@article {pmid41943240,
year = {2026},
author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J},
title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {4},
pages = {e70421},
doi = {10.1002/iid3.70421},
pmid = {41943240},
issn = {2050-4527},
support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; },
mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid/immunology ; *SARS-CoV-2 ; *Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology ; *Area Postrema/virology/pathology ; Middle Aged ; Adult ; Magnetic Resonance Imaging ; Immunoglobulin G/blood/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/blood ; },
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.

METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.

RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.

CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.},
}

Humans
Female
*COVID-19/complications/cerebrospinal fluid/immunology
*SARS-CoV-2
*Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology
*Area Postrema/virology/pathology
Middle Aged
Adult
Magnetic Resonance Imaging
Immunoglobulin G/blood/cerebrospinal fluid
Aquaporin 4/immunology
Autoantibodies/blood

@article {pmid41943413,
year = {2026},
author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J},
title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {75-83},
doi = {10.33073/pjm-2026-008},
pmid = {41943413},
issn = {2544-4646},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; Aged ; Bacteria/genetics/isolation & purification/classification ; *Pneumonia/microbiology/blood/complications/diagnosis ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Adult ; *Sepsis/microbiology/diagnosis ; },
abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology/virology
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Retrospective Studies
Middle Aged
*Metagenomics/methods
Aged
Bacteria/genetics/isolation & purification/classification
*Pneumonia/microbiology/blood/complications/diagnosis
Fungi/genetics/isolation & purification/classification
Aged, 80 and over
Adult
*Sepsis/microbiology/diagnosis

@article {pmid41943678,
year = {2026},
author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J},
title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70843},
doi = {10.1111/gcb.70843},
pmid = {41943678},
issn = {1365-2486},
support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Biodiversity ; China ; *Soil/chemistry ; *Fungi/physiology ; Ecosystem ; *Sodium/analysis ; Salinity ; },
abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.},
}

*Soil Microbiology
*Biodiversity
China
*Soil/chemistry
*Fungi/physiology
Ecosystem
*Sodium/analysis
Salinity

@article {pmid41944124,
year = {2026},
author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W},
title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10074},
pmid = {41944124},
issn = {1520-5851},
abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.},
}

@article {pmid41944276,
year = {2026},
author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R},
title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13821},
pmid = {41944276},
issn = {1520-5851},
abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.},
}

@article {pmid41944309,
year = {2026},
author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L},
title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17245},
doi = {10.1002/advs.202517245},
pmid = {41944309},
issn = {2198-3844},
support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.},
}

@article {pmid41946009,
year = {2026},
author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P},
title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.},
journal = {Enzyme and microbial technology},
volume = {198},
number = {},
pages = {110869},
doi = {10.1016/j.enzmictec.2026.110869},
pmid = {41946009},
issn = {1879-0909},
abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.},
}

@article {pmid41946242,
year = {2026},
author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L},
title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141986},
doi = {10.1016/j.jhazmat.2026.141986},
pmid = {41946242},
issn = {1873-3336},
abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.},
}

@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}

@article {pmid41946403,
year = {2026},
author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y},
title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134561},
doi = {10.1016/j.biortech.2026.134561},
pmid = {41946403},
issn = {1873-2976},
abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.},
}

@article {pmid41946559,
year = {2026},
author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S},
title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.},
journal = {The British journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1136/bjo-2025-328867},
pmid = {41946559},
issn = {1468-2079},
abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.

METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.

RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; κ=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; κ=0.78), though accuracy remained below specialists (87-90%; κ≈0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; κ=0.95; GPT-5 91.7%; κ=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.

CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.},
}

@article {pmid41889817,
year = {2026},
author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL},
title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41889817},
issn = {2692-8205},
abstract = {Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.},
}

@article {pmid41937465,
year = {2026},
author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT},
title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2508050},
doi = {10.4014/jmb.2508.08050},
pmid = {41937465},
issn = {1738-8872},
mesh = {*Petroleum/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Salinity ; Soil Microbiology ; Metagenomics/methods ; Biodegradation, Environmental ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.},
}

*Petroleum/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
*Salinity
Soil Microbiology
Metagenomics/methods
Biodegradation, Environmental
Soil Pollutants/metabolism
Hydrocarbons/metabolism
*Microbiota
Phylogeny

@article {pmid41937665,
year = {2026},
author = {Sizikova, TE and Lebedev, VN and Borisevich, SV},
title = {The Mengla virus (Filoviridae: Dianlovirus).},
journal = {Voprosy virusologii},
volume = {71},
number = {1},
pages = {7-12},
doi = {10.36233/0507-4088-356},
pmid = {41937665},
issn = {2411-2097},
mesh = {Animals ; *Chiroptera/virology/genetics ; *Filoviridae/genetics/classification/pathogenicity/isolation & purification ; Humans ; Phylogeny ; Genetic Variation ; Genome, Viral ; *Filoviridae Infections/virology/epidemiology/genetics ; Asia, Southeastern/epidemiology ; Hemorrhagic Fever, Ebola/virology/genetics/epidemiology ; },
abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.

MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.

RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.

CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.},
}

Animals
*Chiroptera/virology/genetics
*Filoviridae/genetics/classification/pathogenicity/isolation & purification
Humans
Phylogeny
Genetic Variation
Genome, Viral
*Filoviridae Infections/virology/epidemiology/genetics
Asia, Southeastern/epidemiology
Hemorrhagic Fever, Ebola/virology/genetics/epidemiology

@article {pmid41937718,
year = {2026},
author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X},
title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17817},
pmid = {41937718},
issn = {1520-5851},
abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.},
}

@article {pmid41937905,
year = {2026},
author = {Cheng, Y and Peng, L and Liu, D and Zhong, L and Liu, Y and Yang, T},
title = {Case Report: A rare culprit of severe pulmonary infection in children: prevotella.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1782202},
pmid = {41937905},
issn = {2296-2360},
abstract = {BACKGROUND: To characterize the clinical features, diagnostic pitfalls, and treatment of severe pediatric pulmonary infection caused by Prevotella species.

METHODS: We retrospectively reviewed clinical data, the diagnostic workflow, antimicrobial regimens, and outcomes of two children with severe Prevotella pulmonary infection.

RESULTS: Case 1 was an 11-year-old boy with necrotizing pneumonia, and Case 2 was a 13-year-old boy with retained foreign-body aspiration. Both patients responded poorly to initial cephalosporin-based therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid identified Prevotella nanceiensis (sequence count 299,022; relative abundance 92.24%) and Prevotella oralis (210,449; 67.98%) within 24 h, whereas anaerobic culture (Case 1) became positive after 4 days. Based on mNGS results antibiotics were adjusted to metronidazole plus a carbapenem (meropenem for Case 1; imipenem-cilastatin for Case 2), and both children received adjunctive pulmonary rehabilitation before discharge. They subsequently recovered and were discharged.

CONCLUSION: Severe Prevotella pulmonary infection in children has non-specific manifestations and may respond poorly to conventional beta-lactam therapy, leading to delayed diagnosis. mNGS enables rapid pathogen identification and supports targeted anti-anaerobic treatment. For severe or complicated cases refractory to empirical therapy, metronidazole combined with a carbapenem may be an effective option.},
}

@article {pmid41937991,
year = {2026},
author = {Halphen, J and Ahmadzade, M and Mankidy, B and Berenji, A and Ghasemi-Rad, M},
title = {Letter to the Editor: Evidence for a two-step species-level pulmonary nocardiosis diagnostic approach.},
journal = {World journal of radiology},
volume = {18},
number = {3},
pages = {118126},
pmid = {41937991},
issn = {1949-8470},
abstract = {Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The authors also compared traditional cultures to mNGS, finding that traditional cultures and mNGS were concordantly positive in only 3.3% of cases. This letter supports a combined radiologic and molecular diagnostic approach, enabling earlier and more accurate species identification in pulmonary nocardiosis, thereby informing treatment decisions, and enhancing epidemiologic understanding.},
}

@article {pmid41938562,
year = {2026},
author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F},
title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).},
journal = {Veterinary world},
volume = {19},
number = {2},
pages = {864-876},
pmid = {41938562},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.

MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), α- and β-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.

RESULTS: α-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, β-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.

CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.},
}

@article {pmid41938867,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R},
title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779554},
pmid = {41938867},
issn = {2235-2988},
mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.

METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.

RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.

DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.},
}

Female
Humans
Phylogeny
*Candidiasis, Vulvovaginal/virology/microbiology
Genome, Viral
Vagina/virology/microbiology
Metagenomics
Capsid Proteins/genetics
RNA, Viral/genetics
RNA-Dependent RNA Polymerase/genetics
Adult
*Double Stranded RNA Viruses/genetics/isolation & purification/classification

@article {pmid41939082,
year = {2026},
author = {Turner, ML and Nguyen, MT and Kung, Y and Doan, T and Seitzman, GD},
title = {Rhizopus angle abscess, scleritis and endophthalmitis following Kahook Dual Blade goniotomy and phacoemulsification.},
journal = {American journal of ophthalmology case reports},
volume = {42},
number = {},
pages = {102572},
pmid = {41939082},
issn = {2451-9936},
abstract = {PURPOSE: To describe a rare case of Rhizopus angle abscess progressing to scleritis and endophthalmitis after routine cataract surgery with Kahook Dual Blade (KDB) goniotomy in an immunocompetent patient.

OBSERVATION: A 79-year-old male developed hyphema and anterior chamber fibrin three days after uncomplicated phacoemulsification with KDB. Despite intravitreal vancomycin and ceftazidime, inflammation worsened, and by postoperative day nine vision was count fingers with intraocular pressure of 29 mmHg. Slit-lamp exam showed an inferonasal corneal infiltrate with a purulent angle abscess at the goniotomy site and dense vitritis. Intravitreal and oral voriconazole were started for presumed fungal infection. Standard cultures and PCR were negative, but metagenomic RNA deep sequencing of aqueous fluid detected Rhizopus stolonifer. After two months of systemic and intravitreal voriconazole, the infection resolved and visual acuity improved to 20/70, leaving localized limbal thinning.

CONCLUSION AND IMPORTANCE: This case illustrates that Rhizopus angle abscess can occur in an immunocompetent host following anterior segment surgery and may masquerade as bacterial endophthalmitis. Early suspicion of fungal infection and use of metagenomic deep sequencing were critical for diagnosis and successful treatment, emphasizing the need to consider invasive fungal pathogens and advanced molecular diagnostics in culture-negative postoperative ocular infections.},
}

@article {pmid41939697,
year = {2026},
author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M},
title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786817},
pmid = {41939697},
issn = {1664-302X},
abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.},
}

@article {pmid41939705,
year = {2026},
author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP},
title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768977},
pmid = {41939705},
issn = {1664-302X},
abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.},
}

@article {pmid41939707,
year = {2026},
author = {Li, X and Jin, S and Hu, H and Lan, Y and Ni, B and Su, J and Luo, S and Tan, L and Zhang, Y and Huang, H and Xu, Y and Yang, J and Zhou, C and Chen, K and Li, S and Liang, B and Bai, S and Zhang, K and Pan, H and Dong, X and Yan, D},
title = {Feeding Diqing Tibetan pigs with 50% of soybean meal replaced by walnut meal can reduce subcutaneous fat deposition and promote intramuscular fat accumulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794046},
pmid = {41939707},
issn = {1664-302X},
abstract = {BACKGROUND: Protein feed resource shortage is a major constraint to the sustainable development of the livestock industry and a bottleneck problem hindering the growth of the Tibetan pig industry in China's Qinghai-Tibet Plateau region. Walnut meal, rich in protein, holds promise as a substitute for soybean meal. However, the effects and underlying mechanisms of walnut meal substitution on Tibetan pigs in Diqing remain unclear.

RESULTS: The study showed that substituting 50% of soybean meal with walnut meal in the diet of Diqing Tibetan pigs significantly reduced backfat thickness and increased intramuscular fat content (P < 0.05). Integrated multi-omics analyses, including metagenomics, transcriptomics, and lipidomics, revealed that walnut meal substitution significantly reduced the abundance of Clostridium butyricum in the cecum of Diqing Tibetan pigs. The reduction in Clostridium butyricum was linked to the lipolytic capacity of subcutaneous adipose tissue, potentially facilitating the breakdown of triglycerides into free fatty acids (FFAs), which are then released into the bloodstream. When these free fatty acids are transported to muscle tissue, the muscle exhibited inhibited oxidative metabolism (e.g., a decrease in acylcarnitine metabolites), while showing an upregulation in the expression of genes related to adipocyte differentiation (e.g., MEDAG, VDR) and triglyceride synthesis (e.g., PPARGC1A, ANGPTL4). Ultimately, these processes may contribute to the synthesis and storage of triglycerides in muscle, thereby facilitating intramuscular fat deposition.

CONCLUSION: This study reveals that walnut meal can serve as a substitute for soybean meal, and a 50% substitution ratio is conducive to intramuscular fat deposition in Diqing Tibetan pigs. The findings provide valuable insights for the development and application of unconventional protein feed resources, and offer new perspectives for the production of marbled pork.},
}

@article {pmid41939710,
year = {2026},
author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J},
title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741638},
pmid = {41939710},
issn = {1664-302X},
abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.},
}

@article {pmid41939717,
year = {2026},
author = {Navarro-Nieva, A and Martínez-Checa, F and Delgado, R and Párraga, J and Francino, MP and Jiménez-Hernández, N and Del Moral, A},
title = {Airborne microorganisms in muddy rain: microbe-mineral interactions and their ecosystem impact.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1772201},
pmid = {41939717},
issn = {1664-302X},
abstract = {The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.},
}

@article {pmid41940150,
year = {2026},
author = {Luo, H and Wang, Y and Hou, H and Yang, J and Liu, YX},
title = {Advances and applications in sequencing-based pathogen surveillance.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100004},
pmid = {41940150},
issn = {2662-1738},
abstract = {The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.},
}

@article {pmid41940273,
year = {2026},
author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X},
title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.},
journal = {Current zoology},
volume = {72},
number = {1},
pages = {14-29},
pmid = {41940273},
issn = {1674-5507},
abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.},
}

@article {pmid41940285,
year = {2025},
author = {Jeong, GH and Lim, KS},
title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1207-1214},
pmid = {41940285},
issn = {2055-0391},
abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.},
}

@article {pmid41940335,
year = {2026},
author = {Buysse, M and Ballinger, MJ and Bruley, M and Amoros, J and Grillet, J and Farassat, N and Serr, A and Lagrèze, WA and Wennerås, C and Grankvist, A and Schön, T and Berglund, J and Bell-Sakyi, L and Sprong, H and Duron, O},
title = {A human-associated Spiroplasma ixodetis lineage responsible for infantile cataracts and adult febrile illness.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115233},
pmid = {41940335},
issn = {2589-0042},
abstract = {Bacteria of the Spiroplasma ixodetis clade are well characterized as reproductive parasites and defensive endosymbionts of arthropods. Nevertheless, clinical evidence indicates that they can also infect humans, causing neonatal ocular disease and acute febrile illness in adults. Using metagenomic assembly and phylogenomic analyses of Spiroplasma ixodetis-related human infections (SiRHIs), combined with a systematic meta-analysis of public datasets, we identified 25 human cases across ten European countries. Despite the frequent detection of multiple S. ixodetis strains in ticks, our data provide no evidence implicating tick-associated strains in human infections. Instead, SiRHI constitute a distinct monophyletic lineage within the S. ixodetis clade, consistent with a shared evolutionary origin with arthropod-associated relatives. Notably, SiRHI genomes harbor horizontally acquired chaperone genes absent from most arthropod-associated Spiroplasma, while retaining conserved effector genes typical of endosymbionts, suggesting the preservation of ancestral symbiotic traits alongside newly acquired molecular adaptations.},
}

@article {pmid41940665,
year = {2026},
author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X},
title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191125},
doi = {10.1128/spectrum.01911-25},
pmid = {41940665},
issn = {2165-0497},
abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.

IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.},
}

@article {pmid41940696,
year = {2026},
author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M},
title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0190325},
doi = {10.1128/aem.01903-25},
pmid = {41940696},
issn = {1098-5336},
abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.},
}

@article {pmid41940802,
year = {2026},
author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , },
title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2653550},
doi = {10.1080/19490976.2026.2653550},
pmid = {41940802},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Mouth/microbiology ; Female ; *Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Child, Preschool ; Saliva/microbiology ; Infant ; Cross-Sectional Studies ; *Bacterial Translocation ; *Growth Disorders/microbiology ; Child ; *Gastrointestinal Tract/microbiology ; Metagenomics ; },
abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.},
}

Humans
*Gastrointestinal Microbiome
Male
*Mouth/microbiology
Female
*Bacteria/classification/isolation & purification/genetics
Feces/microbiology
Child, Preschool
Saliva/microbiology
Infant
Cross-Sectional Studies
*Bacterial Translocation
*Growth Disorders/microbiology
Child
*Gastrointestinal Tract/microbiology
Metagenomics

@article {pmid41940852,
year = {2026},
author = {Jin, Z and Yuan, Q and Wang, J and Liao, H and Bol, R and Wu, D and Wu, Q and Tang, Y and Guo, W and Liu, Y and Chen, J},
title = {Recycling of Sedimentary Phosphorus Pools in Two Yunnan-Guizhou Plateau Lakes, Southwest China.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c00162},
pmid = {41940852},
issn = {1520-5851},
abstract = {Applying phosphate oxygen isotopes (δ[18]OP) to identify sediment phosphorus (P) sources and its recycling is still challenging due to poor understanding in δ[18]OP variations of sediment P pools and their driving mechanisms. Here, we analyzed the δ[18]OP in inorganic P (Pi) pools of sediment cores and varied P sources from Lake Dianchi and Lake Erhai in the Yunnan-Guizhou Plateau, Southwest China. The δ[18]OP values of sediment detrital Pi (Det-Pi, nonbioavailable P) were consistent with those of watershed soils (within ∼0.4-0.6‰), indicating that the δ[18]OP of sediment Det-Pi inherits the δ[18]OP of soil Det-Pi. The δ[18]OP values of aluminum-bound Pi (Al-Pi) and authigenic Pi (Auth-Pi) in sediment were close to or within the δ[18]OP equilibrium (δ[18]OP-eq) ranges, implying oxygen isotopic exchange equilibrium between phosphate and ambient water prior to the formation of sediment Al-Pi and Auth-Pi. However, the δ[18]OP of iron oxide-bound Pi (Fe-Pi) in sediment was lighter (∼3‰) than δ[18]OP-eq, retaining the negative isotopic signal of organic P (Po) remineralization. Furthermore, [31]P NMR and metagenomic analysis indicated that microbial-mediated Po mineralization and Pi recycling are the driving factors for δ[18]OP changes in sediment Fe-Pi, Al-Pi, and Auth-Pi. These integrated insights deepen our understanding of the biogeochemical cycling for sedimentary P.},
}

@article {pmid41940893,
year = {2026},
author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S},
title = {Establishment of the chromid database and analysis of evolutionary research.},
journal = {Molecular genetics and genomics : MGG},
volume = {301},
number = {1},
pages = {},
pmid = {41940893},
issn = {1617-4623},
mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics/classification ; Polymorphism, Single Nucleotide ; Metagenomics/methods ; Computational Biology/methods ; },
abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.},
}

*Evolution, Molecular
Phylogeny
*Genome, Bacterial/genetics
*Databases, Genetic
*Bacteria/genetics/classification
Polymorphism, Single Nucleotide
Metagenomics/methods
Computational Biology/methods

@article {pmid41941835,
year = {2026},
author = {Hennen, J and Ifrach, J and Morse, C and Charcos, I and Godil, SS and Mossop, CM},
title = {First reported case of Lawsonella clevelandensis brain abscess in the setting of invasive cutaneous squamous cell carcinoma identified via bedside stereotactic aspiration: illustrative case.},
journal = {Journal of neurosurgery. Case lessons},
volume = {11},
number = {14},
pages = {},
doi = {10.3171/CASE25887},
pmid = {41941835},
issn = {2694-1902},
abstract = {BACKGROUND: Brain abscesses associated with malignant skull base invasion pose unique diagnostic and management challenges for neurosurgeons, particularly when routine cultures remain negative. The authors report the first documented intracranial infection caused by Lawsonella clevelandensis, a recently described anaerobe that mimics Nocardia or Mycobacterium sp., diagnosed using bedside stereotactic biopsy as well as metagenomic next-generation sequencing.

OBSERVATIONS: A 74-year-old woman with recurrent, locally invasive facial squamous cell carcinoma presented with recent-onset shaking of her lower extremity and a large right frontal mass extending through the calvarium and orbit. Imaging revealed ring-enhancing lesions consistent with abscess. Bedside stereotactic biopsy and drainage were performed, and metagenomic sequencing identified L. clevelandensis. Antibiotics were narrowed to ceftriaxone and metronidazole, stabilizing her condition, although repeat drainage was required for radiographic progression. She subsequently underwent multidisciplinary skull base resection and reconstruction, with operative cultures isolating Enterococcus faecium but no further Lawsonella sp.

LESSONS: This case represents the first documented intracranial L. clevelandensis infection and demonstrates the diagnostic value of molecular sequencing in culture-negative brain abscesses. It also highlights bedside stereotactic biopsy and drainage as a safe, minimally invasive strategy for managing intracranial infection in medically complex patients. https://thejns.org/doi/10.3171/CASE25887.},
}

@article {pmid41942049,
year = {2026},
author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J},
title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.004},
pmid = {41942049},
issn = {2090-1224},
abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.

OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.

METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.

RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.

CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.},
}

@article {pmid41942192,
year = {2026},
author = {Xia, Y and Kuda, T and Zhou, Q and He, Q},
title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118924},
doi = {10.1016/j.foodres.2026.118924},
pmid = {41942192},
issn = {1873-7145},
mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; *Microbiota/drug effects ; Antioxidants/pharmacology ; Animals ; *Fermented Foods/microbiology ; Humans ; Food Quality ; Taste ; },
abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.},
}

*Gallic Acid/pharmacology
*Meat Products/microbiology/analysis
*Polyphenols/pharmacology
Fermentation
*Tea/chemistry
*Food Microbiology
*Microbiota/drug effects
Antioxidants/pharmacology
Animals
*Fermented Foods/microbiology
Humans
Food Quality
Taste

@article {pmid41942205,
year = {2026},
author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H},
title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118955},
doi = {10.1016/j.foodres.2026.118955},
pmid = {41942205},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Prunus avium/microbiology ; *Metagenomics/methods ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; *Fruit/microbiology ; },
abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.},
}

*Food Storage/methods
*Prunus avium/microbiology
*Metagenomics/methods
*Food Microbiology
*Microbiota
Bacteria/classification/genetics
*Fruit/microbiology

@article {pmid41942425,
year = {2026},
author = {Peña-Valencia, MF and Robaina-Estévez, S and Custer, GF and Turak, O and Sierra, F and Mendes, LW and Rubiano-Labrador, C and Gutiérrez, J and Vaksmaa, A and Dini-Andreote, F and Rosado, AS and Reyes, A and Jiménez, DJ},
title = {Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71548-z},
pmid = {41942425},
issn = {2041-1723},
abstract = {Mangroves are ecosystems located at land-sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.},
}

@article {pmid41942856,
year = {2026},
author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT},
title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04996-8},
pmid = {41942856},
issn = {1471-2180},
support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; },
}

@article {pmid41942925,
year = {2026},
author = {Maimaitiming, A},
title = {Metagenomic next-generation sequencing (mNGS) for severe cat bite infections with negative aerobic culture: a single-center retrospective study in a rabies vaccination center.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13222-9},
pmid = {41942925},
issn = {1471-2334},
}

@article {pmid41943157,
year = {2026},
author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M},
title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00887-7},
pmid = {41943157},
issn = {2524-6372},
support = {2023-21230832//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigación y Desarrollo/ ; 1230084//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; Consolidator grant 865694/ERC_/European Research Council/International ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.

RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.

CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.},
}

@article {pmid41764528,
year = {2026},
author = {Zhang, W and Su, Q and Shi, H and Sun, Y and Li, X and Li, M and Wang, H and Yu, J and Wong, N and Chan, FKL and Zhang, J and Ng, SC},
title = {Discovery and characterization of Christensenella hongkongensis as a novel bacterium in the adenoma-carcinoma progression.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41764528},
issn = {1479-5876},
abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and commonly starts from a pre-cancerous stage. This study aimed to identify potential fecal bacterial candidates associated with progression of CRC from the adenoma-carcinoma sequence and to explore underlying mechanisms of carcinogenesis.

METHODS: Publicly metagenomic datasets were analyzed using MaAsLin2 to identify bacterial species enriched in CRC patients compared to healthy controls. Additionally, we established a large cohort in mainland China, consisting of 686 subjects, including 285 CRC patients, 73 advanced adenoma patients (AA), 134 non-advanced adenoma patients (nAA), and 194 healthy controls (NC). Fecal samples from this cohort were analyzed by duplex quantitative polymerase chain reaction (qPCR) to validate the abundance of key bacterial candidate and its association with tumor node metastasis (TNM) stages. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of Christensenella hongkongensis (C. hongkongensis) alone and in combination with fecal immunochemical test (FIT) across different CRC stages. In vitro experiments and transcriptome sequencing were performed to explore the effects of C. hongkongensis and its mechanisms in CRC progression.

RESULTS: MaAsLin2 analysis identified seven bacterial species were significantly more abundant in fecal samples of CRC patients than in healthy controls (p < 0.05). Among them, C. hongkongensis, an obligately anaerobic, catalase-positive, motile, non-sporulating, gram-positive coccobacillus was distinguished by its lowest abundance in healthy controls and significant enrichment in CRC patients. Validation in our recruited cohort showed that the abundance of C. hongkongensis progressively increased from non-advanced adenomas to advanced adenomas and CRC. For classifying AA from nAA, C. hongkongensis yielded an area under the ROC curve (AUC) of 0.60 (95% CI 0.53–0.68), with 45.2% sensitivity and 85.8% specificity. A combined model integrating C. hongkongensis abundance and FIT further improved diagnostic performance, increasing AUCs from 0.77 to 0.81 for AA vs NC (p < 0.05) and from 0.76 to 0.82 for AA vs nAA (p < 0.001). Linear regression analysis revealed a significant positive association between C. hongkongensis and TNM stages in CRC. In vitro experiments showed that C. hongkongensis promoted CRC cell proliferation, inhibited apoptosis, and enhanced the growth of patient-derived CRC organoids. RNA-seq analysis identified activation of the Wnt/β-catenin signaling pathway, which was further validated by elevated protein levels of active β-catenin, reduced phosphorylation of GSK3β, and the upregulation of downstream targets c-Jun and Cyclin-D1.

CONCLUSIONS: Our findings suggest that C. hongkongensis promotes colorectal tumorigenesis via Wnt/β-catenin activation, and highlight its potential as a novel non-invasive bacterial marker for early detection and monitoring of CRC progression.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07886-9.},
}

@article {pmid41935438,
year = {2026},
author = {Bai, Y and Zhao, J and Wang, Z and Zheng, J and Zhu, X and Shao, Y and Zhang, X},
title = {A case of Rickettsia felis caused pneumonia and diagnosed by clinical analysis and Targeted Next-Generation Sequencing (tNGS) using Bronchoalveolar Lavage Fluid (BALF): A case report and literature review.},
journal = {Journal of infection and public health},
volume = {19},
number = {5},
pages = {103217},
doi = {10.1016/j.jiph.2026.103217},
pmid = {41935438},
issn = {1876-035X},
abstract = {Feline rickettsia pneumonia is a rare lung disease caused by feline R. felis infection, which is mainly transmitted by feline fleas. A 57-year-old male patient was hospitalized with pain in the back of the sternum. Chest CT showed bilateral diffuse interstitial lung disease with multiple nodules. After the empirical anti-infection treatment was ineffective, the second-generation meta-genome sequencing (mNGS) of bronchoalveolar lavage (BALF) was diagnosed as feline rickettsia infection. In terms of treatment, inject tegacycline intravenously and then sequentially take minocycline. The patient's symptoms were relieved quickly, and the imaging improved significantly. This report summarizes the clinical and imaging characteristics and diagnosis and treatment experience of the case, aiming to provide reference for the early identification and treatment of such rare infections.},
}

@article {pmid41935631,
year = {2026},
author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , },
title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.},
journal = {JHEP reports : innovation in hepatology},
volume = {},
number = {},
pages = {101848},
doi = {10.1016/j.jhepr.2026.101848},
pmid = {41935631},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.

METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.

RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.

CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.

CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.},
}

@article {pmid41935814,
year = {2026},
author = {Sambucci, KM and Samaš, P and Ssebide, B and Petrželková, KJ and Okello, RO and Nizeyimana, F and Bukamba, N and Smiley-Evans, T and Gilardi, K and Pafčo, B and Červená, B},
title = {Shifts in strongylid communities associated with chronic wasting in mountain gorillas.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104848},
doi = {10.1016/j.ijpara.2026.104848},
pmid = {41935814},
issn = {1879-0135},
abstract = {Host-parasite relationships are typically maintained in a dynamic equilibrium, but disruptions to this balance can lead to clinical disease and population-level health impacts. Chronic wasting, characterized by chronic loss of body condition, alopecia, a browning hair coat and pot belly, is an emerging health concern in mountain gorillas of Bwindi Impenetrable National Park, Uganda. Deworming of suspected cases has led to marked short-term health improvements, implicating intestinal helminths. To investigate, we analysed faecal samples from human-habituated gorillas collected in 2018 and 2021, and unhabituated gorillas in 2018, using high-throughput sequencing of strongylid nematodes (ITS-2) and gut bacteria (16S). Strongylid community composition varied with chronic wasting occurrence, with Oesophagostomum emerging as a key taxon driving this difference, while bacterial communities remained relatively stable. Strongylid diversity increased between 2018 and 2021, and habituated gorillas exhibited reduced strongylid genetic diversity, higher relative abundance of Oesophagostomum and lower relative abundance of Murshidia compared to unhabituated gorillas. These results suggest that a higher abundance of Oesophagostomum is associated with chronic wasting in mountain gorillas due to either a causative association or because of other genetic, immunological or environmental causes allowing Oesophagostomum, a common member of the gut eukaryote community of the Bwindi gorillas, to overpopulate.},
}

@article {pmid41935918,
year = {2026},
author = {Lazarevic, V and Ruppé, E and Schrenzel, J},
title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.008},
pmid = {41935918},
issn = {1878-4380},
abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.},
}

@article {pmid41936200,
year = {2026},
author = {Uematsu, S},
title = {Programming systemic and mucosal immunity through co-adjuvant-based prime-boost vaccination.},
journal = {Current opinion in virology},
volume = {76},
number = {},
pages = {101525},
doi = {10.1016/j.coviro.2026.101525},
pmid = {41936200},
issn = {1879-6265},
abstract = {The development of effective mucosal vaccines has been limited by the limited availability of mucosal adjuvant approaches with established clinical track records and an incomplete understanding of how systemic and mucosal immunity are coordinated. Recent studies indicate that the priming phase of vaccination plays a decisive role in programming the quality, durability, and anatomical distribution of subsequent immune responses. This review discusses emerging evidence that co-adjuvant-based priming strategies can establish long-lasting immune programs that enable adjuvant-free mucosal boosting. Focusing on the combination of CpG DNA and curdlan as a prototypical example, this review highlights how coordinated activation of innate immune receptors during priming imprints dendritic cells, B cells, and T cells to support robust mucosal IgA and tissue-resident immunity. This review further discusses translational advances demonstrating that this immune programming paradigm can be maintained using translationally oriented formulations designed with clinical development in mind and validated in non-human primates. Independent studies using mRNA and protein-based vaccines support the general principle that the quality of priming, rather than the boosting modality, determines successful mucosal immunity. Together, these findings redefine vaccine adjuvants as tools for immune programming and provide a conceptual framework for next-generation vaccine design.},
}

@article {pmid41936930,
year = {2026},
author = {Zhou, Z and Song, Y and Zhou, Y},
title = {Metagenomic Next-Generation Sequencing Profiling of Primary versus Iatrogenic Osteoarticular Infections: Unveiling Distinct Pathogen Spectra and Diagnostic Implications.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108688},
doi = {10.1016/j.ijid.2026.108688},
pmid = {41936930},
issn = {1878-3511},
abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus microbial culture in primary osteoarticular infection (POI) and iatrogenic osteoarticular infection (IOI), and to analyze pathogen spectrum differences and clinical implications.

METHODS: Ninety-two patients with confirmed osteoarticular infection (POI, n=42; IOI, n=50) were retrospectively analyzed. All specimens were tested using both mNGS and conventional culture. The pathogen detection rates, pathogen spectrum composition, detection of mixed infections, and concordance of results between the two methods were compared.

RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (72.83% vs. 43.48%; P < 0.001), particularly in IOI (78.00% vs. 34.00%; P < 0.001). Pathogen profiling showed predominance of Staphylococcus aureus in POI, whereas IOI exhibited greater microbial diversity with increased detection of Staphylococcus epidermidis (31.03%) and anaerobes (13.79%). Polymicrobial infections were more frequently identified by mNGS (14.13% vs. 4.35% by culture; P = 0.024), primarily in the IOI group. Concordance between mNGS and culture was substantial in POI (κ = 0.66; 95% CI: 0.42-0.89) but only slight in IOI (κ = 0.12; 95% CI: -0.12 to 0.35), largely attributable to the high rate of mNGS-exclusive positives in IOI (48.00%).

CONCLUSION: mNGS improves pathogen detection in osteoarticular infections, especially in IOI where it identifies complex and polymicrobial infections more effectively than culture, providing critical support for guiding antimicrobial therapy.},
}

@article {pmid41936935,
year = {2026},
author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F},
title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134553},
doi = {10.1016/j.biortech.2026.134553},
pmid = {41936935},
issn = {1873-2976},
abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.},
}

@article {pmid41936957,
year = {2026},
author = {Ghaly, TM and Shah, BS and Coleman, NV and Elbourne, LDH and Le Roux, JJ and Gillings, MR and Paulsen, IT and Tetu, SG},
title = {Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124428},
doi = {10.1016/j.envres.2026.124428},
pmid = {41936957},
issn = {1096-0953},
abstract = {Humans are a major evolutionary force, yet our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase (Nar) were specific to Burkholderiales, a major group of denitrifying bacteria. Nar protein regions under positive selection flanked the enzyme's substrate channel, favouring smaller amino acids, likely resulting in the widening of the channel entrance. We present a novel hypothesis that this channel widening could increase rates of substrate turnover, which we propose would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant nitrate reducers globally, such evolutionary consequences of agriculture on this lineage could have cascading environmental impacts, including increased nitrous oxide emissions. These findings indicate that anthropogenic selection might be altering protein-level evolution of vital microbial biogeochemical processes.},
}

@article {pmid41937023,
year = {2026},
author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H},
title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102978},
doi = {10.1016/j.tmaid.2026.102978},
pmid = {41937023},
issn = {1873-0442},
abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.

METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.

RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).

CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.},
}

@article {pmid41937144,
year = {2026},
author = {Bočaj, V and Pongrac, P and Likar, M},
title = {Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00890-y},
pmid = {41937144},
issn = {2524-6372},
support = {P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; },
abstract = {BACKGROUND: Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.

RESULTS: The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log2 fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.

CONCLUSION: Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.},
}

@article {pmid41937169,
year = {2026},
author = {Mullin, CE and Louca, S},
title = {Effects of heat-assisted sample desiccation on microbiome surveys.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00889-5},
pmid = {41937169},
issn = {2524-6372},
abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.},
}

@article {pmid41857392,
year = {2026},
author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J},
title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41857392},
issn = {1432-184X},
support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science & Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; },
abstract = {UNLABELLED: Cold seep is a distinctive deep-sea environment mainly formed by methane-rich fluids leaking on the seafloor, gaps remain regarding the influence of seepage on microorganisms inhabiting water column across vertical and horizontal dimensions. Site F cold seep, located at 1,120 m depth on the northern South China Sea (SCS) slope, is one of the most active cold seeps in SCS. We performed 16S rRNA gene and metagenomic sequencing on samples collected by Niskin bottles mounted on Conductivity-Temperature-Depth profiler and Remote Operated Vehicle to analyze the structure and metabolic potentials of microbial communities throughout the water column at Site F. Microbial abundance generally decreased with depth at all sampling spots and was higher at sites adjacent to the seepage compared to those farther away, indicating a potential vertical and horizonal influence of methane seepage on water microbial community. High microbial abundance at deeper depths may attribute to a higher proportion of Gammaproteobacteria, comprised mainly of Alcanivoracaceae, Alteromonadaceae, Marinobacteraceae, methylotrophs represented by Methylophagaceae and Methylococcales (mainly Methylomonadaceae), and sulfur-oxidizing bacteria represented by SUP05 and Ectothiorhodospiraceae. Consistently, the aerobic methane oxidation gene pmoA was more prevalent in the deeper water and was found in four bacterial classes in addition to Gammaproteobacteria. Sulfur-oxidizing genes also exhibited higher abundances at depths and were primarily affiliated with Rhodobacteraceae. These microbes likely play important roles in aerobic oxidation of methane and sulfur, contributing to methane depletion during upward diffusion. By integrating sampling across vertical and horizontal dimensions, we demonstrate that seepage shapes the microbial community and biogeochemical functions in the water column at Site F.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02722-5.},
}

@article {pmid41933601,
year = {2026},
author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y},
title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134536},
doi = {10.1016/j.biortech.2026.134536},
pmid = {41933601},
issn = {1873-2976},
abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.},
}

@article {pmid41933710,
year = {2026},
author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105932},
doi = {10.1016/j.meegid.2026.105932},
pmid = {41933710},
issn = {1567-7257},
abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.},
}

@article {pmid41933826,
year = {2026},
author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D},
title = {The Health Threat of Wild Animals by Rank I ARGs from Habitat Soils: Metagenomic and Metabolomic Evidence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128041},
doi = {10.1016/j.envpol.2026.128041},
pmid = {41933826},
issn = {1873-6424},
abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.},
}

@article {pmid41934012,
year = {2026},
author = {Moraïs, S and Mizrahi, I},
title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.005},
pmid = {41934012},
issn = {1878-4380},
abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.},
}

@article {pmid41934196,
year = {2026},
author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ},
title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {7},
pages = {e70450},
doi = {10.1002/mnfr.70450},
pmid = {41934196},
issn = {1613-4133},
support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; },
mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; },
abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.},
}

Humans
*Diet, Mediterranean
Male
Female
Adult
Bacteria/genetics/classification
*Microbiota
Metagenomics
Middle Aged
Olive Oil
*Gastrointestinal Microbiome
Feces/microbiology
Fruit
Vegetables
Multiomics

@article {pmid41934511,
year = {2026},
author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM},
title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41934511},
issn = {1572-9699},
mesh = {*Chitosan/administration & dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; },
abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.},
}

*Chitosan/administration & dosage/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Animal Feed/analysis
*Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Diet
Dietary Supplements
*Fishes/microbiology
Biodiversity
Aquaculture

@article {pmid41934651,
year = {2026},
author = {Zhang, N and Li, L and Chen, F and Kang, X and Liu, L and Kuang, D},
title = {Rapid Cavitary Pneumonia and Reversible Hepatic Injury in Burkholderia pseudomallei ST271 Infection.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e951729},
doi = {10.12659/AJCR.951729},
pmid = {41934651},
issn = {1941-5923},
mesh = {Humans ; Male ; *Melioidosis/drug therapy/diagnosis/complications/microbiology ; Middle Aged ; *Burkholderia pseudomallei/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; },
abstract = {BACKGROUND Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease endemic to tropical and subtropical regions that displays highly variable clinical presentations, ranging from localized abscesses to severe septicemia. Sequence type (ST) 271 has been rarely reported; data concerning its clinical and epidemiological characteristics remain limited. This report describes a rare case of ST271 infection presenting with rapidly progressive cavitary pneumonia and reversible hepatic injury. CASE REPORT A previously healthy 50-year-old male construction worker from Haikou, China, presented with a 2-week history of intermittent fever, hemoptysis, and persistent cough. Chest computed tomography revealed a thick-walled cavitary mass in the right upper lobe. Laboratory findings demonstrated substantially elevated liver enzymes, indicating acute hepatic injury. Metagenomic sequencing of bronchoalveolar lavage fluid identified B. pseudomallei, and whole-genome sequencing classified the isolate as ST271. The strain was sensitive to imipenem, ceftazidime, and trimethoprim-sulfamethoxazole; preliminary in vitro bacteriophage susceptibility also was observed. After initiation of intravenous ceftazidime followed by oral trimethoprim-sulfamethoxazole, the patient showed rapid clinical improvement that included robust resolution of the pulmonary lesion and normalization of liver enzymes, consistent with reversible hepatic injury. CONCLUSIONS This case highlights the aggressive clinical course of the rare B. pseudomallei ST271 strain, characterized by rapidly progressive cavitary pneumonia and concurrent hepatic injury in an immunocompetent host. Early identification using sequencing techniques facilitated timely targeted therapy and a favorable recovery. The observed in vitro phage susceptibility may provide preliminary insight for future research into alternative management strategies for resistant strains.},
}

Humans
Male
*Melioidosis/drug therapy/diagnosis/complications/microbiology
Middle Aged
*Burkholderia pseudomallei/isolation & purification/genetics
Anti-Bacterial Agents/therapeutic use
*Pneumonia, Bacterial/microbiology/drug therapy/diagnosis

@article {pmid41934839,
year = {2026},
author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B},
title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141959},
doi = {10.1016/j.jhazmat.2026.141959},
pmid = {41934839},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.},
}

@article {pmid41934858,
year = {2026},
author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F},
title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141965},
doi = {10.1016/j.jhazmat.2026.141965},
pmid = {41934858},
issn = {1873-3336},
abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.},
}

@article {pmid41935109,
year = {2026},
author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J},
title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46434-9},
pmid = {41935109},
issn = {2045-2322},
support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; },
abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.},
}

@article {pmid41935274,
year = {2026},
author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S},
title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03152-y},
pmid = {41935274},
issn = {1743-422X},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.

METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.

RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.

CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.},
}

@article {pmid41935328,
year = {2026},
author = {Li, XX and Li, BY and Fu, GW and Zhao, H and Li, J and Zhou, YH and Zhang, X and Zhao, YC},
title = {Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12702-2},
pmid = {41935328},
issn = {1471-2334},
}

@article {pmid41935339,
year = {2026},
author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R},
title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00885-9},
pmid = {41935339},
issn = {2524-6372},
abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.

RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.

CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.},
}

@article {pmid41928235,
year = {2026},
author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE},
title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-026-02359-w},
pmid = {41928235},
issn = {1755-8794},
}

@article {pmid41928361,
year = {2026},
author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S},
title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02392-y},
pmid = {41928361},
issn = {2049-2618},
support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; },
abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.

RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.

CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.},
}

@article {pmid41928791,
year = {2026},
author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A},
title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9142184/v1},
pmid = {41928791},
issn = {2693-5015},
abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.},
}

@article {pmid41929040,
year = {2026},
author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ},
title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.714183},
pmid = {41929040},
issn = {2692-8205},
abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.

IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.},
}

@article {pmid41929113,
year = {2026},
author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R},
title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714056},
pmid = {41929113},
issn = {2692-8205},
abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.},
}

@article {pmid41929272,
year = {2026},
author = {Biesheuvel, MM and Barkema, HW and Morley, PS and Pinnell, LJ and Doster, E and Valeris-Chacin, R},
title = {In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1770245},
pmid = {41929272},
issn = {2297-1769},
abstract = {Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of a targeted enrichment (TE) shotgun sequencing approach to detect and classify M. bovis strains in milk metagenomic samples. As a proof of concept, the accuracy of this approach was assessed using milk-derived M. bovis strains. A total of 620 M. bovis whole-genome sequences were downloaded from NCBI, of which 162 (26.1%) originated from milk samples. Genomes were grouped into Genomically Clustered Sequence Variants (GSVs) using MashTree and TreeCluster to enable strain-level classification. To simulate TE sequencing data, genomes from different milk-associated GSVs were randomly selected and fragmented in silico into 150-bp reads. Mock milk samples were generated by sampling reads with replacement from these genomes. Sequencing depth was modeled using a Poisson distribution, while mixed-strain DNA samples were simulated by including 1, 3, 6, or 9 GSVs per sample. Enrichment proportions were set at 0.3, 0.5, 0.7, and 0.9. Two classification tools, Kraken2 and Themisto/mSWEEP, were evaluated for their ability to detect and classify the simulated TE reads. Themisto/mSWEEP consistently outperformed Kraken2, achieving an average read classification accuracy of 84.9% compared with 1.4% for Kraken2. Sensitivity for Themisto/mSWEEP was 100% with a single spiked GSV and declined slightly to 97.0% with nine GSVs, whereas Kraken2 achieved sensitivities of only 17.3% and 4.7%, respectively. Positive predictive value (PPV) showed a similar pattern: 98% for Themisto/mSWEEP vs. 4.7% for Kraken2 with a single GSV, and 65.5% vs. 10% with nine GSVs. While Kraken2's PPV increased slightly with additional GSVs, Themisto/mSWEEP's PPV decreased. Both methods maintained high specificity and negative predictive value (>91%) across all scenarios. Enrichment proportion had no measurable effect on performance. Overall, Themisto/mSWEEP demonstrated superior accuracy for GSV-level identification of M. bovis strains. Enrichment to at least 30% of total reads was sufficient to recover strain-level data. Further work is needed to assess the biological relevance and practical applications of these genomic clusters.},
}

@article {pmid41929449,
year = {2026},
author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ},
title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1725666},
pmid = {41929449},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation & purification ; *Lung/physiology ; Metagenomics ; Aged ; },
abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.

METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.

RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.

DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.},
}

Humans
*Microbiota
Male
*Periodontitis/therapy/microbiology
Female
Middle Aged
*Mouth/microbiology
Longitudinal Studies
Adult
Bacteria/classification/genetics/isolation & purification
*Lung/physiology
Metagenomics
Aged

@article {pmid41929455,
year = {2026},
author = {Geng, Y and Yuan, Y and Lin, X and Wei, J and Zhang, Q and Mao, X and Zhang, X and Zhang, X and Zhang, Y and Zhao, J and Guo, F and Zheng, P},
title = {Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1653022},
pmid = {41929455},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/virology/epidemiology ; China/epidemiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/genetics/isolation & purification/classification ; *Coinfection/virology/epidemiology/microbiology ; Aged ; Adult ; Risk Factors ; Mycoplasma pneumoniae/isolation & purification ; Severity of Illness Index ; Hospitalization ; High-Throughput Nucleotide Sequencing ; Pneumonia, Mycoplasma/epidemiology ; Respiratory Tract Infections ; },
abstract = {BACKGROUND: Reports on mixed infection with different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in China remain scarce. In this study, we analyzed the clinical characteristics of mixed infections involving different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in central China.

METHODS: Nested polymerase chain reactions and metagenomic next-generation sequencing were employed to identify severe acute respiratory syndrome coronavirus 2 variants. Clinical data, including hospitalization days, severity classification, outcomes, and laboratory data, were collected and analyzed.

RESULTS: Seven patients had mixed infections with different severe acute respiratory syndrome coronavirus 2 variants in samples collected on different dates. Overall, 54.6% (83/152) of patients had co-existing respiratory pathogen infection. The most common co-existing respiratory pathogen was Mycoplasma pneumoniae. Longer hospital stays, intensive care unit admission, and prolonged duration from admission to positive severe acute respiratory syndrome coronavirus 2 sample detection were independent risk factors for acute coronavirus disease infection with different respiratory pathogens. Severity classification, mixed infection, cerebral fraction, and fever were independent risk factors for failed treatment. Early detection of white blood cell count, procalcitonin, and D-dimer concentrations can help predict mixed respiratory infections and treatment outcomes.

CONCLUSIONS: The phenomenon of mixed infection with different variants in patients with coronavirus disease may have been underestimated. Therefore, active surveillance of severe acute respiratory syndrome coronavirus 2 variants should be performed in older patients with comorbidities.},
}

Humans
*COVID-19/virology/epidemiology
China/epidemiology
Male
Female
Middle Aged
*SARS-CoV-2/genetics/isolation & purification/classification
*Coinfection/virology/epidemiology/microbiology
Aged
Adult
Risk Factors
Mycoplasma pneumoniae/isolation & purification
Severity of Illness Index
Hospitalization
High-Throughput Nucleotide Sequencing
Pneumonia, Mycoplasma/epidemiology
Respiratory Tract Infections

@article {pmid41929479,
year = {2026},
author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X},
title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1760881},
pmid = {41929479},
issn = {1664-3224},
mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; },
abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.

MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.

RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.

CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.},
}

Male
*Dysbiosis/complications/microbiology/metabolism
Animals
*Gastrointestinal Microbiome
*Asthenozoospermia/metabolism/etiology/microbiology
Humans
Mice
Case-Control Studies
Fecal Microbiota Transplantation
Adult
Fatty Acids, Volatile/metabolism
Butyrates/metabolism
Sperm Motility
Metabolomics
Testis/metabolism

@article {pmid41929693,
year = {2026},
author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z},
title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729476},
pmid = {41929693},
issn = {1664-302X},
abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.

METHODS: Vaginal swabs (sPTB, n = 37; term, n = 62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.

RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p < 0.05), and distinct community structure (PERMANOVA p < 0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC = 0.82), and a multi-metabolite model improved classification (AUROC = 0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.

CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.},
}

@article {pmid41929767,
year = {2026},
author = {Peng, W and Yang, W and Ma, L and Wang, Q and Yang, R and Ji, A and She, M and Wang, T and Gong, W and Yan, L},
title = {Flower vinegar prepared from Yunnan large-leaved tea tree prevents high-fat diet-induced obesity in mice by regulating gut microbiota.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1749951},
pmid = {41929767},
issn = {2296-861X},
abstract = {Obesity and its metabolic complications are major public health concerns. The gut microbiota plays a pivotal role in regulating host adiposity. Fermented products from Camellia sinensisvar. Assamica (Yunnan large-leaved tea) flowers, a novel food ingredient, may offer therapeutic potential, but their effects on obesity and gut microbiota remain unexplored. We investigated the anti-obesity effects of vinegar fermented from Camellia sinensisvar. Assamica flowers (TTFV) in a high-fat diet (HFD)-induced obese mouse model. Body weight, glucose and lipid metabolism, hepatic injury, steatosis, inflammation, and oxidative stress were assessed. Metabolomic analysis and metagenomic sequencing of gut microbiota were performed. Key metabolic pathways were analyzed. TTFV supplementation significantly attenuated HFD-induced body weight gain, improved glucose and lipid profiles, alleviated hepatic steatosis and injury, and reduced systemic inflammation and oxidative stress. TTFV modulated host metabolite profiles and related metabolic pathways. Crucially, TTFV reshaped the gut microbiota structure: it increased the relative abundance of Bacteroidota and decreased the Firmicutes/Bacteroidota ratio at the phylum level. At the family level, it promoted beneficial bacteria (Oscillospiraceae, Eubacteriaceae) and suppressed potentially harmful ones (Erysipelotrichaceae). Metabolic pathway analysis indicated TTFV's positive role in maintaining cellular homeostasis and regulating metabolic disturbances. Our findings demonstrate that TTFV exerts protective effects against HFD-induced obesity in mice. These benefits are closely associated with the remodeling of gut microbiota composition and the modulation of key metabolic pathways. This study is the first to report the anti-obesity potential and microbiota-regulating effects of TTFV, suggesting its promise as a functional food ingredient for promoting intestinal health and mitigating obesity-related metabolic disorders.},
}

@article {pmid41929953,
year = {2026},
author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE},
title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.},
journal = {Journal of Alzheimer's disease reports},
volume = {10},
number = {},
pages = {25424823261436287},
pmid = {41929953},
issn = {2542-4823},
abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.

OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.

METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.

RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (ε4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.

CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.},
}

@article {pmid41930262,
year = {2025},
author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C},
title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1757196},
pmid = {41930262},
issn = {1664-302X},
abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.},
}

@article {pmid41930266,
year = {2026},
author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J},
title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag041},
pmid = {41930266},
issn = {2730-6151},
abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.},
}

@article {pmid41930333,
year = {2026},
author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T},
title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.},
journal = {MedComm},
volume = {7},
number = {4},
pages = {e70705},
pmid = {41930333},
issn = {2688-2663},
abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.},
}

@article {pmid41930475,
year = {2026},
author = {Tan, Y and Zou, D and Ni, C and Zeng, Q and Li, M},
title = {From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12277},
pmid = {41930475},
issn = {1520-5851},
abstract = {Picocyanobacteria, represented by Prochlorococcus and Synechococcus, are major photosynthetic organisms in aquatic ecosystems, and their viruses (cyanophages) significantly impact cyanobacterial ecology and evolution. Here, we combined metagenomics of Synechococcus communities along four representative estuaries in China and whole-genome analyses of laboratory-evolved Synechococcus mutants to link viral diversity to host adaptation and evolution. We assembled 83 cyanophage genomes (mainly cyanomyoviruses), with expanded auxiliary metabolic genes encoding glycosyltransferases and radical S-adenosyl methionine proteins involved in amino acid and lipopolysaccharide metabolism. Metagenome-assembled cyanobacterial genomes revealed mutations predominantly in membrane-associated functions linked to phage infection. In parallel, we identified genetic pathways conferring phage resistance in 18 evolved Synechococcus mutant strains that are resistant to phage infection. Notably, mutations in carbohydrate (rfbA) and photosynthetic energy transfer (cpeT) of Synechococcus mutants recurred in both cultured isolates and recovered metagenomes. These results indicate that cyanophages in estuaries leverage broader metabolic toolkits, while Synechococcus repeatedly evolves resistance. Together, these findings outline a reciprocal adaptive landscape that helps explain the persistence and turnover of picocyanobacterial populations in estuarine environments.},
}

@article {pmid41930516,
year = {2026},
author = {Wang, W and Li, M and Liu, X and Li, Y and Yang, K and Tuovinen, OH and Wang, H},
title = {Anaerobic antimony oxidation by mine groundwater bacteria: The energy-detoxification trade off governed by carbon source and Sb concentration.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141926},
doi = {10.1016/j.jhazmat.2026.141926},
pmid = {41930516},
issn = {1873-3336},
abstract = {Microorganisms drive anaerobic antimony (Sb) oxidation and detoxification in groundwater, how carbon source (organic vs. inorganic) regulates this process and shapes microbial adaptive strategies remains unclear. To fill this knowledge gap, microcosms were conducted with groundwater from Xikuangshan mining-area, integrating with hydrochemistry, genes quantification, and metagenomics. The results demonstrated efficient anaerobic Sb(III) oxidation coupled with NO3[-] reduction, regulated synergistically by Sb concentration and carbon sources. The concentration of 0.5 mM Sb(III) served as a critical threshold that triggered changes in bacterial diversity, composition, and Sb(III)-oxidation behavior. Below this, NaHCO3 promoted higher oxidation rates (P < 0.05), linked to enrichment of Hydrogenophaga, Aquabacterium, Acidovorax, and aioA genes (Sb-oxidizing gene). Above 0.7 mM Sb(III), Na-lactate activated aioA and narrowed the rate gap, accompanied by increases in both abundance and niche of Dechloromonas. In addition, elevated Sb stress reshaped the metabolic networks across microcosms. The communities prioritized energy allocation to nitrogen fixation (nifH) with multiple benefits over redundant carbon fixation (cbbL). This research expands the known range of Sb and carbon drive microbial metabolic remodeling, advancing our predictive understanding of Sb biogeochemical cycling in contaminated aquifers.},
}

@article {pmid41930813,
year = {2026},
author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S},
title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158039},
doi = {10.1016/j.phymed.2026.158039},
pmid = {41930813},
issn = {1618-095X},
abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.

PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.

METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-γ-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.

RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-κB signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-κB signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.

CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-κB signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.},
}

@article {pmid41931872,
year = {2026},
author = {Ren, Z and Wen, Y and Ma, Y and Li, M and Wang, L and Yu, R and Wu, L},
title = {Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.},
journal = {Water research},
volume = {298},
number = {},
pages = {125791},
doi = {10.1016/j.watres.2026.125791},
pmid = {41931872},
issn = {1879-2448},
abstract = {Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a key process regulating methane emissions from wetland ecosystems. However, the species-specific mechanisms that enable N-DAMO bacteria to adapt and occupy distinct niches along environmental gradients (such as salinity) remain largely unknown. This makes it difficult to predict the ecological function of these bacteria. In this study, the structure, functional diversity, and species-specific salinity adaptation mechanisms of N-DAMO bacterial community in the Ulansuhai Wetland along a natural salinity gradient were investigated. An integrated approach combining metagenomic sequencing, isotopic tracer experiment, quantitative PCR, and biogeochemical measurements was employed for this research. The results show that salinity significantly reshaped the community structure and diversity of N-DAMO bacteria, while their potential activity remained functionally stable. This functional resilience was underpinned by distinct niche partitioning among four dominant species of Candidatus Methylomirabilis, species. Each species exhibited unique genomic potential for exopolysaccharide biosynthesis, osmoregulation, and stress response. Furthermore, the N-DAMO process constituted a significant methane sink, representing 39.5% of the observed anaerobic methane oxidation activity. Path analysis further explained that salinity regulated N-DAMO bacterial communities directly and through indirect pathways mediated by soil carbon and nitrogen pools. This research provides the first mechanistic framework linking species-specific genomic traits of N-DAMO bacteria to salinity adaptation and niche partitioning. The study offers novel insights for predicting wetland methane emissions.},
}

@article {pmid41931886,
year = {2026},
author = {Xiao, S and Han, Z and Tang, Y and Wu, X and Huang, J and Zeng, W},
title = {Dual roles of tetracycline-degrading bacteria in pollutant detoxification and resistome reshaping under tetracycline-copper co-contamination.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141951},
doi = {10.1016/j.jhazmat.2026.141951},
pmid = {41931886},
issn = {1873-3336},
abstract = {Combined contamination of soils with antibiotics and heavy metals represents a growing environmental challenge, yet remediation strategies addressing their synergistic toxicity remain limited. In this study, the bioremediation potential of a tetracycline-degrading bacterial consortium (Raoultella sp. XY-1 and Pandoraea sp. XY-2) was evaluated in tetracycline-copper (TC-Cu) co-contaminated soils by integrating chemical, biological, and ecological assessments. Soil column experiments demonstrated that bioaugmentation significantly enhanced TC degradation (48.57-53.71% after 90 days) compared to uninoculated controls (<12%), while simultaneously reducing copper bioavailability by shifting acid-extractable and reducible fractions toward more stable oxidizable forms. Inoculation further alleviated the strong inhibition of soil enzymatic activities (sucrase, urease, phosphatase), reflecting improved soil functional recovery. Metagenomic sequencing revealed that TC-Cu co-contamination reshaped microbial community composition, particularly increasing the relative abundance of Actinomycetota and Campylobacterota. Bioaugmentation further facilitated the establishment of Raoultella and indirectly stimulated indigenous resistant taxa through community interactions. Correlation network analysis further revealed that Raoultella was a highly connected genus in co-occurrence networks of antibiotic resistance gene (ARG)- and metal resistance gene (MRG)-hosting genera. LC-MS detection of intermediate products during TC microbial degradation proposed three microbial degradation pathways and inferred microbial resistance mechanisms under TC-Cu coexistence. Collectively, these findings highlight that TC-degrading bacteria not only reduce pollutant toxicity but also reshape microbial and genetic landscapes in co-contaminated soils, potentially suppressing the diffusion risk of resistance genes at low TC-Cu level. This work provides novel insights into the ecological trade-offs of bioremediation and supports the development of targeted, sustainable strategies for complex antibiotic-metal pollution scenarios.},
}

@article {pmid41931897,
year = {2026},
author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y},
title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141890},
doi = {10.1016/j.jhazmat.2026.141890},
pmid = {41931897},
issn = {1873-3336},
abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.},
}

@article {pmid41932005,
year = {2026},
author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A},
title = {A survey of bacterial and fungal communities of table olives.},
journal = {International journal of food microbiology},
volume = {455},
number = {},
pages = {111759},
doi = {10.1016/j.ijfoodmicro.2026.111759},
pmid = {41932005},
issn = {1879-3460},
abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.},
}

@article {pmid41932427,
year = {2026},
author = {Bao, C and Ren, Y and Tang, C and Su, Y and Yue, H and Chen, X},
title = {Viral Isolation and Genomic Characteristics of the First Bovine Parainfluenza Virus Type 3 Isolated from Water Buffaloes (Bubalus bubalis) in China.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106655},
doi = {10.1016/j.tvjl.2026.106655},
pmid = {41932427},
issn = {1532-2971},
abstract = {Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease. In this study, we report the isolation and genomic characterization of BPIV3 from a water buffalo with respiratory symptoms in China. Virus isolation was performed using susceptible cell cultures, followed by identification via RT-qPCR, transmission electron microscopy, and indirect immunofluorescence. Metagenomic sequencing of the near-complete genome showed that the isolate shared 89.9%-91.1% nucleotide identity with BPIV3 genotype A strains. Notably, several distinct mutations were identified in the structural protein genes, and phylogenetic analysis demonstrated that the isolate formed a separate cluster within genotype A, suggesting that it may represent a novel subtype within this genotype. To our knowledge, this is the first report describing the isolation and genomic characterization of BPIV3 from water buffaloes in China. These findings provide baseline molecular data for further studies on the genetic diversity and evolution of BPIV3.},
}

@article {pmid41932524,
year = {2026},
author = {Qian, J and Li, X and Xu, X and Zhang, D and Xiang, G and Wang, Z and Zhang, Z and Liu, M and Hao, W and Wu, D},
title = {Thiosulfate-Driven redox buffering enables efficient nitrogen removal and norfloxacin degradation in mixed denitrifying systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134550},
doi = {10.1016/j.biortech.2026.134550},
pmid = {41932524},
issn = {1873-2976},
abstract = {Wastewaters often contain both conventional pollutants and recalcitrant antibiotics, posing challenges to biological treatment. This study investigated a mixed autotrophic-heterotrophic denitrification system driven by sodium acetate and sodium thiosulfate for simultaneous nitrate and norfloxacin removal. A sequencing batch reactor was operated in four stages, culminating in norfloxacin exposure (0.5 mg/L). Results showed stable nitrogen removal (>95%) and norfloxacin degradation (>90%) under sustained antibiotic stress. Batch tests confirmed that the co-presence of thiosulfate and acetate enhanced norfloxacin biodegradation via co-metabolic pathways, with negligible abiotic removal. Three-dimensional excitation-emission matrix spectroscopy revealed a shift toward humic-like extracellular polymeric substances under norfloxacin, supporting biofilm integrity. 16S rRNA sequencing and metagenomics indicated dynamic microbial restructuring, with persistent core taxa (Thauera, Desulfofustis) and enrichment of stress-tolerant groups (norank_o_SJA-15). Functional analysis showed upregulation of carbon metabolism (pta, ackA), denitrification (nirS, nosZ), and sulfur oxidation (SUOX, SoxX, SoxA) genes, alongside oxidative stress mitigation genes (catB, gst) and xenobiotic degradation genes (HGD, E1.13.11.4). Antibiotic resistance gene profiles shifted toward multidrug (>29%), peptide resistance (14.0%→15.4%), and glycopeptide resistance (7.0%→9.4%), dominated by multidrug efflux and target alteration mechanisms, enabling community resilience while minimizing energetically costly defenses. This work elucidates the synergistic roles of dual electron donors in pollutant co-removal and stress mitigation, offering a robust, sustainable strategy for treating antibiotic-laden wastewater.},
}

@article {pmid41932525,
year = {2026},
author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J},
title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134546},
doi = {10.1016/j.biortech.2026.134546},
pmid = {41932525},
issn = {1873-2976},
abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-l-Proline, l-Histidine, and Hypaphorin, with l-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.},
}

@article {pmid41932647,
year = {2026},
author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L},
title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2026.03.023},
pmid = {41932647},
issn = {1673-8527},
abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.},
}

@article {pmid41932883,
year = {2026},
author = {Silva, RMB and Slyvka, A and Lee, YJ and Guan, C and Lund, SR and Raleigh, EA and Skowronek, K and Kuska, MS and Bochtler, M and Weigele, PR},
title = {A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70671-1},
pmid = {41932883},
issn = {2041-1723},
support = {FNP, POIR.04.04.00-00-5D81/17-00//Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)/ ; },
abstract = {Nucleic acid modifying enzymes drive diverse defense and counter-defense measures in the evolutionary arms race between viruses and their cellular hosts. Abundant and widespread bacterial viruses (bacteriophage or phage) encode for biosynthetic pathways that install elaborate DNA hypermodifications which protect their genomic DNA from host endonucleases. Here, we establish the molecular basis for the multistep biosynthesis of 6-aminocarboxymethyl-2'-deoxyadenosine (6-NcmdA), a nucleobase hypermodification found in the virion DNA of bacteriophage Mu that leads to restriction evasion in the context of phage-host conflicts. In the first step, we show that Mu-encoded Mom enzyme catalyzes the formation of 6-NcmdA by transferring glycine from charged tRNA[Gly] to the N6 position of adenine within double-stranded DNA. We uncover a second step where the glycyl-dA intermediate undergoes an on-base rearrangement to form 6-NcmdA. Examination of the proposed reaction pathways by quantum chemical calculations confirms the instability of acyl exocyclic groups at N6-adenine and reveals an energetically favorable orientation of 6-NcmdA that restores canonical base pairing. An X-ray structure confirms Mom is a member of the GNAT superfamily and suggests binding sites for both tRNA and DNA. Guided by the Mom structure and patterns of sequence conservation across metagenomic space, we show residues R111 and S124 are essential for catalysis. This work demonstrates that the Mom enzyme defines a new category of acetyltransferases utilizing charged tRNA to modify DNA.},
}

@article {pmid41932890,
year = {2026},
author = {Zhao, L and Zheng, J and Shen, Y and Xu, X and Liu, X and Yu, J and Li, J and Yang, B and Chen, L and Wang, F and Liu, S and Peng, X and Du, J and Dong, R},
title = {Composite polyphenols mitigate microplastic exposure-related immune disturbances: a two-phase population trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71167-8},
pmid = {41932890},
issn = {2041-1723},
abstract = {Microplastics (MPs) are widespread, making it urgent to elucidate their toxicity and identify intervention strategies. Here, we designed a two-phase population trial, comprising a baseline pilot population (n = 151) and a 28-day randomized, double-blind, placebo-controlled trial (n = 98). Primary outcomes include fecal MP concentration and blood parameters (complete blood count, glycemic and lipid, and cytokines), with exploratory outcomes comprising fecal metagenomics and plasma metabolomics. The median MP concentration in 151 participants' fecal samples is 158.28 μg/g dry weight, correlating with levels of 7 inflammatory indexes, 4 cytokines, and 2 lipid indicators. Composite polyphenols (CP) significantly reduced plasma levels of IL-1β (P = 0.045, effect sizes = -0.463), IL-6 (P = 0.023, effect sizes = -0.576) and IL-8 (P = 0.022, effect sizes = -0.529). 507 differentially expressed microbiotas (DEMs; P < 0.05) and 144 significantly different metabolites (SDMs; P-FDR < 0.25, VIP ≥ 1) are observed between the high and low MP exposure groups; 108 DEMs and 85 SDMs are identified following CP intervention. Notably, CP could mitigate the pro-inflammatory effects of high MP exposure by modulating gut microbiota and up-regulating glycerophospholipid metabolism and arginine biosynthesis. The gut bacteria Staphylococcus and the plasma metabolite PC (22:5/0:0) are identified as potential mediators in this protective effect. Trial registration: ClinicalTrials.gov: NCT06437119.},
}

@article {pmid41932913,
year = {2026},
author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M},
title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00976-y},
pmid = {41932913},
issn = {2055-5008},
abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.},
}

@article {pmid41933095,
year = {2026},
author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W},
title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44972-w},
pmid = {41933095},
issn = {2045-2322},
abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.},
}

@article {pmid41933201,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41933201},
issn = {2058-5276},
support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.},
}

@article {pmid41933302,
year = {2026},
author = {Wu, L and Pu, J and Xi, X and Bao, Y and Luo, L},
title = {Streptomyces morookaense spinal suppurative infection: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13238-1},
pmid = {41933302},
issn = {1471-2334},
support = {2025M781412//The China Postdoctoral Science Foundation/ ; },
abstract = {PURPOSE: Streptomyces species are ubiquitous soil actinomycetes and a major source of antibiotics, but invasive human infection with spinal involvement is exceedingly rare and may mimic tuberculous or fungal spondylodiscitis. We report a thoracic suppurative vertebral infection caused by Streptomyces morookaense and highlight an integrated diagnostic approach.

METHODS: A 66-year-old woman with no known immunodeficiency developed progressive thoracic back pain one month after severe trauma with open wounds. CT/MRI showed osteolytic endplate destruction at T3-T4 with paravertebral abscess formation. Fluoroscopy-guided percutaneous biopsy of the T4 vertebral body was performed for histopathology, culture, and metagenomic next-generation sequencing (mNGS).

RESULTS: Histopathology demonstrated fibrinous exudate, necrosis, and inflammatory granulation tissue with fragmented trabeculae, without granuloma or caseous necrosis; acid-fast staining was negative. Vertebral tissue culture grew Streptomyces spp, and mNGS identified high-abundance sequences matching S. morookaense. Intravenous piperacillin/tazobactam led to rapid pain relief and normalization of inflammatory markers within one week, and no recurrence was observed during follow-up.

CONCLUSION: This case suggests that Streptomyces morookaense has the potential to involve the thoracic spine in immunocompetent individuals. For unexplained spinal infections with negative routine tests, percutaneous vertebral sampling with integrated interpretation of pathology, culture, and mNGS can improve detection of rare pathogens and help avoid inappropriate empirical therapy.},
}