial communities drive phosphorus (P) transformation and activation, yet their responses to potassium (K) gradients and the underlying regulation of functional potential remain unclear. Accordingly, a field trial was conducted on 7- to 8-year-old Korla pear trees to evaluate changes in microbial community structure and functional potential across topsoil (0-20 cm) and subsoil (40-60 cm) layers under different K gradients (0, 75, 150, and 225 kg/ha K2O). Results indicated that microbial communities under K treatments were distinctly separated from the control. Microbial responses in subsoil were more pronounced than in topsoil, with soil available phosphorus and pH associated with these shifts. At the functional gene level, under K150, microorganisms were characterized by a reduced relative abundance of genes annotated for phosphorus-acquisition-related functions (ugpE, phy) and genes associated with nucleotide biosynthesis (guaA). With increasing K application, the relative abundance of phosphorus-cycling genes in microbial communities exhibited notable differences across K gradients. Soil available K and microbial biomass nitrogen were closely linked to these functional gene profile variations. Furthermore, K fertilization correlated with fruit yield variations, peaking under K150. PLS-PM showed that the community composition of phosphorus-cycling microorganisms and related functional genes had positive relationships with fruit yield. Overall, these results suggest that the K150 treatment corresponded to a favorable balance between fruit yield and microbial genetic potential for nutrient cycling under the conditions of this study.},
}

@article {pmid42798947,
year = {2026},
author = {Yin, Y and Ma, Y and Wang, Y and Gao, P and Jia, C and Li, C and Yang, Q and Zhang, F and Bo, H and Wang, R and Chen, J},
title = {Chemical heterogeneity and mixed pollution are associated with microbial functional potential across soils in a coal mining subsidence landscape.},
journal = {RSC advances},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6ra03694e},
pmid = {42798947},
issn = {2046-2069},
abstract = {Coal mining subsidence occurs when underground coal extraction removes structural support for overlying strata, causing ground deformation and localized surface collapse. However, it remains unclear whether soils across a subsidence landscape respond in a similar way, or whether different habitats develop distinct nutrient conditions and mixtures of heavy metals and PAHs that are associated with different microbial communities and carbon, nitrogen, and sulfur cycling potentials. Local ecological risks would be overlooked if the entire subsidence zone is generalized as one disturbed ecosystem. Here, we sampled surface soils (0-20 cm) in September 2024 from four ordered habitats along a local subsidence associated topographic habitat in Jining, China: subsidence soil (SS), ditch soil adjacent to the subsidence area (SL), ditch soil near farmland (SR), and farmland soil (SF). We quantified soil physicochemical properties, heavy metals, polycyclic aromatic hydrocarbons (PAHs), and enzyme activities, and characterized bacterial and fungal communities and functional genes using metagenomic sequencing and downstream multivariate analyses. Soil chemical conditions differed consistently across habitats, with clear separation along nutrient related gradients and distinct contaminant profiles among habitats. Microbial α-diversity and β-diversity showed specific habitat patterns, and community composition differed among habitats for both bacteria and fungi. Functional profiles related to carbon, nitrogen, and sulfur cycling also varied across habitats, indicating that chemical heterogeneity and mixed pollution coincided with reconfiguration of microbial metabolic potential at the pathway and gene levels. Ordination analyses further showed that microbial community structure and functional potential were strongly associated with soil physicochemical gradients and pollutant variables, while enzyme activities covaried with key soil properties and contaminants. Our results indicate that coal mining subsidence landscapes contain multiple habitat-specific chemical and contaminant filters rather than a single uniform "subsidence effect", supporting chemically informed, habitat-stratified assessment of soil condition and microbial functional potential in mining-affected ecosystems.},
}

@article {pmid42799486,
year = {2026},
author = {Ibrahim, AD and Ibrahim, UB and Abdulkadir, N and Dandare, SU and Rao, JR},
title = {Microbial niches at the One Health interface: linking environmental factors, biomes, and disease dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1800305},
doi = {10.3389/fmicb.2026.1800305},
pmid = {42799486},
issn = {1664-302X},
abstract = {Microbial communities shape life at every stratum of environmental hierarchy, ranging from a wide spectrum of functionalities such as nutrient cycling processes that support ecosystem functioning in soil biome to those of intricate balance between disease causal and responsive immune defenses in animals. This review explores the roles of microbial niches in shaping pathogen persistence, antimicrobial resistance (AMR) dissemination, and host-microbe interactions at the human-animal-environment interface. Emphasis is placed on microbial community assembly, environmental drivers of pathogen survival, zoonotic reservoirs, and the contribution of metagenomics and genome-resolved approaches, including metagenome-assembled genomes (MAGs). We examine how microbial diversity is structured by environmental factors, host behaviors, and microbial interactions, with particular attention to the conditions that allow pathogens and antimicrobial resistance genes to emerge or persist. The review highlights how abiotic and biotic factors regulate microbial succession and disease spread across interconnected ecosystems. Literature used in this review was retrieved through a comprehensive search of peer-reviewed publications using major scientific databases using relevant search terms. Findings from this review demonstrate that microbial niches are not passive habitats but dynamic systems that regulate microbial adaptation, pathogen invasion, and ecosystem resilience. Recent advances in metagenomics, genome-resolved metagenomics, and MAG reconstruction and multi-omics technologies have improved the detection and characterization of unculturable microorganisms, antimicrobial resistance genes, and complex microbial interactions. Nevertheless, important knowledge gaps remain regarding how microbial communities respond to environmental pressures and how these responses influence pathogen persistence and antimicrobial resistance dissemination. Therefore, sustained investment in interdisciplinary One Health and MAG-based research, especially in under-resourced regions, will assist in building a resilient and equitable preparedness against emerging infectious diseases and AMR threats.},
}

@article {pmid42799671,
year = {2026},
author = {Joyce, GH and Zhang, X and Leu, AO and Gumulya, Y and Guo, J and Tyson, GW and Hu, S and McIlroy, SJ},
title = {Arsenate reduction coupled to anaerobic oxidation of methane by members of the Methanoperedenaceae.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag251},
pmid = {42799671},
issn = {1751-7370},
abstract = {Anaerobic methanotrophic 'Candidatus Methanoperedenaceae' play a key role in mitigating methane emissions from freshwater sediments. Members of the family are metabolically versatile, with species coupling anaerobic oxidation of methane (AOM) to the reduction of nitrate, metal oxides and/or humic compounds. Metagenomic analyses have indicated further uncharacterised metabolic diversity, including the potential for AOM coupled to arsenate reduction (As-AOM). While As-AOM has been confirmed as an important methane sink and contributor to arsenic mobilisation in freshwater environments, the underlying microbiological mechanisms remain to be empirically demonstrated. In this study stoichiometric coupling of dissimilatory arsenate reduction to methane oxidation was demonstrated using enrichment cultures of the uncultured type species 'Ca. Methanoperedens nitroreducens'. Meta-omics revealed that arsenate oxidoreductases were exclusively encoded by 'Ca. M. nitroreducens' and upregulated under As-AOM conditions, confirming this species was directly responsible. These findings expand our understanding of 'Ca. Methanoperedenaceae' physiology and demonstrate microbial mechanisms underpinning arsenic mobilisation in freshwater systems, with important implications for climate and public health.},
}

@article {pmid42785439,
year = {2026},
author = {Wang, W and Beever, J and Cho, S and Li, X},
title = {Long-read metagenomic characterization of the microbial DNA and resistome recovered from a peracetic acid immersion chiller in a commercial poultry processing facility: a pilot study.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100931},
doi = {10.1016/j.jfp.2026.100931},
pmid = {42785439},
issn = {1944-9097},
abstract = {Peracetic acid (PAA)-based immersion chillers are a critical pathogen intervention in commercial poultry processing, yet the microbial DNA recoverable from these systems remains poorly characterized. Here, we applied long-read Oxford Nanopore Technology (ONT) metagenomics to characterize the taxonomic composition, resistance gene content and mobile element context of the microbial DNA recovered from the mid-stage immersion chiller of a commercial poultry processing facility. From 14.47 GB of sequencing data (median Q-score 19.1), we reconstructed three near-complete metagenome-assembled genomes (MAGs) assigned to the putative species Comamonas sp., Flavobacterium sp., and Pseudomonas veronii (completeness >99.5%), each encoding oxidative stress defense, mercury detoxification, and efflux gene repertoires. Assembly graph analysis revealed a high-depth Tn21-family transposon junction node shared between contigs binned to Comamonas sp. and P. veronii, indicating that the genetic determinants recovered from these two genomes occur within a common mobile-element context. In addition, forty-four circular contigs were recovered, including one classified as a near-complete Myoviridae phage genome (1.45% of assembled bases). Community-level resistome profiling identified a prevalent mercury resistance (mer) cluster spanning multiple genera, alongside the biocide resistance gene qacE and antibiotic resistance genes on reads taxonomically assigned to Salmonella and Escherichia. These findings describe the resistance gene content and genomic organization of the DNA recoverable from a single immersion chiller. Because total DNA metagenomics cannot distinguish viable from inactivated cells, no inference regarding microbial survival, selection or ongoing gene transfer is drawn. Nevertheless, these pilot findings provide a foundation for viability‑resolved and multisite investigations that can more fully define microbial dynamics in immersion chillers.},
}

@article {pmid42785505,
year = {2026},
author = {Jiang, Y and Liu, B and Ding, Y and Li, L and Li, Z and Ren, Y and Zhong, C and Chen, J and Cui, X and Lu, A and Liu, J},
title = {Mineral-supported microbial functional differentiation across a vertical gradient in a vanadium-titanium magnetite mine.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125725},
doi = {10.1016/j.envres.2026.125725},
pmid = {42785505},
issn = {1096-0953},
abstract = {Vanadium-titanium magnetite (VTM) mines are often associated with metal contamination, organic carbon depletion, and ecological degradation, yet how indigenous microbiomes respond to vertical geochemical heterogeneity remains poorly understood. Here, we investigated a ∼260 m vertical gradient in the Zhulan Iron Mine, China, by integrating elemental and mineralogical analyses with 16S rRNA gene amplicon and metagenomic profiling. Pronounced vertical stratification was observed. The lower-elevation section was enriched in vanadium (V) and Fe(II)-bearing minerals and harbored microbial communities with lower diversity but a more highly connected co-occurrence network. Representative lower-section taxa, including Thiobacillus, Sulfuricaulis, and Chloroflexota members, were linked to functional potentials for V-associated redox transformation, Fe/S metabolism, extracellular electron transfer, and autotrophic carbon fixation. These patterns suggest that Fe(II)-bearing minerals, particularly magnetite, may serve as potential inorganic electron sources supporting mineral-based lithotrophy and carbon fixation under metal-rich and organic-carbon-limited conditions. In contrast, the upper-elevation section exhibited lower V stress, higher microbial diversity, sparse vegetation, and enrichment of heterotrophic and plant- associated taxa, such as Sphingomonas, Flavisolibacter, and Actinomycetota, indicating a shift toward plant-supported microbial functions during early ecological recovery. Overall, this study links vertical geochemical stratification to microbial functional differentiation and highlights indigenous mineral-microbe interactions as a potential basis for targeted, low-input restoration strategies in metal-contaminated mining ecosystems.},
}

@article {pmid42785511,
year = {2026},
author = {Imaizumi, K and Nozaki, R and Kondo, H and Hirono, I},
title = {A dominant, genome-reduced symbiont of the whiteleg shrimp gastric microbiome retains an atypical peptidoglycan biosynthesis pathway: Genomic characterization of Candidatus Penaeiplasma gastricola gen. Nov., sp. nov.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108754},
doi = {10.1016/j.jip.2026.108754},
pmid = {42785511},
issn = {1096-0805},
abstract = {Symbiotic bacteria belonging to the class Mollicutes are widely associated with arthropods, yet their ecological roles in crustaceans remain poorly understood. Our previous 16S rRNA gene amplicon surveys revealed that Mollicutes consistently dominated the gastric microbiota of the whiteleg shrimp Penaeus vannamei. To characterize this dominant lineage, genome-resolved metagenomic analysis was conducted on Mollicutes-dominated samples from aquaculture ponds in Thailand, where a single lineage accounted for >95% of the community. A high-quality metagenome-assembled genome (MAG) was reconstructed (98.55% completeness, 1.33% contamination), with a small genome (~1.28 Mb) and low GC content (29.7%). Phylogenomic analyses placed this lineage within the order Enteroplasmatales but clearly separated it from Enteroplasma. Genomic relatedness metrics, including average nucleotide identity (~68%), average amino acid identity (~57%), and POCP values (43-46%), support its classification as a novel genus and species. Functional annotation revealed a highly reduced metabolic repertoire consistent with host association, including loss of amino acid biosynthesis and respiratory chain components, while retaining glycolysis and fermentative metabolism and expanded ABC transport systems for nutrient uptake. Notably, genes for nearly complete peptidoglycan biosynthesis were retained, an unusual feature in Mollicutes that may reflect incomplete cell wall loss or functional repurposing of these genes. Overall, this study identifies a previously uncharacterized Enteroplasmatales lineage dominating the shrimp gastric microbiota and exhibiting strong signatures of reductive evolution and host adaptation. This lineage is proposed as Candidatus Penaeiplasma gastricola gen. Nov., sp. nov., representing a distinct crustacean-associated clade within Enteroplasmatales and likely encompassing lineages previously assigned to Candidatus Bacilloplasma based on 16S rRNA gene similarity. These findings provide a genomic framework for understanding the ecological roles and evolutionary history of dominant gastric symbionts in penaeid shrimp, and a foundation for future studies of shrimp microbiome function and health.},
}

@article {pmid42785658,
year = {2026},
author = {Zhang, RR and Gong, Z and Chen, Z and Ho, MM and Lam, WY and Chu, CH and Yu, OY},
title = {The oral microbiome of prediabetes: a scoping review.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {107076},
doi = {10.1016/j.jdent.2026.107076},
pmid = {42785658},
issn = {1879-176X},
abstract = {OBJECTIVE: To map evidence on oral bacterial microbiome shifts in adults with prediabetes and compare them with normoglycemic and type 2 diabetes populations.

DATA AND SOURCES: A scoping review in accordance with PRISMA-ScR was conducted. PubMed, Cochrane Central Register of Controlled Trials, Web of Science, Embase, and Scopus, were searched from inception to May 1, 2026, including English-language original clinical studies using high-throughput sequencing of oral samples from adults with prediabetes and normoglycemic and/or type 2 diabetes comparison groups. Findings were narratively synthesized by sample size, diversity measure, taxonomic composition and relative abundance, and predicted microbial function.

STUDY SELECTION/RESULTS: 2,320 publications were screened, and nine cross-sectional studies met eligibility criteria. Samples composed of saliva, tongue coating, oral rinse, and dental plaque; all studies used 16S rRNA gene sequencing. Alpha and beta-diversity findings were heterogeneous, partly reflecting differences in sample size, glycemic definitions, study populations, and analytical methods. Prediabetes was not consistently distinguishable from normoglycemia, while diabetes more frequently differed from normoglycemia and/or prediabetes. Actinomyces and Prevotella were among the taxa more often reported as enriched at higher glycemic status, whereas Haemophilus and Neisseria were more frequently reported as depleted; however, taxonomic findings were not uniform across studies. Only one study reported computationally predicted functional profiles.

CONCLUSION: Current evidence suggests that prediabetes may be associated with subtle oral microbiome alterations, but there is insufficient consistency to define a reproducible prediabetes-specific microbial signature. Standardized, longitudinal, and functionally resolved studies are needed to establish temporality, clinical utility, and potential mechanisms.

CLINICAL SIGNIFICANCE: Identifying prediabetes-associated oral microbiome shifts may support earlier recognition of metabolic dysregulation and inform future preventive strategies. Longitudinal and functionally oriented studies are needed to determine whether oral microbiome changes precede, accompany, or result from progression toward diabetes.},
}

@article {pmid42785694,
year = {2026},
author = {Sun, ML and Qin, HL and Cui, ZY and Ren, Y and Yang, J and Ren, JH and Xu, M and Wang, JW and Ye, JR and Sun, H and Huang, L},
title = {Fungal-augmented biofertilizer increases soil nutrient availability, alters rhizosphere community structure, and improves plant growth.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135934},
doi = {10.1016/j.biortech.2026.135934},
pmid = {42785694},
issn = {1873-2976},
abstract = {Converting lignocellulosic waste into biofertilizers offers a sustainable practice for waste valorization, yet the mechanistic links underpinning how such amendments affect the soil-plant system remain poorly elucidated. We hypothesized that fungal-augmented biofertilizers improve plant growth through direct nutrient release and shifts in rhizosphere microbial community composition. To test this hypothesis, we isolated a white-rot fungus, Bjerkandera adusta strain QX3-19, which exhibited high ligninolytic activity. Inoculation with QX3-19 during composting of forest residues substantially enhanced lignocellulose degradation and yielded a nutrient-rich biofertilizer (BBF; QX3-19-augmented biofertilizer). Soil amendment with BBF significantly promoted the growth of Capsicum annuum and Cunninghamia lanceolata. Integrated metagenomic and culture-based analyses showed that BBF shifted the rhizosphere microbiome, increasing community diversity and network complexity. Specifically, BBF application was associated with the enrichment of plant growth-promoting rhizobacteria (PGPR) with complementary functional traits, alongside higher abundances of functional genes potentially involved in bacterial chemotaxis, flagellar assembly, and nutrient mineralization. Furthermore, a synthetic microbial community (SynCom) constructed from these enriched PGPR recapitulated the plant growth-promoting phenotype, suggesting a potential association between these taxa and improved plant performance. Collectively, our results suggest that QX3-19-mediated composting yields an effective biofertilizer that benefits plant growth via direct nutrient supplementation and indirect rhizosphere microbiome modulation. This integrated investigation provides empirical insights into forest residue valorization to support agroforestry sustainability.},
}

@article {pmid42785696,
year = {2026},
author = {Li, J and Zheng, D and Tang, Y and Ran, Y},
title = {Fe stabilizes syntrophic volatile fatty acid oxidizing consortia under high organic load in chicken manure anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135907},
doi = {10.1016/j.biortech.2026.135907},
pmid = {42785696},
issn = {1873-2976},
abstract = {Volatile fatty acid (VFA) accumulation driven by thermodynamic constraints on syntrophic oxidation is a critical bottleneck in high-load anaerobic digestion (AD) of nitrogen-rich feedstocks. Using metagenomic and metatranscriptomic analyses of 172 bacterial genomes, thermodynamic calculations, and granule morphology, we investigated how Fe reshaped syntrophic VFA-oxidizing consortia during 310-day AD of chicken manure under escalating organic loading rates (OLR 1-6 g VS/L/d). Fe attenuated VFA accumulation by 65.0-46.5 % (OLR 4-6), and acted as a stabilizer of core syntrophic consortia: Pelotomaculum persisted as the dominant propionate oxidizer (67.7 % of methylmalonyl-CoA pathway transcription at OLR 6), whereas the control shifted to Fermentimonas; Gallicola and unclassified Clostridiaceae maintained acetate oxidation redundancy; and Syntrophomonas and unclassified Bacteroidales sustained butyrate oxidation capacity. This guild-level stabilization was corroborated at the system level, where methylmalonyl-CoA pathway transcription remained 20.9 % higher (OLR 6), while β-oxidation twofold higher (OLR 4) in the Fe reactor. From this root, a cascade followed: preserved consortia kept VFA concentrations substantially lower, producing more favorable thermodynamic conditions with wider allowable H2 partial pressure windows for all four VFAs, and limiting bicarbonate alkalinity consumption, thereby delaying acidification. Granule analysis further revealed Fe-dependent structural changes, with more uniform granules at moderate load and larger-irregular aggregates at extreme load. These findings suggest Fe sustains syntrophic VFA oxidation by stabilizing the syntrophic consortia network that integrates VFA oxidation, thermodynamics, alkalinity buffering, and granule architecture into a coherent stress-response system, offering a rational basis for microbiome-targeted strategies to improve AD resilience.},
}

@article {pmid42786178,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Li, S and Zhang, Y and Wang, C and Yao, X and Chang, K and Lu, B and Guo, R and Xing, G and Yu, H and Yin, J and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42786178},
issn = {2055-5008},
support = {2025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; XLYC2403207//Young Top Talents Program of the Liaoning Revitalization Talents Initiative/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program/ ; 2024RJ018//Dalian Outstanding Young Scientific and Technological Talents Program/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; Metagenome ; *Respiratory System/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Metagenomics/methods ; Phylogeny ; Case-Control Studies ; },
abstract = {The human oral cavity and airway harbor diverse microbiomes that are implicated in oral and respiratory diseases, yet comprehensive genomic catalogs remain scarce. Here, we present the Oral and Airway Prokaryotic Genome Catalog (OAPGC), comprising 99,215 high-quality, non-redundant genomes reconstructed from public and newly sequenced metagenomes and isolates. OAPGC was clustered into 2474 species using refined, phylum-specific nucleotide identity thresholds, and 29.5% of them are uncultured. Habitat-driven divergence was evident across 15 oral and 8 airway sites, with airway microbiomes showing greater inter-individual variability and enriched antibiotic resistance genes. Across 25 case-control comparisons covering 12 diseases, disease status explained significant community shifts in 19 datasets, with classifiers achieving an AUC > 0.70 in 20 datasets. Shared microbial signatures were identified for diseases such as periodontitis and pneumonia, including uncultured taxa. We also detected 12.3% of OAPGC species in the gut, whose enrichment was linked to multiple diseases and improved cross-cohort classification performance. OAPGC establishes a foundational, disease-relevant genomic framework for oral and airway microbiome studies.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
Metagenome
*Respiratory System/microbiology
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Metagenomics/methods
Phylogeny
Case-Control Studies

@article {pmid42787023,
year = {2026},
author = {Kitsios, G and Sy, MA and Wang, X and Craig, A and Rizzo, A and Francisco, JR and Qin, S and Hensley, M and Kramer, KH and Noda, K and Benos, P and Hage, C and Sanchez, P and Morris, A and Haidar, G and Snyder, ME},
title = {Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {42787023},
abstract = {BACKGROUND: Conventional bronchoalveolar lavage (BAL) culture has limited sensitivity in lung transplant recipients due to universal antimicrobial prophylaxis and inability to detect non-culturable organisms. Metagenomic sequencing of BAL offers culture-independent pathogen identification, but concordance with conventional culture and clinical utility in the immediate post-transplant period have not been evaluated.

METHODS: We prospectively enrolled 19 adult lung transplant recipients undergoing serial bronchoscopies during the immediate post-transplant period. BAL samples (n=33) were tested in parallel with conventional culture, microbial cell-free DNA (mcfDNA) sequencing (Karius Focus BAL; with quantitation determined by research analysis), and Oxford Nanopore sequencing using a unified three-tier organism classification framework. BAL host-response biomarkers were profiled concurrently.

RESULTS: Karius reported Tier 1 pathogens in 19/33 episodes (58%) versus 8/33 by conventional culture (24%); organism-level concordance was low (Cohen's kappa 0.18). In 16 episodes where Karius reported a pathogen not recovered by culture, 8 across 3 participants represented predictive reports, defined as the same organism subsequently confirmed as causing invasive infection 2-46 days later, including fatal Pseudomonas pneumonia, Enterococcal surgical site infection, and Candidemia. Nanopore sequencing had low yield due to contaminating human DNA. Quantitative mcfDNA burden correlated positively with multiple alveolar inflammatory biomarkers including total protein, IL-6, and sST2.

INTERPRETATION: BAL mcfDNA metagenomics identified clinically relevant pathogens not recovered by conventional culture, including predictive reports and non-culturable organisms. Quantitative mcfDNA signal correlated with alveolar inflammatory mediators, supporting the biological relevance of mcfDNA detection beyond conventional diagnostic classification and a role for metagenomic surveillance in the early post-transplant period.},
}

@article {pmid42787064,
year = {2026},
author = {Guimarães, GNF and Barrett, DW and Gonzalez-Lima, F},
title = {Combined abdominal and transcranial photobiomodulation is associated with fecal microbiome restructuring: a systems microbiology pre-post case report.},
journal = {Frontiers in systems biology},
volume = {6},
number = {},
pages = {1920618},
pmid = {42787064},
issn = {2674-0702},
abstract = {Photobiomodulation (PBM) has been proposed as a non-invasive strategy capable of modulating mitochondrial, inflammatory, vascular, and gut-brain axis-related pathways. However, its potential effects on fecal microbiome ecology in neurobehavioral conditions remain poorly characterized. This case report describes paired fecal microbiome findings before and after a 90-day combined abdominal and transcranial PBM protocol in a 6-year-old female with autism spectrum disorder and chronic constipation. PBM was delivered daily using a 1064-nm near-infrared LED device with 54 mW/cm[2] irradiance, applied for 10 min over the right prefrontal cortex and for 10 min over the infraumbilical and right lower abdomen. Fecal samples collected before and after the intervention were analyzed by 16 S rRNA amplicon sequencing. The baseline sample showed limited taxonomic resolution, with 93.14% assigned to "Other/unclassified," whereas the post-intervention sample showed a more taxonomically resolved microbial profile, including Firmicutes (53.37%), Bacteroidetes (29.66%), Actinobacteria (7.97%), Verrucomicrobia (4.21%), Euryarchaeota (2.89%), Proteobacteria (1.14%), and a markedly reduced unclassified fraction (0.03%) at the phylum level. At the genus level, the post-intervention profile showed detection or increased representation of taxa commonly discussed in relation to gut microbial ecology, mucosal biology, and short-chain fatty acid metabolism, including Faecalibacterium (7.03%), Bifidobacterium (4.25%), Bacteroides (18.82%), Alistipes (5.38%), preserved Akkermansia (3.92%-4.21%), and low-abundance Roseburia. Taxa with context-dependent or uncertain significance, including Sarcina, Collinsella, Parabacteroides, and residual unclassified genera, were also observed and are reported transparently. Caregiver behavioral observations included improved bowel regularity, reduced abdominal distension, more stable mood, reduced irritability and impulsivity, improved communication, and greater social tolerance. The intervention was well tolerated with no reported adverse effects. As a single-patient pre-post case report without sham control, repeated baseline sampling, or functional metagenomic confirmation, these findings cannot establish causality. Nevertheless, they provide a biologically plausible systems-level observation linking combined abdominal and transcranial PBM with a shift in fecal microbiome structure and gastrointestinal-behavioral regulation, supporting future controlled studies integrating longitudinal microbiome profiling, metabolomics, inflammatory biomarkers, autonomic measures, and validated behavioral outcomes.},
}

@article {pmid42787096,
year = {2026},
author = {Ren, Z and Du, C and Wang, Y and Ji, S and Chi, X and Ma, Y and Lu, Z and Li, X and Zhang, B and Shi, C},
title = {Earthworm-associated microbial community reassembly accompanies higher inorganic-N concentrations in spent mushroom substrate.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1935901},
pmid = {42787096},
issn = {1664-302X},
abstract = {INTRODUCTION: Spent mushroom substrate (SMS) is a major residual stream from edible mushroom production and a potential feedstock for organic fertilizer. Although earthworm composting can alter SMS transformation, the microbial processes associated with nitrogen transformation remain poorly resolved.

METHODS: Seven mixtures of black fungus SMS (AhSMS) and golden needle mushroom SMS (FfSMS) were subjected to conventional composting or Eisenia fetida-mediated composting and sampled after 0, 30, and 60 d.

RESULTS: Earthworm composting was associated with higher bacterial alpha-diversity values and a transition from early Bacteroidota-dominated communities to later communities enriched in Pseudomonadota and Actinomycetota. At the treatment level, mean NH4[+]-N in Group E increased from 2.34 to 44.17 mg kg[-1] between day 0 and day 60 (1788%), while NO3[-]-N increased from 10.33 to 26.10 mg kg[-1] (153%). These changes coincided with candidate taxa associated with predicted nitrogen-cycling functions, including Arenimonas, Pseudoxanthomonas, Croceibacterium and Kineobacterium. PICRUSt2-based functional prediction and network analysis further identified coordinated changes in predicted nitrogen-cycle EC categories and candidate hub taxa, including Mesorhizobium and Flavobacterium.

DISCUSSION: Earthworm composting was associated with higher inorganic-N concentrations and bacterial community reassembly. However, these concentration changes do not by themselves demonstrate greater total nitrogen retention because dry-matter loss was not measured. Moreover, as the functional profiles were inferred from 16S rRNA gene data, metagenomic and transcriptomic analyses are required to verify the underlying mechanisms. These findings provide a framework for optimizing earthworm-assisted SMS valorization and prioritizing microbial taxa and nitrogen-cycling pathways for functional validation.},
}

@article {pmid42787116,
year = {2026},
author = {Doster, E and Pinnell, LJ and Parker, JK and Wolfe, CA and Morley, PS},
title = {Different DNA input amounts and library preparation kits yield comparable resistome characterization using target-enriched metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1907850},
pmid = {42787116},
issn = {1664-302X},
abstract = {INTRODUCTION: Target-enriched metagenomic sequencing improves detection of antimicrobial resistance genes (ARGs) relative to standard shotgun metagenomics, but whether DNA input amount influences resistome characterization has not been systematically evaluated.

METHODS: We evaluated target-enriched sequencing using fecal microbial communities from multiple host species and compared results across library preparation kits, DNA input amounts, and sequencing approaches. Composite fecal samples from livestock and humans and individual canine samples were processed using three library preparation kits and DNA input amounts ranging from 50 to 800 ng.

RESULTS: Target-enriched libraries from composite samples were compared with shotgun metagenomic sequences generated from the same samples. Target-enriched sequencing achieved a 7.9-fold increase in on-target read proportions and detected 12-fold more unique antimicrobial resistance gene groups than shotgun metagenomics. Resistome composition was driven primarily by sample source, which explained 66%-79% of within-species variance, while library preparation kit accounted for 13%-26% and DNA input amount had no consistent effect. Kit-associated differences were systematic and affected primarily low-abundance resistance classes but were small relative to biological variation among samples.

DISCUSSION: These findings demonstrate that target-enriched metagenomic sequencing substantially improves resistome detection and provides comparable resistome characterization DNA input amounts ranging from 50 to 800 ng. Differences associated with library preparation were small relative to biological variation, supporting the flexibility of using differing DNA inputs for resistome characterization.},
}

@article {pmid42787187,
year = {2026},
author = {Zhang, L and Wu, X and Chen, X and Xin, H and Yan, J and Zhuo, M and Ma, X and Liu, X and Liu, M and Huang, G and Ma, F},
title = {Dietary patterns and osteoporosis risk in a high-altitude population: the roles of gut microbiota and plasma metabolites in a case-control study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1865666},
pmid = {42787187},
issn = {2296-861X},
abstract = {BACKGROUND: This study investigated the association between dietary pattern and osteoporosis, exploring gut microbiota and plasma metabolites as potential mediators.

METHODS: This case-control study included 90 osteoporosis patients and 90 healthy controls. All participants completed a validated semi-quantitative food frequency questionnaire (FFQ) to assess their dietary intake over the past year. Principal component analysis (PCA) was performed on the FFQ data to identify major dietary patterns. Gut microbiota composition was analyzed using metagenomic sequencing (Illumina HiSeq platform, PE150). Plasma metabolites were analyzed using untargeted metabolomics with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Binary logistic regression was employed to examine the association between dietary pattern and osteoporosis; Multivariate linear regression was used to investigate the association between dietary pattern and gut microbiota/metabolites. Additionally, mediation analysis was conducted to assess whether gut microbiota or plasma metabolites mediated the association between dietary patterns and osteoporosis, and the proportion of mediation was calculated.

RESULTS: The osteoporosis group showed significant differences in age (61.89 ± 7.86 vs. 56.10 ± 7.29 years), sex (72.2% vs. 36.7% female), and anthropometrics (all P < 0.05). Among six identified dietary patterns, "animal offal and seeds" was associated with higher osteoporosis risk (OR = 2.21, 1.21-4.06; P = 0.010). osteoporosis patients exhibited gut microbiota dysbiosis (enriched Enterobacteriaceae) and seven metabolites exerted mediating effects on the association between dietary pattern and osteoporosis.

CONCLUSION: In high-altitude population, the "animal offal and seeds" dietary pattern elevates osteoporosis risk, partially mediated by metabolite. Gut microbiota composition also differs significantly between osteoporosis patients and controls.},
}

@article {pmid42787375,
year = {2026},
author = {Li, H and Shi, Z and Zhang, R and Yao, J and Li, J and Liu, D},
title = {Metagenomic landscape of peripancreatic necrotic pus in acute pancreatitis: pathogen ecology, resistance gene profiles, and disease-associated microbial patterns.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1950013},
pmid = {42787375},
issn = {1664-302X},
abstract = {OBJECTIVE: To characterize the metagenomic landscape of intra-abdominal pus from surgical ICU patients using metagenomic next-generation sequencing (mNGS), compare pathogen ecology and resistance gene profiles between acute pancreatitis (AP)-associated and non-pancreatitis abdominal infection, and examine the association between pancreatitis-associated microbial features and persistent organ failure status.

METHODS: A total of 115 patients undergoing abdominal paracentesis and drainage in a surgical ICU were stratified into three groups: the POF group (AP with persistent organ failure, n = 35), the Non-POF group (AP without persistent organ failure, n = 49), and the Non-AP group (non-pancreatitis intra-abdominal infection, n = 31). Pus samples were analyzed by mNGS to characterize pathogen profiles, antimicrobial resistance gene (ARG) carriage, and microbial community structure.

RESULTS: Compared with Non-AP infections, both AP groups showed a convergent microbial profile dominated by ICU-associated pathogens, including Enterococcus faecium, Klebsiella pneumoniae, Acinetobacter baumannii complex, and Pseudomonas aeruginosa, with broad ARG detection profiles. ARG positivity was higher in AP patients than Non-AP controls (69.0% vs. 45.2%; P = 0.029), with frequent detection of Beta-lactam resistance genes, including carbapenemase-related genes. At sampling, alpha and beta diversity did not differ between POF and Non-POF groups, whereas both AP groups were clearly separated from Non-AP infections (P < 0.01). Among species enriched in Non-AP pus, Enterococcus faecalis remained inversely associated with AP status after adjustment for comorbidity burden, disease severity, antibiotic exposure, and ICU exposure (all P ≤ 0.006). The family-level random forest model achieved exploratory discriminatory performance for AP identification (AUC = 0.843).

CONCLUSION: AP-associated peripancreatic pus harbored a distinct microbial ecological profile characterized by reduced community diversity, predominance of ICU-associated pathogens, and broad ARG detection profiles. This pattern was associated with AP status but not with POF at sampling. These findings may complement antimicrobial risk assessment and empirical treatment decisions when interpreted alongside culture-based susceptibility testing and clinical factors, but require validation in prospective multicenter studies.},
}

@article {pmid42787428,
year = {2026},
author = {Patil, S and Rudragouda, CS},
title = {Coffee phytobiome dynamics: integrating multitrophic interactions and plant physiology for climate-resilient production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1951767},
pmid = {42787428},
issn = {1664-302X},
abstract = {Coffee (Coffea arabica L. and Coffea canephora Pierre ex A. Froehner) is a globally important perennial plantation crop that sustains the livelihoods of millions of smallholder farmers while making substantial contributions to agricultural economies worldwide global agricultural economies. Nevertheless, sustainable coffee production is increasingly constrained by climate change, declining soil fertility, emerging pests and diseases and the environmental costs associated with intensive use of synthetic agrochemicals. Recent advances in plant microbiome research have transformed the understanding of coffee from an individual organism to a holobiont, where the host plant and its associated microorganisms operate as an integrated biological system. The coffee phytobiome encompasses diverse microbial communities inhabiting the rhizosphere, rhizoplane, endosphere, phyllosphere, anthosphere, carposphere and spermosphere, together with complex multitrophic interactions involving shade trees, soil fauna, insects and the surrounding environment. These interactions collectively regulate nutrient acquisition, carbon assimilation, water-use efficiency, hormonal balance, stress tolerance, immune responses and overall plant productivity. This review critically examines current advances in multitrophic plant-microbe interactions that influence physiological adaptation in coffee, with particular emphasis on sustainable production under Indian agroecological conditions. It highlights the functional functions of plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), endophytic microorganisms and other beneficial microbes in enhancing root development, nutrient cycling, and resilience to biotic and abiotic stresses. Furthermore, the review evaluates recent progress in metagenomics, metatranscriptomics, metabolomics and microbiome engineering for harnessing indigenous microbial resources. Finally, it outlines future research priorities integrating plant physiology, microbial ecology, systems biology, and precision agriculture to develop climate-resilient, resource-efficient, and environmentally sustainable coffee production systems.},
}

@article {pmid42787483,
year = {2026},
author = {Zarkasi, KZ and Kamal, MHA and Ronidean, MD and Zaludin, MSM and Daud, MF and Purwantisari, S and Ghazali, AHA and Salim, H},
title = {Metagenomic Profiling of Barn Owl (Tyto javanica javanica) Regurgitated Pellets Reveals Spatially Structured Environmental Microbiota in Paddy Agroecosystems.},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74429},
pmid = {42787483},
issn = {2045-7758},
abstract = {The tropical barn owl (Tyto javanica javanica) is a major biocontrol agent against rodents in paddy fields. While raptors are frequently monitored for zoonotic diseases, they may also facilitate beneficial microbial redistribution. This study evaluated bacterial communities in barn owl regurgitated pellets to assess their role as environmental biosensors and vectors for microbe dispersal. We collected 90 fresh pellets from three paddy field locations during the growing season. Samples underwent bacterial enumeration and metagenomic sequencing of the 16S rRNA V3-V4 domains via the Illumina MiSeq platform. Results revealed significant spatial variation in bacterial communities across locations (PERMANOVA, F(2, 87) = 3.14, p < 0.05). Firmicutes (28.1%-63.2%) and Proteobacteria (17.7%-45.6%) dominated all sites. Notably, Sporosarcina sp., known for eco-friendly biocementation and soil enhancement, was highly abundant across all locations (up to 40.6%). The high abundance of Escherichia sp. at the AV site (32.1%) highlighted the pellet's ability to capture transient environmental and prey-derived coliforms. Ultimately, these pellets act as critical environmental proxies capturing localized microbiota. This supports the perspective that barn owls contribute significantly more to microbial ecological redistribution than to disease spread, offering valuable agricultural ecological services.},
}

@article {pmid42787553,
year = {2026},
author = {Kumar, B and Lorusso, E and Fosso, B and Pesole, G},
title = {A data-driven universal gut microbiome health assessment: a machine learning framework trained on large metagenomic data.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925500},
pmid = {42787553},
issn = {1664-302X},
abstract = {The gut microbiota is essential to maintain host physiology, and its disruption (dysbiosis) is associated with a wide range of diseases. Machine learning (ML) offers a powerful tool to model species-level microbiome profiles, but classifiers that reliably separate healthy from diseased individuals across independent cohorts are still lacking. In this study, we developed a ML classifiers trained on 7,452 publicly available stool metagenomes spanning 32 studies and 12 diseases, designed to distinguish healthy individuals (absence of a clinically diagnosed disease) from non-healthy individuals (presence of a clinically diagnosed disease) based on species-level gut microbiome profiles. We trained 16 supervised models combining four algorithms (RF, SVM-LIN, SVM-RBF, and LR-ElasticNet) combined with all feature sets and three feature-selection algorithms. Performance was assessed by F1 score and ROC-AUC on held-out test data and externally validated on 642 samples from six independent cohorts, including previously unseen diseases. On the test set, all models achieved F1 scores of 78-86% and ROC-AUC values of 89-95%. An SVM-RBF model using permutation-based feature selection performed best (F1 = 86.6%, ROC-AUC = 95.5%; healthy F1 = 86.6%, non-healthy F1 = 88.7%). Importantly, external validation confirmed the generalizability of the full-feature SVM-RBF model (overall F1 = 70.6%; ROC-AUC = 84.7%), including unseen disease types such as Clostridioides difficile infection (F1 = 90.3%) and type 2 diabetes (F1 = 77.4%). Feature-importance and multivariate analyses revealed both shared and disease-specific microbial signatures, suggesting that the model captures biologically meaningful patterns rather than cohort-specific artifacts. Disease-associated taxa included Klebsiella pneumoniae, Raoultella ornithinolytica, Sutterella wadsworthensis, Gemmiger formicilis, and Lactobacillus crispatus. In contrast, healthy status was consistently associated with commensal species such as Extibacter hylemonae and Ruthenibacterium lactatiformans. These results show that models trained on pooled metagenomes predict gut health status accurately and transfer to independent cohorts, providing a scalable, non-invasive framework and a set of candidate microbial biomarkers for further clinical evaluation.},
}

@article {pmid42787881,
year = {2026},
author = {Zhang, X and Li, H and Han, Y and Li, Q and Yang, H and Hu, C},
title = {Stage-specific cyanobacterial handoffs and heterotrophic subsidies underpin biocrust carbon accumulation.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag254},
pmid = {42787881},
issn = {2730-6151},
abstract = {Inoculating cyanobacteria is a widely adopted strategy to accelerate biocrust formation and restore dryland soil functions, yet the in situ mechanisms sustaining microbial biomass carbon (MBC) accumulation under seasonal stress remain poorly understood. Here, we combined a field inoculation experiment with multi-omic profiling (amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics) and genome-scale metabolic modeling to track the circannual development of induced cyanobacterial biocrusts in Hopq Desert, China. Although the inoculated Konicacronema strain (formerly Microcoleus) maintained significant taxonomic dominance, metatranscriptomic and metaproteomic data revealed a striking functional handoff. Microcoleus-like populations drove rapid initial biocrust formation via the oxidative pentose-phosphate pathway and enzymatic antioxidant systems, whereas Oscillatoria assumed transcriptional dominance during harsher seasonal transitions through enhanced light harvesting, cyclic electron transport, and non-enzymatic photoprotection. Genome-scale metabolic modeling predicted that dominant cyanobacteria acted primarily as net importers, receiving amino acids, vitamins, cell-wall precursors, and phosphate from heterotrophic partners, while supplying inorganic sulfur and iron-sulfur clusters. Co-occurrence networks and life-history analyses further revealed that MBC maintenance was associated with a shift from growth-oriented resource mobilization toward acquisition-oriented strategies mediated by ABC transporters. Structural equation modeling confirmed that solar radiation and soil salinity govern MBC indirectly by influencing cyanobacterial composition and the balance between phototrophic assimilation and resource-acquisition strategies. These findings demonstrate that biocrust carbon accumulation is sustained by temporal functional division among cyanobacterial guilds and metabolic subsidies from heterotrophic partners, rather than by the persistent activity of a single pioneer strain, and provide a trait-based roadmap for designing resilient, multifunctional synthetic inocula for dryland restoration.},
}

@article {pmid42788735,
year = {2026},
author = {Shi, H and Chen, Y and Liu, X and Yang, J and Yan, D and Zhang, H and Chen, J and Wu, Z and Yuan, D and Lu, H and Li, L},
title = {Clinical severity score-guided metagenomic analysis identifying gut microbial taxonomic and functional markers for severe hepatitis E progression.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095626},
doi = {10.1128/msystems.00956-26},
pmid = {42788735},
issn = {2379-5077},
abstract = {Although gut microbiome alterations have been reported in hepatitis E (HE), the taxonomic and functional determinants of disease severity remain poorly defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 125 individuals spanning acute non-icteric hepatitis (ANIH), acute icteric hepatitis (AIH), acute liver failure (ALF), and healthy controls. We constructed a surrogate clinical severity index from routine blood parameters and developed an integrative analytical framework that combined XGBoost-based taxonomic modeling with LASSO-driven functional feature selection to explore microbiome-severity associations. The taxonomic model discriminated patients from controls (area under the curve [AUC] = 0.944) and identified nine bacterial species significantly associated with severity, independent of age, sex, and body mass index (BMI) (permutation test, P < 0.05), with Veillonella atypica emerging as the most robust candidate biomarker. The signature featured enrichment of lactate-utilizing Veillonella spp. and Ligilactobacillus salivarius, alongside depletion of beneficial commensals (Dorea longicatena, Ruminococcus timonensis, Eubacterium ramulus), collectively suggesting a pathogenic "lactate axis." The HE-enriched lactate utilizers were positively associated with 13 core severity-increasing KOs involved in oxidative stress adaptation (npr, hemQ, NUDT1, nfr1) and secretion/biofilm formation (gspD, fhaC, vpr, sinR) and negatively with three severity-decreasing KOs, including the butyrate fermentation gene (K14534). Strikingly, the stringent 16-KO core (intersection of four methods) explained more variance in disease severity than the broader set identified by at least three methods (R[2] = 0.61 vs. 0.47). Collectively, these findings reveal a strong link between microbiome-derived lactate metabolism and HE severity, highlighting its potential as a basis for microbiome-based severity stratification and motivating further mechanistic exploration.IMPORTANCEHepatitis E virus (HEV) infection ranges from ANIH to ALF, yet the role of the gut microbiome remains poorly understood across the severity spectrum. By performing shotgun metagenomic sequencing on fecal samples from 125 individuals and applying an integrative framework combining XGBoost-based taxonomic modeling with LASSO-driven functional selection, we identified robust microbiome-severity associations as quantified by a surrogate clinical severity index derived from routine blood parameters. These associations were characterized by enrichment of lactate-utilizing Veillonella species (notably Veillonella atypica), depletion of beneficial butyrate-producing commensals, and severity-linked shifts in microbial functional gene profiles. Such patterns are consistent with a perturbed microbial "lactate axis" in gut-liver crosstalk, although all associations remain correlational. Our findings nominate candidate microbial markers for severity stratification in hepatitis E and provide a hypothesis-generating framework to guide future mechanistic studies and microbiome-based therapeutic strategies.},
}

@article {pmid42759909,
year = {2026},
author = {Hou, J and Li, Q and Li, Y and Liu, M and Xue, M and An, Y and Yao, Y and Xu, H},
title = {Intraspecific rice intercropping reduces the rhizosphere resistome in association with organic acid and low-ARG-burden microbiota enrichment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129180},
doi = {10.1016/j.envpol.2026.129180},
pmid = {42759909},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils are an emerging environmental concern. However, sustainable strategies for reducing ARG in crop rhizospheres remain limited. Here, we investigated associations among rhizosphere metabolites, microbial communities, and ARG profiles in an intraspecific rice intercropping system. Compared with monoculture, intraspecific intercropping reduced the relative abundances of total ARGs and ARGs assigned to the Ranks I and II. Intercropping also altered rhizosphere metabolite profiles, with increased organic acid abundance, and was associated with convergent changes in microbial community composition. Nitrospirales, particularly Candidatus Sulfobium, was enriched under intercropping. Metagenome-assembled genomes (MAGs) assigned to this lineage contained relatively few annotated ARGs, which were predominantly classified as ARGs assigned to the Rank IV. Exogenous supplementation reproduced this field-associated pattern: citric acid treatment reduced total ARG and ARGs assigned to the Ranks I and II abundance and concurrently increased the relative abundance of Candidatus Sulfobium. These results support an association among rhizosphere organic acids, low-ARG-burden taxa, and reduced ARG abundance. Collectively, these findings highlight intraspecific rice intercropping as a low-input, source-control approach for cleaner rice production and ARG-risk mitigation.},
}

@article {pmid42777464,
year = {2026},
author = {Wang, YC and Zhang, YF and He, G and Wang, ZX and Zhang, BN and Wang, C},
title = {Unveiling the overlooked nitrous oxide reduction enzyme in wastewater treatment systems.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126987},
doi = {10.1016/j.watres.2026.126987},
pmid = {42777464},
issn = {1879-2448},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas with steadily rising atmospheric concentrations. N2O reductase (N2OR), encoded by the nosZ gene, is the key enzyme capable of reducing N2O to dinitrogen. While the canonical nosZ clades (I and II) have been extensively investigated, the recently proposed clade III (L-nosZ) remains largely uncharacterized in engineered ecosystems. Here, by analyzing 226 metagenomes from globe 114 wastewater treatment plants (WWTPs), we demonstrate that l-nosZ is both widespread and phylogenetically diverse within activated sludge communities. Although its abundance is generally lower than that of clade II nosZ, integrating l-nosZ into emission estimates reduces the predicted microbial N2O emission potential by up to 12% in some systems. Environmental association analyses show that the distribution and functional contribution of l-nosZ are shaped primarily by sludge retention time and temperature (Rs > 0.2; p < 0.001), and that its response to dissolved oxygen differs from that of canonical nosZ. Comparisons across representative habitats further reveal that WWTPs act as important reservoirs for nosZ genes, whereas l-nosZ exhibits broad environmental occurrence and marked taxonomic conservatism. Collectively, our findings uncover a previously overlooked component of microbial N2O reduction in WWTPs and highlight the need to incorporate l-nosZ into current emission assessments to improve predictions and inform mitigation strategies in engineered nitrogen-cycling systems.},
}

@article {pmid42777608,
year = {2026},
author = {Liu, YN and Zhou, LS and Peng, YX and Liu, HM and Tang, XJ and Jia, SY and Ming, Z and Li, YC and Lin, JY},
title = {Quercetin alleviates painful diabetic neuropathy in association with gut microbial remodeling and spinal betaine-related metabolic changes.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158812},
doi = {10.1016/j.phymed.2026.158812},
pmid = {42777608},
issn = {1618-095X},
abstract = {BACKGROUND: Painful diabetic neuropathy (PDN) involves metabolic, inflammatory, and neuroimmune disturbances. Quercetin may alleviate diabetic neuropathy, but the associated gut-spinal mechanisms remain unclear.

PURPOSE: To investigate whether quercetin improves PDN in association with gut microbial remodeling, spinal betaine-related metabolism, and magnetic resonance imaging-derived spinal gadopentetate dimeglumine signal dynamics.

STUDY DESIGN: A two-stage study combined quercetin intervention, antibiotic-associated gut perturbation, multi-omics analyses, and independent betaine validation in a diet/streptozotocin-induced rat model of PDN.

METHODS: PDN rats received quercetin (30 or 60 mg/kg) or metformin. The 60 mg/kg dose was also evaluated during antibiotic co-treatment. Behavioral, metabolic, histological, inflammatory, oxidative-stress, immunofluorescence, western blot, fecal metagenomic, targeted spinal metabolomic, and magnetic resonance imaging assessments were performed. A separate cohort received intraperitoneal betaine.

RESULTS: Quercetin improved pain hypersensitivity, metabolic dysfunction, intestinal barrier-associated readouts, inflammation, spinal oxidative stress, magnetic resonance imaging-derived gadopentetate dimeglumine signal dynamics, and the overlap between aquaporin-4 and glial fibrillary acidic protein, with stronger overall effects at 60 mg/kg. Antibiotic co-treatment attenuated several quercetin-associated effects. Multi-omics analyses highlighted betaine-related metabolic changes, while exploratory protein changes related to the spinal choline-betaine metabolic branch were attenuated by antibiotics. Betaine partially reproduced selected downstream effects and was accompanied by lower exploratory inflammatory-pathway protein readouts.

CONCLUSION: Quercetin alleviated PDN and was associated with coordinated gut, systemic, and spinal changes. Betaine may represent one candidate functional contributor, although microbiota-specific causality and the directionality of the proposed gut-spinal connection remain unestablished.},
}

@article {pmid42777747,
year = {2026},
author = {Pearse, O and Lester, R and Zuza, AM and Mangochi, H and Siyabu, P and Tewesa, E and Edwards, T and Thomson, NR and Kawaza, K and Musicha, P and Cornick, J and Heinz, E and Feasey, NA and Jewell, C},
title = {Transmission of extended-spectrum β-lactamase-producing Klebsiella pneumoniae in a Malawian neonatal unit: a clinical and genomic analysis of a prospective cohort study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101516},
doi = {10.1016/j.lanmic.2026.101516},
pmid = {42777747},
issn = {2666-5247},
abstract = {BACKGROUND: Klebsiella pneumoniae is an important cause of neonatal sepsis in sub-Saharan Africa and is frequently antimicrobial resistant. In this study, we investigated key transmission routes of extended-spectrum β-lactamase-producing K pneumoniae (ESBL-K pneumoniae) within a single neonatal unit to inform development of contextually appropriate infection prevention and control practices.

METHODS: We recruited a prospective mother and neonate cohort of babies admitted for less than 48 h and expected to stay for 24 h or more, where the mother or guardian was aged 18 years or older. Participants were followed up until day 7 of admission or discharge, with samples taken on day 1 and 3, and at the final follow-up (maternal stool, neonatal stool, maternal hands, cots, and swaddling cloth [day 1 only]). We sampled the ward environment weekly and included contemporaneous invasive ESBL-K pneumoniae isolates in our analysis. The primary outcome was ESBL-K pneumoniae colonisation. K pneumoniae single-colony isolates were subjected to single-colony whole-genome sequencing, and plate-sweeps had post-enrichment metagenomics performed, before evaluation of multilocus sequence types and single-nucleotide polymorphisms. Statistical analyses (Kaplan-Meier, state-transition models, source-attribution models, transmission analysis combining single-nucleotide polymorphisms and timing of sample collection, and exponential random graph models) were used to infer whether transmission occurred and from which sources.

FINDINGS: We recruited 94 neonate-mother pairs (from July 23, 2019, to March 30, 2020). Median gestational age was 37 (IQR 35-38) weeks, 41 (44%) of the 94 neonates were girls, all were of Black ethnicity, and 69 (73%) of 94 neonates were antibiotic exposed. ESBL-K pneumoniae rapidly colonised neonates (Kaplan-Meier analyses indicated median 5 days [95% CI 4-6]), with 44 (49%) of 90 of neonates being colonised at least once. State-transition model indicated females had increased colonisation risk (hazard ratio 2·33 [95% credible interval 1·07-5·40]). Invasive isolates (13 [76%] of 17) clustered with stool and environmental isolates. Results of transmission analysis using single-colony whole-genome sequencing and post-enrichment metagenomics were consistent with ESBL-K pneumoniae transmission from cots (13-29%), ward surfaces (37-65%; especially sinks and oxygen delivery equipment), mother's hands (6-13%), and other neonates (8-13%). The results of network analysis (exponential random graph models) were consistent with shared cots increasing transmission risk from 5·7 × 10[-5] (95% CI 1·4 × 10[-5] to 2·3 × 10[-4]) to 5·9 × 10[-4] (3·1 × 10[-4] to 1·1 × 10[-3]).

INTERPRETATION: The hospital environment is implicated in colonisation and invasive infection with ESBL-K pneumoniae. Infection prevention and control interventions should focus on containing neonatal stool, maternal hand hygiene, cot decontamination, single-use oxygen delivery equipment, and surface cleaning, particularly sinks.

FUNDING: Medical Research Council (UK); National Institute for Health Research (UK); Gates Foundation (USA); Wellcome (UK).},
}

@article {pmid42778005,
year = {2026},
author = {Wang, X and Bai, M and Yan, Y and Wang, YN and Gao, Y and Zhao, J and Wang, H},
title = {Roles of salt-tolerant Halobacillus sp. YJT-1 and Bacillus sp. TX-1 in efficient benzo[a]pyrene removal from contaminated water and saline soils.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125738},
doi = {10.1016/j.envres.2026.125738},
pmid = {42778005},
issn = {1096-0953},
abstract = {Benzo[a]pyrene (BaP) contamination in high-salinity environments has received increasing attention; however, few efficient, salt-tolerant microorganisms that can degrade BaP in contaminated soil have been explored. Here, we isolated two salt-tolerant Mn(II)-oxidizing bacteria, Halobacillus sp. YJT-1 and Bacillus sp. TX-1, and evaluated their performance in removing BaP and the relevant underlying mechanisms in saline soils. Extracellular superoxide (O2[•-]) was identified as a major reactive oxygen species involved in Mn(II) oxidation by both strains, as supported by reactive oxygen species quenching experiments and extracellular O2[•-] measurements. During in situ biogenic Mn oxide (BMO) formation, the generated extracellular O2[•-] and BMOs jointly promoted BaP hydroxylation, aromatic ring cleavage, and further transformation to low molecular weight organic matter. Inoculation with YJT-1 and TX-1 significantly increased BaP removal from three saline soils within 14 d, with strain YJT-1 exhibiting significantly greater removal efficiency (51.04-59.62%) than strain TX-1 (43.30-53.84%) (p < 0.05). BaP removal in soils was significantly positively correlated with the presence of amorphous Mn oxides, and laccase activity. Quantitative polymerase chain reaction and metagenomic analyses revealed that inoculation with strains YJT-1 and TX-1 increased the total bacterial abundance, the relative abundance of the polycyclic aromatic hydrocarbon-degradation-related phe gene and the enrichment of pathways associated with biogenic Mn(II) oxidation and the Na[+] stress response. These findings provide a microbial strategy for the bioremediation of BaP in high-salinity environments.},
}

@article {pmid42778008,
year = {2026},
author = {Zhang, Y and Wang, H and Ling, Y and Wang, H and Tian, Z and Wang, X and Liu, F and Wang, S},
title = {Mixotrophic denitrification with Arundo donax straw and elemental sulfur in constructed wetlands: enhanced nitrogen removal, carbon-sulfur interactions, and greenhouse gas mitigation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125726},
doi = {10.1016/j.envres.2026.125726},
pmid = {42778008},
issn = {1096-0953},
abstract = {Surface flow constructed wetlands (SFCWs) treating low carbon-to-nitrogen ratio wastewater are often limited by insufficient electron donor availability, leading to inefficient denitrification and greenhouse gas emissions. This study evaluated mixotrophic SFCWs integrated with Arundo donax straw and elemental sulfur (S[0]) over 160 days. The total nitrogen (TN) removal rate of 794.45 mg N/(m[2]·d) was achieved, exceeding those of the straw-only and S[0]-only SFCWs by 24.16% and 213.15%, respectively. Sequential operation further reduced effluent TN to 3.07 ± 0.16 mg/L (78.90% removal). The global warming potential per unit of nitrogen removed was 24.75% lower than that of the heterotrophic SFCW. Metagenomics indicated that straw supplementation enriched heterotrophic genera (e.g., Trichlorobacter and Dechloromonas) and favored their co-occurrence with sulfate-reducing bacteria (e.g., Desulfobulbus), suggesting a potential microbial link between straw-derived carbon metabolism and sulfur transformation. Moreover, genes encoding pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (KOR) were enriched following straw supplementation, suggesting an enhanced metabolic potential for reduced ferredoxin (Fdred) generation. This candidate Fdred-associated route may provide a low-potential electron transfer pathway complementary to NADH-dependent processes. Non-targeted metabolomics further revealed the enrichment of sulfur-containing metabolites (e.g., octyl hydrogen sulfate and sulfated phenolics) and the quinone menadione, providing complementary evidence for sulfur transformation and redox mediator-associated electron transfer potential, respectively. These findings provide new insights into carbon, sulfur, and nitrogen metabolism and inform the design of wetland systems that combine advanced nitrogen removal with reduced operational greenhouse gas intensity.},
}

@article {pmid42778012,
year = {2026},
author = {Fu, X and He, H and Li, C and Huang, Q and Bu, Y and Zhang, D and Hashim, JH and Hashim, Z and Wispriyono, B and Sary, L and Pratama, S and Wieslander, G and Norback, D and Sun, Y},
title = {Classroom dust microbiome-metabolome signatures and ocular health in students: Cross-sectional associations with putative pollutant-transformation and microbial functional profiles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129217},
doi = {10.1016/j.envpol.2026.129217},
pmid = {42778012},
issn = {1873-6424},
abstract = {Ocular irritation and tear-film instability are common among school-aged children, yet the microbial and chemical features of classroom dust associated with these outcomes remain poorly characterized. We conducted a cross-sectional multi-omics study in 32 classrooms from eight Indonesian junior high schools, integrating shotgun metagenomics and untargeted LC-MS metabolomics of settled dust with ocular symptoms and tear film break-up time (TFBUT) from 380 students. Classrooms with a low prevalence of ocular irritation were enriched in Actinobacteriota such as Allosaccharopolyspora coralli, Saccharopolyspora dendranthemae, and Brevibacterium epidermidis (LDA > 2, P < 0.05, LEfSe), and in microbial pathways annotated for the degradation of aromatic pollutants and xenobiotics, including xylene, benzoate, toluene and polycyclic aromatic hydrocarbons (LDA > 2, P < 0.05). Consistent with this, classrooms with more stable tear film showed higher signals of metabolites consistent with aromatic-compound and xenobiotic transformation, including 4-hydroxyphenylpyruvic acid, the phthalate-degradation intermediate 4-hydroxyphthalate, 3-hydroxybenzoic acid and 4-hydroxycinnamic acid (q < 0.05), indicating potential microbial degradation of aromatic pollutants in these classrooms. Statistical interactions linked specific genera to these features (e.g. Brevibacterium with trans-cinnamate and p-hydroxyphenylacetic acid, and Sphingomonas with 3-hydroxyphenylacetic acid) in relation to TFBUT, and taxa such as Janibacter and Nocardioides co-occurred with multiple degradation intermediates. These signatures point to microbial pollutant-transformation potential as a candidate modifier of the indoor exposome, warranting longitudinal and mechanistic follow-up.},
}

@article {pmid42778553,
year = {2026},
author = {Meng, JX and Li, WD and Tao, WF and Tu, S and Gao, J and Zhao, X and Li, J and Wu, J and Liu, C and Zhang, Y and Zhu, SJ},
title = {An atlas of colonization factors in the human gut microbiome reveals ecological strategies and inflammatory bowel disease signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778553},
issn = {2041-1723},
support = {82572567//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome ; Metagenomics ; Dysbiosis/microbiology ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Long-term residence in the gut enables microbes to interact with the host and influence intestinal health. However, many microbiome studies focus on taxonomic profiles or broad metabolic pathway annotations and provide limited insight into the conserved genes that support microbial residence. Here we show that colonization factors (CFs), defined as gut-enriched genes associated with microbial residence, offer a colonization-centered functional framework for profiling the human gut microbiome. By mapping 79 CF families across 289,231 surveyed microbial genomes, we identify more than seven million CF homologs and reveal their widespread distribution, phylogenetically structured organization and functional stratification into three putative lineage-associated colonization strategies centered on metabolism, stress resistance and microbial communication. Applying this framework to 3,666 metagenomic and metatranscriptomic samples from 10 inflammatory bowel disease (IBD) cohorts, we find that disease-associated dysbiosis is accompanied by recurrent remodeling of CF repertoires. These alterations can be traced to specific colonization-associated functions and microbial carrier species, and are captured by a compact feature panel that discriminates disease status within cohorts. These results establish CF profiling as a mechanism-oriented approach for interpreting the ecological organization of the gut microbiome and prioritizing colonization-associated targets for future disease monitoring and intervention studies.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Metagenome
Metagenomics
Dysbiosis/microbiology
Phylogeny
*Bacteria/genetics/classification/isolation & purification

@article {pmid42778565,
year = {2026},
author = {Lv, Y and Liu, P and Liu, Y and Dong, L and Li, J and Zhang, Y},
title = {Redox-stratified macromolecule degradation supports microbial survival in the oligotrophic Kermadec Trench sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778565},
issn = {2041-1723},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122043//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Geologic Sediments/microbiology ; Oxidation-Reduction ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Ecosystem ; Phylogeny ; *Microbiota/genetics ; Pacific Ocean ; },
abstract = {Kermadec Trench is a hadal ecosystem in the South Pacific with the water depth 10,047 m. The trench bottom harbors a highly active and populated microbial community, despite the surface sediment is characterized as extremely pressurized, oligotrophic and with low oxygen concentration. It is intriguing, as well as technically challenging, to investigate the microbial adaptation strategies therein. Here we performed the in situ RNA fixation on sediment samples with the assistant of Fendouzhe manned submersible, to approach natural status of microbial metabolisms on both genomic and transcriptomic levels. We reconstructed 1369 metagenome-assembled genomes (MAGs), revealing dominant heterotrophic lineages encoding carbohydrate-active enzymes targeting complex macromolecules such as peptidoglycan and β-1,4-mannan. These degradation processes were transcriptionally coupled with flexible respiratory pathways utilizing oxygen, nitrate, and nitrite as electron acceptors. Co-expression analyses and microbial co-occurrence networks demonstrated niche partitioning driven by redox stratification, with slope communities favoring oxidative pathways and bottom communities enriched in reductive metabolisms, including denitrification and N2O reduction. Despite compositional divergence, both habitats exhibited conserved functional strategies centered on macromolecule recycling and redox-coupled respiration. Our findings highlight a coordinated system of organic matter remineralization and electron acceptor versatility that underpins microbial survival in Earth's deepest seafloor ecosystems.},
}

*Geologic Sediments/microbiology
Oxidation-Reduction
Metagenome
*Bacteria/genetics/metabolism/classification
Ecosystem
Phylogeny
*Microbiota/genetics
Pacific Ocean

@article {pmid42778848,
year = {2027},
author = {Vidal, P and Almendral, D and Fernandez-Lopez, L and V Cervantes, F and Molina-Espeja, P and Bargiela, R and Ferrer, M},
title = {Quantitative Methods for Assessing True Lipase Activity Using Long-Chain Triglycerides and Complex Lipid Substrates.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3064},
number = {},
pages = {65-73},
pmid = {42778848},
issn = {1940-6029},
mesh = {*Lipase/metabolism ; *Triglycerides/metabolism/chemistry ; Substrate Specificity ; *Enzyme Assays/methods ; Colorimetry/methods ; Animals ; Fatty Acids, Nonesterified/metabolism ; Fatty Acids/metabolism ; Detergents/chemistry ; Hydrolysis ; },
abstract = {Lipases (E.C. 3.1.1.3) are enzymes that catalyze the hydrolysis of triacylglycerols (TAGs) into glycerol and fatty acids (FAs), making them essential for various industrial applications, including food processing, detergents, pharmaceuticals, and biofuels. This chapter focuses on methods used to assess true lipase activity, specifically those for measuring the release of FAs from long-chain triglycerides with varying saturation levels (e.g., C8:0, C10:0, C12:0, C14:0, C16:0, C18:0, C18:1), as well as complex, standardized lipid substrates such as oils, mayonnaise, lipstick, sebum, beef fat, and butterfat. These are assessed using the non-esterified free fatty acid (NEFA/FFA) colorimetric assay. The combined use of triglycerides, standardized test materials (e.g., stained fabrics), and the NEFA assay provides a more practical and realistic evaluation of true lipase activity, particularly relevant for industrial applications such as detergents.},
}

*Lipase/metabolism
*Triglycerides/metabolism/chemistry
Substrate Specificity
*Enzyme Assays/methods
Colorimetry/methods
Animals
Fatty Acids, Nonesterified/metabolism
Fatty Acids/metabolism
Detergents/chemistry
Hydrolysis

@article {pmid42779148,
year = {2026},
author = {Sáez-Sandino, T and Singh, BK and Xiong, C and Wang, J and Ren, C and Delgado-Baquerizo, M},
title = {Microbial Functional Genes Help Explain Soil Carbon Sensitivity to Temperature Across Global Biomes.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71101},
pmid = {42779148},
issn = {1365-2486},
support = {DP230101448//Australian Research Council/ ; TED2021-130908B-C41//URBANCHANGE/ ; P20_00879//Junta de Andalucía/ ; 647038/ERC_/European Research Council/International ; LRB17\1019//BES/ ; 702057//Marie Sklodowska-Curie/ ; PID2020-115813RA-I00//Spanish Ministry of Science and Innovation/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Temperature ; Climate Change ; Ecosystem ; *Genes, Microbial ; Carbon Cycle ; },
abstract = {The temperature sensitivity of soil microbial respiration (Q10) is a major factor underpinning global soil carbon emissions under climate change. While microbial biomass is a key driver of Q10 values, the role of microbial functional traits in explaining Q10 values remains largely undetermined. Here, we combined temperature-gradient incubations with a metagenomic database generated from a collection of surface soils collected across 196 natural ecosystems spanning all major biomes. We found that microbial functional traits related to carbohydrate metabolism and hemicellulose degradation, quantified as transcripts-per-million (TPM), are significantly correlated with Q10 values. Moreover, Q10 values display abrupt non-linear shifts once thresholds of microbial functional traits are crossed. Global mapping further provides evidence that microbial functional traits associated with carbon degradation and high Q10 values are concentrated within the planet's largest soil carbon reservoirs at high latitudes in the Northern Hemisphere. These regions could represent critical hotspots of vulnerability to soil carbon losses under climate warming. Our results provide a new step towards incorporating metagenomic data and non-linear microbial responses into next-generation carbon-climate models.},
}

*Soil Microbiology
*Carbon/metabolism
*Soil/chemistry
*Temperature
Climate Change
Ecosystem
*Genes, Microbial
Carbon Cycle

@article {pmid42779556,
year = {2026},
author = {Ehiosun, KI and Chapleur, O and Mazéas, L},
title = {Diagnosing Anaerobic Digesters' Function and Performance: From Meta-Omics to Integrated Meta-Omics Analyses.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70417},
doi = {10.1111/1758-2229.70417},
pmid = {42779556},
issn = {1758-2229},
support = {ANR-22-CE43-0014-01//Agence Nationale de la Recherche/ ; },
mesh = {Multiomics ; Anaerobiosis ; Metabolomics/methods ; *Bioreactors/microbiology ; Biofuels ; Metagenomics/methods ; Methane/metabolism ; Proteomics ; *Bacteria/metabolism/genetics ; },
abstract = {Anaerobic digestion (AD) of organic wastes by microorganisms into biomethane contributes significantly towards bioenergy generation. However, the bioprocess remains challenging due to its complex microbial ecology, dynamic biochemical pathways and sensitivity to perturbations. Over the past decade, using meta-omics like metataxonomics, metagenomics, metatranscriptomics, metaproteomics and metabolomics to diagnose its functioning has become necessary and common. However, a single meta-omics method can only provide limited biological understanding of the bioprocess. This led to the use of multi-meta-omics analyses in tandem; however, most studies still examine and interpret each meta-omics separately, limiting their ability to uncover functional interactions across molecular levels. Currently, the frontier is integrated meta-omics, where multi-meta-omics and process data are systematically combined into a single and interpretable system to unlock mechanistic understanding, diagnostic and predictive control of AD. This review critically examines specific application of meta-omics in AD, discussing their strengths, limitations and distinct position in integrated meta-omics approach. Importantly, it explores the computational frameworks, methodologies and challenges of integrated meta-omics. Discovering diagnostic biomarkers with high predictive power and transferability across AD systems through cross-omics validation is highlighted. As workflows standardise and technologies mature, integrated meta-omics would significantly contribute to the advancement of AD bioprocess for bioenergy.},
}

Multiomics
Anaerobiosis
Metabolomics/methods
*Bioreactors/microbiology
Biofuels
Metagenomics/methods
Methane/metabolism
Proteomics
*Bacteria/metabolism/genetics

@article {pmid42779939,
year = {2026},
author = {Coker, MO and Kumar, A and Peter, O and Abulude, IJ and Sheng, Q and Akhigbe, P and Osagie, E and Pan, Q and Aliyu, AT and Liu, J and Idemudia, NL and Obuekwe, O and Shiau, S},
title = {Unique Oral Microbiota Signatures and Neurocognitive Function in Adolescents with and without Perinatally Acquired HIV.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10920507/v1},
pmid = {42779939},
issn = {2693-5015},
abstract = {Adolescents with perinatally acquired HIV (PHIV) on antiretroviral therapy (ART) face early neurocognitive and oral disease, yet links between the oral microbiome and cognition remain underexplored. We analyzed baseline data from 53 PHIV and 47 age-, sex-, and socioeconomically matched HIV-unexposed-uninfected (HUU) adolescents (10-13 years) in Nigeria. Cognition was assessed with NeuroScreen and the NIH Toolbox. Oral rinse shotgun metagenomes were profiled for microbial diversity, community structure, and species-level differential abundance using five complementary methods stratified by HIV serostatus. Taxa were considered robust when concordant across at least two methods. Diversity and community structure did not significantly differ by HIV (Bray-Curtis PERMANOVA R [2] = 0.017, p = 0.11) or across cognitive gradients, however at the species level, reproducible taxon-level signals emerged. In PHIV, Leptotrichia , Tannerella , Actinomyces , and Prevotella were associated with higher performance. In HUU, Neisseria sp. was associated with lower-cognitive performance across analyses in the HUU groups. Streptococcus associations differed in direction by HIV stratum. In this cross-sectional analyses, distinct oral taxa are associated with neurocognitive health in an HIV-context-dependent manner, identifying candidate markers of the oral-brain axis. Longitudinal, multi-omic studies are needed to test directionality and mechanism of action as candidate intervention targets.},
}

@article {pmid42779957,
year = {2026},
author = {Turner, D and Ottesen, A and Kocurek, BJ and Lane, J and Findlay, V},
title = {Ultra processed microbiome: Effects of dietary Stable Carbonyl adducts (SCars) on developing microbiota of mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752391},
pmid = {42779957},
issn = {2692-8205},
abstract = {Consumption of ultra-processed food (UPF) is increasing and is causally linked with noncommunicable disease onset, however specific compounds within UPFs that influence disease risk remain poorly defined. The acronym 'SCars', for Stable Carbonyl Adducts, is introduced herein as an umbrella term encompassing advanced glycation end-products (AGEs), advanced lipoxidation end-products (ALEs), and other carbonyl-derived modifications. These molecules arise as products of spontaneous carbonyl chemistry, a reaction accelerated by industrial food processing. Dietary SCars have been associated with metabolic dysfunction; however, their impact on microbiome composition during windows of developmental vulnerability has not been well studied. Puberty in mice represents a period of developmental plasticity during which the gut microbiome is susceptible to dietary exposures. We tested whether transient exposure to high levels of dietary SCars during puberty remodels the developing gut microbiome. Using metagenomic sequencing of fecal samples from mice exposed to high-SCars or control diets, we found that high-SCars exposure profoundly impacted microbial community structure and metabolic potential. Dietary SCars reduced microbial diversity and depleted short-chain fattyacid producing taxa while enriching pathways related to membrane remodeling, branched-chain amino acid biosynthesis, and nucleotide anabolism. These data identify SCars as features of UPFs capable of reprogramming the developing gut microbiota.},
}

@article {pmid42779984,
year = {2026},
author = {Kitsios, G and Sy, MA and Bain, WG and Hensley, M and Qin, S and Wang, X and Inman, KW and Dela Cruz, C and Robinson, K and Nouraie, SM and Shah, FA and Benos, P and McVerry, BJ and Morris, A},
title = {Microbiome Profiling Reveals Prognostic Heterogeneity in Staphylococcus aureus Pneumonia.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.26363347},
pmid = {42779984},
abstract = {BACKGROUND: Staphylococcus aureus is a leading cause of severe pneumonia in mechanically ventilated patients. Clinical cultures identify pathogen presence but may not reflect lower respiratory tract microbial ecology. Whether culture-confirmed S. aureus pneumonia encompasses compositional heterogeneity with prognostic implications remains unknown.

METHODS: We performed 16S rRNA gene sequencing and shotgun nanopore metagenomics on endotracheal aspirate samples from mechanically ventilated patients with culture-confirmed S. aureus pneumonia in a prospective ICU registry. We quantified Staphylococcus abundance, assessed correlations with culture characteristics and host inflammatory biomarkers, and examined associations with 60-day mortality using Kaplan-Meier and Cox hazards analyses.

RESULTS: Among 109 patients, semi-quantitative culture growth and methicillin resistance showed no associations with outcomes. 16S sequencing (n=54) revealed marked heterogeneity in Staphylococcus relative abundance (range 0-96.7%), with only 33% demonstrating dominance (>50%). Dominance was associated with worse 60-day survival (50% vs. 80%,p=0.013) and remained independently predictive after adjusting for age, sex, and methicillin resistance (adjusted HR 3.24 [95%CI 1.12-9.36],p=0.030). Patients with dominance exhibited elevated pentraxin-3 (p=0.01) and reduced fractalkine (p=0.02). Nanopore metagenomics (n=28) validated these findings, with high absolute S. aureus read counts independently predicting mortality (adjusted HR 11.23 [95%CI 2.25-55.9],p=0.003). In an exploratory analysis of virulence genes (n=19), staphylokinase detection was associated with the hyperinflammatory phenotype (p=0.003) and mortality (p=0.046).

CONCLUSIONS: Metagenomic profiling reveals clinically meaningful heterogeneity within culture-confirmed S. aureus pneumonia, masked by conventional diagnostics. Staphylococcus dominance identifies a high-risk phenotype with elevated bacterial burden, dysregulated host responses, and increased mortality, challenging the assumption that culture positivity represents a uniform clinical entity.},
}

@article {pmid42780003,
year = {2026},
author = {Fodor, KE and Ritter, AC and Nickerson, K and Prasad, A and Ricart Arbona, RJ and Krumbeck, J and Lipman, NS},
title = {Skin and Gut Microbiome Features Associated with Resistance to Corynebacterium bovis -Associated Disease in Nude Mice (Mus musculus).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.15.751397},
pmid = {42780003},
issn = {2692-8205},
abstract = {Corynebacterium bovis is an important opportunistic pathogen of immunodeficient mice and the etiologic agent of Corynebacterium -associated hyperkeratosis (CAH). Although disease severity varies, specific vendor-derived microbiomes have been shown to protect against CAH. Preinoculation with nonpathogenic Corynebacterium amycolatum prior to C. bovis infection has been demonstrated to limit disease severity. To define community features associated with protection, axenic outbred athymic nude mice stocks (A, B, and C) were reassociated with donor microbiomes from four vendor sources (A1, A2, B, and C) and topically challenged with C. bovis . C. amycolatum was added to the A1 microbiome in a separate group. Skin (Stock A) and fecal (Stocks A, B, and C) microbiomes were evaluated at 21 days post-inoculation via shotgun metagenomic sequencing. The A2 microbiome, previously associated with resistance to clinical disease and minimal skin pathology, exhibited greater cutaneous microbial evenness after challenge and significantly lower relative abundance of C. bovis than all other microbiome groups. Addition of C. amycolatum to the A1 microbiome did not fully confer disease protection and relative abundance was low, suggesting that sustained colonization by this organism was insufficient to explain the protective phenotype seen with the A2 microbiome. C. kroppenstedtii was detected in all A2 skin samples and was absent from all other groups. Several anaerobic taxa, including Duncaniella dubosii, D. muris, Bacteroides caecimuris , and Muribaculum gordoncarteri , were uniquely detected or enriched in the A2-associated microbiome, whereas Mammaliicoccus lentus and Staphylococcus nepalensis were absent from A2 but present in all nonprotective groups. Gut alpha diversity did not differ significantly among microbiomes, although several taxa, including segmented filamentous bacteria, were enriched in A2 feces. These findings associate resistance to CAH with preservation of cutaneous community structure, suppression of C. bovis prominence, and distinct microbial taxa. The identified organisms represent candidates for future mechanistic studies of microbiome-mediated colonization resistance.},
}

@article {pmid42780034,
year = {2026},
author = {Long, W and Tantry, A and Tran, J and Cyphert, EL},
title = {Validating a high-throughput in vitro model for culturing antibiotic-altered microbiome communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.16.752229},
pmid = {42780034},
issn = {2692-8205},
abstract = {The gut microbiome plays a central role in host health, and its disruption is associated with metabolic, infectious, and immune conditions. Stool sampling is frequently used to characterize snapshots of the gut microbiota. To screen microbiota communities in vitro, multi-stage bioreactors have been developed that model distinct physiological environments along the gastrointestinal tract. However, such bioreactors are often operationally complex and provide limited throughput. Stool-derived in vitro communities offer several advantages to study microbiota due to their ease of use, high-throughput nature, and have previously been shown to remain stable following repeat passaging. Yet, prior characterization of stool-derived cultures has relied on 16S rRNA sequencing of unaltered gut microbiota, leaving several key questions unanswered: 1) how closely does in vitro culture recapitulate the functional potential and resistome composition of its inoculum and 2) can these cultures model antibiotic disrupted microbial communities? In this work, we generated stool-derived in vitro cultures from male and female mice with both unaltered and antibiotic altered gut microbiomes and applied shotgun metagenomic sequencing to characterize taxonomic composition, functional pathway capacity, and antimicrobial resistance gene (ARG) content. Antibiotic-altered microbiota communities, dominated by Enterobacteriaceae, were faithfully recapitulated in culture with preservation of both taxonomy and ARGs. By contrast, unaltered communities underwent substantial restructuring in culture, with Bifidobacterium and Enterococcus blooming and driving sex-divergent shifts in functional capacity and a substantial amplification of the resistome. Together, these findings validate a high-throughput stool-derived in vitro culture as a tractable proxy for an antibiotic altered gut microbiome to screen interventions.},
}

@article {pmid42780152,
year = {2026},
author = {Cui, D and Ren, X and Li, N},
title = {Integrating metagenomics, transcriptomics, and molecular docking to reveal core gene biomarkers and gut microbiota regulatory mechanisms in tuberculous meningitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1844914},
pmid = {42780152},
issn = {1664-3224},
mesh = {Humans ; *Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology ; Molecular Docking Simulation ; *Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; Biomarkers ; Female ; Male ; Gene Expression Profiling ; *Transcriptome ; Dysbiosis/microbiology ; Adult ; Macrophages/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: Tuberculous meningitis (TBM) is a severe extrapulmonary tuberculosis with high mortality and neurological sequelae, while the role of gut microbiota and its metabolites in TBM pathogenesis remains poorly understood. This study aimed to characterize gut microbiota alterations in TBM patients and elucidate the "microbiota-metabolite-gene" regulatory axis.

METHODS: Fecal samples from 11 TBM patients and 11 healthy controls were subjected to 16S rRNA sequencing. Core target genes were identified via differential expression screening, machine learning, immune infiltration analysis and gene set enrichment analysis based on the public GSE40586 dataset. The regulatory axis was constructed by database prediction and molecular docking, and the regulatory effect was verified by in vitro functional assays in THP-1-derived macrophages.

RESULTS: TBM patients exhibited significant gut dysbiosis. Two core genes (PIK3CB and JAK2) were identified, which were positively correlated with pro-inflammatory immune cells and enriched in bacterial infection pathways. The constructed regulatory axis showed that upregulated gut bacteria produced bile acid metabolites targeting PIK3CB/JAK2, with strong binding affinity verified by molecular docking. In vitro experiments verified that CDCA dose-dependently upregulated PIK3CB and JAK2 expression and promoted pro-inflammatory activation of macrophages, while silencing of target genes significantly reversed this effect.

CONCLUSION: This study identifies a "gut microbiota-bile acid-PIK3CB/JAK2" regulatory axis in TBM, thus providing novel insights into gut-brain crosstalk and potential diagnostic biomarkers and therapeutic targets.},
}

Humans
*Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology
Molecular Docking Simulation
*Metagenomics/methods
*Gastrointestinal Microbiome/immunology
Biomarkers
Female
Male
Gene Expression Profiling
*Transcriptome
Dysbiosis/microbiology
Adult
Macrophages/immunology/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42780282,
year = {2026},
author = {Sóki, J},
title = {Description and evolution of a nimB gene-coding, composite mobilizable transposon, MTnBf8, of Bacteroides fragilis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923328},
pmid = {42780282},
issn = {1664-302X},
abstract = {BACKGROUND: In Bacteroides strains, metronidazole resistance is encoded mainly by the so-called nim genes, which are usually carried on plasmids; however, chromosomal presence is also known (e.g., nimB). Usually, the nim genes are activated by insertion sequence (IS) elements, conferring resistance. Molecular epidemiological observations predict that this configuration most likely arose before the formation of the best-known carrier mobile genetic elements.

OBJECTIVE: To determine the nimB genetic element and study its evolution.

METHODS: To fulfill the goals, the whole-genome sequence of B. fragilis BF8, inverse PCRs, and bioinformatic analyses were used.

RESULTS: A novel mobilizable transposon, MTnBf8, is described, with an integrated part, TnNimB1, that carries the chromosomal nimB gene. Cassettes similar to TnNimB1 were found in Bacteroides-related species in fecal metagenomes, but these species did not harbor IS1168. In inverse PCR, the excised intermediates of MTnBf8 and TnNimB1 were detected, thereby confirming their mobility. In alignments of nucleotide and protein sequences, the existence of the TnNimBs and at least three groups of integrative elements of Bacteroides could be confirmed, and a scheme for the emergence of different nimB-carrying elements was drawn.

CONCLUSION: The data presented here could explain the above-mentioned emergence of MTnBf8/TnNimB1 and the IS-nimB configurations and their expected spread.},
}

@article {pmid42780326,
year = {2026},
author = {Li, J and Ran, L and Xue, S and Sun, Y},
title = {Animal type outweighs growth stage in shaping the active antibiotic resistome in livestock manure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1898413},
pmid = {42780326},
issn = {1664-302X},
abstract = {Animal manure is a major reservoir of antibiotic resistance genes (ARGs), yet the factors governing their composition and activity remain insufficiently understood. In this study, metagenomics, metatranscriptomics, and quantitative PCR (qPCR) were integrated to characterize microbial communities and resistome profiles in manure from five animal types across multiple growth stages. Results demonstrated that animal type was the dominant factor shaping both microbial community structure and ARG composition at DNA and RNA levels, whereas growth stage did not significantly influence overall community structure. Metagenomic analysis identified 944 ARG subtypes, predominantly associated with tetracycline, multidrug, and macrolide-lincosamide-streptogramin (MLS) resistance. Metatranscriptomic analysis further revealed 579 actively transcribed ARG subtypes, among which 29 [e.g., tet(W), sul1, and erm(B)] were consistently detected at both DNA and RNA levels, indicating their active nature. Among tested animal types, layer litter showed the highest ARG number at the DNA level, with qPCR results further revealing significantly higher abundances of specific ARGs, including bla TEM and erm(B). Although growth stage had limited influence on overall resistome composition, stage-dependent variations in ARG abundance were observed, with higher levels during early-life and juvenile stages. Procrustes analysis revealed strong correlations between microbial community composition and resistome profiles in both DNA and RNA levels, suggesting that microbiome structure plays a key role in shaping ARG dynamics and activity. Overall, animal type was the dominant measured correlate of resistome composition, whereas growth stage was associated mainly with variation in selected ARG abundances. These observational findings require validation in multi-farm longitudinal studies before management or environmental-risk conclusions are drawn.},
}

@article {pmid42780330,
year = {2026},
author = {Belenky, P and Meyer, F},
title = {Grand challenge in microbiome data science: recovering the microbiome as a system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1970739},
pmid = {42780330},
issn = {1664-302X},
}

@article {pmid42780358,
year = {2026},
author = {Huang, L and Sun, J and Tian, G and Liu, C and Li, C and Ma, X and Zhao, Y and Pei, Z and Lu, W and Wang, H},
title = {Bifidobacterium breve alleviates dry eye disease by regulating gut microbiota and vitamin A metabolism.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1956357},
doi = {10.3389/fnut.2026.1956357},
pmid = {42780358},
issn = {2296-861X},
abstract = {The gut microbiota can metabolize vitamin A and may thereby alleviate symptoms of dry eye disease. Bifidobacterium breve CCFM1489 was investigated, a commensal strain capable of converting vitamin A (VA) into retinoic acid (RA), in a benzalkonium chloride-induced DED mouse model. The results demonstrated that CCFM1489 alleviated dry eye symptoms, as evidenced by reduced fluorescein sodium staining of the cornea, improved corneal and conjunctival histopathology. These effects were accompanied by reducing oxidative stress and inflammation whilst elevating systemic RA levels. Integration of gut metagenomic and faecal/serum metabolomic analyses provided preliminary insights into the underlying mechanisms. CCFM1489 reshaped the gut microbial composition and structure, increasing the abundance of specific taxa, including Parabacteroides goldsteinii and Lactiplantibacillus plantarum, that were associated with metabolic improvements. Functional shifts indicated enhanced microbial VA metabolism and modulation of host-microbiota pathways. Collectively, CCFM1489 regulates gut microbiota involved in VA metabolism and represents a promising microbiota-targeted strategy for ameliorating dry eye disease.},
}

@article {pmid42780395,
year = {2026},
author = {Ma, C and Lei, S and Zhang, G and Hu, X and Qiu, X and Wang, Q and Kang, X},
title = {Multiorgan and gut microbial alterations in ovariectomized mice: a multiomics analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847257},
doi = {10.3389/fimmu.2026.1847257},
pmid = {42780395},
issn = {1664-3224},
mesh = {Animals ; *Ovariectomy ; Female ; Multiomics ; *Gastrointestinal Microbiome ; Mice ; Liver/metabolism ; Metabolomics/methods ; Colon/metabolism/microbiology ; Muscle, Skeletal/metabolism ; Metabolome ; Mice, Inbred C57BL ; Transcriptome ; },
abstract = {INTRODUCTION: Postmenopausal metabolic dysfunction is increasingly recognized as a multisystem disorder associated with estrogen deficiency, yet how gut microbial, metabolic, and tissue-level alterations co-occur across organs remains incompletely characterized.

METHODS: Here, we used an ovariectomy (OVX) mouse model and an integrated multiomics strategy to characterize systemic alterations in gut microbiota, metabolites in colonic contents and circulation, and tissue-level molecular profiles across the colon, liver, skeletal muscle, and bone.

RESULTS: OVX mice showed higher body weights at multiple postoperative time points, lower serum estradiol concentrations, differences in selected inflammatory and bone-turnover markers, representative histological differences across multiple tissues, and OVX-Sham differences in femoral microarchitecture. Shotgun metagenomic profiling showed significant differences in gut microbial composition, with lower evenness-sensitive diversity and differences in dominant taxa. Metabolomic profiling of colonic contents demonstrated global differences in the luminal metabolic profile, including lower relative abundances of major short-chain fatty acids, differences in bile acid composition, and prominent tryptophan-related features. At the host interface, colonic transcriptomic analysis identified annotations related to epithelial membrane polarity, vesicle trafficking, endoplasmic reticulum protein processing, and bile acid- and energy-sensing pathways. Among the 19 differential circulating bile acids and short-chain fatty acids, most were lower in OVX mice. Feature-level analyses identified multiple hepatic metabolite and bile acid differences, whereas the hepatic transcriptome did not show significant global separation; differential-expression and gene-set enrichment analyses nonetheless identified selected differences related to lipid metabolism, energy metabolism, and molecular transport. Distal tissues also displayed molecular differences, including a significant global transcriptomic difference in skeletal muscle and a significant global metabolomic difference in bone; differential bone metabolites were annotated to energy-, amino-acid-, lipid-, and cyclic guanosine monophosphate-protein kinase G (cGMP-PKG)-related pathways.

DISCUSSION: Collectively, these findings define a gut-associated, multiorgan pattern of OVX-related remodeling characterized by concurrent microbial, metabolite, and tissue-level differences. This descriptive, associative, and hypothesis-generating dataset provides a reference for future studies testing the relevance of these OVX-associated patterns to menopause-associated metabolic dysfunction.},
}

Animals
*Ovariectomy
Female
Multiomics
*Gastrointestinal Microbiome
Mice
Liver/metabolism
Metabolomics/methods
Colon/metabolism/microbiology
Muscle, Skeletal/metabolism
Metabolome
Mice, Inbred C57BL
Transcriptome

@article {pmid42780415,
year = {2026},
author = {Zhou, Y and Zhang, L and Liu, X and Wu, D},
title = {Case Report: Suspected Mycobacterium abscessus-associated polyserositis following coronary stenting, diagnosed with the aid of metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1910932},
doi = {10.3389/fmed.2026.1910932},
pmid = {42780415},
issn = {2296-858X},
abstract = {BACKGROUND: Mycobacterium abscessus (M. abscessus), a rapidly growing non-tuberculous mycobacterium (NTM), rarely causes extrapulmonary disease involving more than one serosal compartment.

CASE PRESENTATION: An 83-year-old man developed intermittent fever about 6 weeks after coronary stent implantation. Multiple antibiotics were ineffective, and he was admitted for fever of unknown origin. Echocardiography showed newly developed pericardial adhesion with echocardiographic changes suggestive of possible early constrictive physiology. These were absent on the echocardiogram performed on the day of percutaneous coronary intervention. During admission, he underwent surgery for mechanical small-bowel obstruction, in which dense omental adhesions were found. With no prior abdominal surgery, the synchronous pericardial, pleural, and peritoneal abnormalities raised suspicion of a systemic inflammatory or infectious process. A single blood-culture draw at the outside hospital grew coagulase-negative staphylococcus, but blood cultures repeated after admission and a bone-marrow culture were negative. Blood metagenomic next-generation sequencing (mNGS) detected M. abscessus at very low abundance (three species-level reads, below the ≥8-read threshold), reported as a suspected organism. Temperature improved during the administration of agents with recognized activity against M. abscessus (linezolid, tigecycline) and relapsed during the administration of β-lactams not active against this organism. Integrating the clinical course, treatment response, and consultation from a tuberculosis specialty hospital, a clinically suspected diagnosis of M. abscessus infection supported by mNGS was made, although microbiological confirmation was not obtained. Temperature normalized on tigecycline and the patient's condition improved, and he was transferred for continued anti-NTM therapy. He was subsequently lost to follow-up, and therefore, the long-term outcome is unknown.

CONCLUSION: We report a rare presentation of suspected M. abscessus-associated polyserositis following coronary stenting, in which mNGS provided the etiologic clue when cultures were unrevealing. NTM should be considered in older patients with unexplained fever after cardiovascular intervention. Low-abundance mNGS results, although below reporting thresholds, may be clinically meaningful when interpreted alongside the clinical course and treatment response, while remaining open to contamination and misclassification. NTM-associated myeloperoxidase-antineutrophil cytoplasmic antibody positivity is non-specific and must be distinguished from primary vasculitis.},
}

@article {pmid42780416,
year = {2026},
author = {Yan, J and Ren, Q and He, X and Du, H and He, L and Zheng, Z and Qi, Y and Xian, X},
title = {Spatiotemporal characteristics of environmental microbial communities and resistomes in intensive care units of a tertiary hospital in northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1909107},
doi = {10.3389/fmicb.2026.1909107},
pmid = {42780416},
issn = {1664-302X},
abstract = {BACKGROUND: Intensive care units (ICUs) are high-risk settings for healthcare-acquired infections (HAIs). It is essential to characterize the microorganisms and antimicrobial resistance genes (ARGs) in ICU environments for prevention and control of HAIs.

METHODS: Totally, 206 environmental and patient samples were collected from general ICU (GICU), emergency ICU (EICU), pediatric ICU (PICU), and neonatal ICU (NICU). Longitudinal sampling was conducted in PICU at four time points from May 2024 to March 2025. All samples were subjected to metagenomic sequencing. The differences of microbial and ARG profiles were further analyzed across different ICU types as well as sampling areas and times.

RESULTS: Alpha diversity did not differ among ICU types. In contrast, microbial community composition varied across ICUs (PERMANOVA, p = 0.001). GICU and EICU samples clustered together, enriched with Acinetobacter baumannii and Klebsiella pneumoniae, whereas NICU and PICU samples showed greater similarity, with enrichment of Streptococcus pneumoniae and Burkholderia cepacia. Sampling areas also exhibited differences in both alpha diversity (p < 0.001) and beta diversity (p = 0.001). Similar spatial patterns were observed for ARGs. Although ARG alpha diversity remained relatively stable, beta diversity differed significantly among ICU types and sampling areas (p = 0.001). Temporal variation was also evident in the PICU, where both microbial and ARG profiles changed over time (p = 0.001), and clinically relevant pathogens reached their highest abundance in November.

CONCLUSIONS: These findings demonstrate obvious spatial and temporal variability in microbial and ARG profiles across ICU environments, supporting the development of targeted infection control strategies.},
}