@article {pmid42945246,
year = {2026},
author = {Wang, Y and Qu, G and Huang, ZYX and Zhang, X and Li, H and Wei, X and Hu, L and Xu, S and Becker, DJ and Wei, F and Xu, Y},
title = {Viral metagenomics reveals heterogeneity in mammalian virus hosting, sharing, and spillover.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2610672123},
doi = {10.1073/pnas.2610672123},
pmid = {42945246},
issn = {1091-6490},
mesh = {Animals ; *Metagenomics/methods ; Humans ; *Mammals/virology ; Phylogeny ; Zoonoses/virology ; *Virome/genetics ; *Viruses/genetics/classification ; Chiroptera/virology ; },
abstract = {Zoonotic viruses originating from mammals pose a persistent threat to global health. While rodents and bats are often considered "special reservoirs," it is debated if spillover risk is driven by specific taxa or merely reflects mammalian species richness. However, most tests have focused on published host-virus association datasets, which can reflect systematic biases in host and virus sampling effort. To address this limitation, we analyzed a comprehensive repository of 4,685 metagenomic datasets, minimizing bias toward any one viral taxon and spanning 296 species across 14 mammalian orders. We characterized the global mammalian virome and found substantial heterogeneity in the capacity of different mammalian orders to harbor and share human-associated viruses. Counter to conventional wisdom, carnivores exhibited significantly higher propensities to carry human-associated viruses, with bats ranked lower in this metric of zoonotic risk. Network analyses of viral sharing further revealed higher cross-order virus sharing among specific mammalian orders (e.g., carnivores and artiodactyls). Phylogenetic comparative analyses revealed that host life-history traits (e.g., longevity) and anthropogenic factors (e.g., urban land use) were key ecological drivers of both virus richness and transmission centrality. Our study provides a data-driven framework that challenges prevailing narratives of zoonotic risk and offers a refined strategy for prioritizing surveillance and mitigating emerging zoonotic threats.},
}

Animals
*Metagenomics/methods
Humans
*Mammals/virology
Phylogeny
Zoonoses/virology
*Virome/genetics
*Viruses/genetics/classification
Chiroptera/virology

@article {pmid42945300,
year = {2026},
author = {Andrade, B and Ramírez, M and Reyes, G},
title = {Microbial community structure of Penaeus vannamei post-larvae naturally infected with multiple viruses in hatchery tanks.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361576},
pmid = {42945300},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/virology/microbiology ; Larva/virology/microbiology ; Aquaculture ; *Microbiota ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This study offers an observational evaluation of how viral and bacterial infections co-occur with alterations in the microbiome and survival of Penaeus vannamei post-larvae, one of the most economically important species in global aquaculture.

METHODS: Eleven commercial larval production tanks were classified into three distinct infection scenarios using histology and PCR: Baculovirus penaei (BP) monoinfection, mixed infections (BP, white spot syndrome virus [WSSV], and acute hepatopancreatic necrosis disease [AHPND]-causing bacteria), and non-infected controls. High-molecular-weight DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform, followed by evaluation of microbial diversity, community structure, and infection-associated microbial signatures.

RESULTS: Although BP was the most abundant viral genus across infected groups, severe mortality was observed only under mixed-infection conditions, which were closely associated with AHPND-causing bacteria presence and microbiome disruption rather than with BP alone. Deep metagenomic sequencing revealed reduced, distinct microbiome structures in shrimp infected with BP and in those with mixed infections, compared to non-infected individuals. Non-infected post-larvae maintained complex and well-balanced bacterial communities, predominantly composed of Donghicola and Muricauda. Nudiviridae and Oscillospiraceae showed comparable relative abundances in BP-only and mixed-infection groups. In contrast, mixed infections were characterized by a relative increase in Vibrio, together with the PCR-detection of PirAB toxin genes, whereas WSSV remained detectable in the metagenomic dataset despite its comparatively low relative abundance, while the infection remained thermally suppressed and asymptomatic in the larvae. Functionally, infected larval microbiomes were enriched for transposases, retrotransposons, and virulence-factor genes. The near-complete BP-GR25 genome (119,245 bp) was assembled and annotated from larval metagenomes.

CONCLUSION: These results highlight the value of high-throughput sequencing in the early detection of pathogens in aquaculture, where subtle microbial shifts during postlarval stages can be valuable indicators of health status for production.},
}

Animals
*Penaeidae/virology/microbiology
Larva/virology/microbiology
Aquaculture
*Microbiota
Metagenomics
Metagenome

@article {pmid42945345,
year = {2026},
author = {Zang, C and Tang, L and Deek, RA},
title = {Supervised and covariate-adjusted dimension reduction for prediction and visualization using microbiome data.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42945345},
issn = {1477-4054},
support = {R56LM014522/LM/NLM NIH HHS/United States ; S10OD028483/OD/NIH HHS/United States ; //University of Pittsburgh's CTSI Trans-disciplinary Collaboration Pilot Award/ ; RRID:SCR_022735//University of Pittsburgh Center for Research Computing and Data/ ; },
mesh = {Humans ; Principal Component Analysis ; Algorithms ; *Microbiota ; Dimensionality Reduction ; *Gastrointestinal Microbiome ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {Given that the gut microbiome has been shown to play a critical role in human health, discerning the relationship between microbial taxa and disease outcomes or phenotypes is of interest. Often, this involves association testing, predictive modeling, and visualizing trends in the data. Principal coordinates analysis (PCoA) is a commonly used dimension reduction technique in microbiome studies. PCoA relies on pairwise distances between samples and serves as a nonlinear alternative to the classic principal component analysis when non-Euclidean distances are used. Its low-dimensional embeddings provide intuitive visualizations but do not incorporate outcome-related information. Therefore, the low-dimensional principal coordinates may have poor performance in visualizing outcome differences, as well as in downstream disease prediction tasks. Additionally, covariates, such as demographics, lifestyle factors, and technical artifacts, can obscure true biological signals, leading to masked or spurious associations and limited generalizability. To address these limitations, we propose a supervised and covariate adjusted PCoA algorithm. By utilizing outcome information, while simultaneously minimizing the influence of nuisance variables, our method produces low-dimensional embeddings that better separate disease outcomes in visualizations and result in improved accuracy in downstream regression and classification tasks. We demonstrate the effectiveness of the proposed method and highlight its ability to extract important associations between the microbiome and disease outcomes while mitigating nuisance variation through simulations and application to real microbiome profiling studies.},
}

Humans
Principal Component Analysis
Algorithms
*Microbiota
Dimensionality Reduction
*Gastrointestinal Microbiome
*Computational Biology/methods
Prediction Algorithms

@article {pmid42945621,
year = {2026},
author = {Brîncuș, AV and Angebault, C and Wesner, N and Leonard-Louis, S and Le Joncour, A and Blandin, C and Richette, P and Poirier, P and Benveniste, O and Rodriguez, C and Botterel, F and Allenbach, Y},
title = {Pathogen identification by shotgun metagenomics in inflammatory myopathies: a prospective observational study reporting the first European case of Anncaliia algerae myositis.},
journal = {Neuromuscular disorders : NMD},
volume = {69},
number = {},
pages = {107458},
doi = {10.1016/j.nmd.2026.107458},
pmid = {42945621},
issn = {1873-2364},
abstract = {This study highlights the utility of shotgun metagenomics (SMg) in the diagnosis of infectious myositis, focusing on a rare case of Anncaliia algerae infection in an immunocompromised patient. This is among the first reports of SMg application in inflammatory myopathies. We conducted a monocentric prospective observational study at Pitié-Salpêtrière Hospital (2021-2024), including patients with inflammatory myopathies and suspected infectious etiologies. Diagnosis was based on clinical symptoms, paraclinical findings, myopathological examination, and SMg performed using DNA/RNA sequencing with the Illumina NextSeq 500® sequencing system and the MetaMIC® bioinformatics pipeline. Among nine patients, SMg identified A. algerae in a kidney transplant recipient with severe myositis and myocarditis. Standard microbiological techniques, including blood tests and muscle biopsy staining, failed to accurately identify the pathogen. Despite specific therapy (albendazole), the infection was fatal, underscoring the pathogen's aggressiveness in immunocompromised hosts. Other patients either recovered spontaneously or with immunosuppressants. This study demonstrates the diagnostic advantage of SMg in infectious myopathies, especially for rare pathogens like A. algerae. The unbiased nature of SMg enables pathogen identification when conventional methods fail, guiding targeted treatments. Early SMg use could improve outcomes in immunocompromised patients and warrants integration into diagnostic workflows for inflammatory myopathies. As an unbiased and culture-free pan-pathogenic method, SMg enables the identification of pathogens, including unexpected ones, and can be used in addition to routine procedures for inflammatory myopathy diagnosis.},
}

@article {pmid42945792,
year = {2026},
author = {An, Z and Ma, WJ and Hou, Y and Gao, L and Tian, Y and Zhang, H},
title = {Macro-scale oxygen pulsing engineers dynamic microbial niches and endogenous carbon cycling for energy-efficient nitrogen removal from low C/N high-strength wastewater.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127163},
doi = {10.1016/j.watres.2026.127163},
pmid = {42945792},
issn = {1879-2448},
abstract = {Low-cost and efficient nitrogen removal from low-C/N high-strength ammonium wastewater remains challenging. Herein, a novel macro-scale oxygen pulsing-driven anaerobic/micro-aerobic/anoxic (MOP-AMA) system was developed to treat low-C/N high-strength ammonium wastewater, achieving TN, NH4[+]-N, and COD removal efficiencies of 97.0 ± 2.2%, 99.1 ± 1.9%, and 97.5 ± 1.6%, respectively, with a specific aeration energy consumption of 20.0 Wh L[-1]. Functional gene analysis revealed strong enrichment of denitrification-related genes (1635.79 RPKM), while concurrent enrichment of glycogen degradation genes and gltA indicated coordinated glycogen metabolism and TCA cycle activity supplying reducing power and energy for polyhydroxyalkanoates (PHAs) synthesis. At KEGG Level 3, "Metabolic pathways" was the dominant functional category, accounting for 16.78% of the total RPKM-normalized functional abundance. Metagenome-assembled genomes and metatranscriptomics showed that glycogen-accumulating organisms (GAOs) (Candidatus Contendobacter and Candidatus Competibacter) had the highest transcriptional activity in the anaerobic phase (18.57% and 4.73%), while synergistic interactions among AOB, Candidatus Nitrospira defluvii (NOB), and Candidatus Competibacter denitrificans (GAOs) enabled coupled nitrification and endogenous denitrification. Nitrification genes peaked under micro-aerobic conditions, whereas denitrification genes (narGHI, nirKS, norB, nosZ) were highly expressed in the micro-aerobic (930.81, 864.93, 122.59, 277.11 TPM) and anoxic phases (756.21, 688.40, 142.64, 128.22 TPM). These findings demonstrate that macro-scale oxygen pulsing can temporally steer redox processes and electron partitioning for carbon-efficient nitrogen removal, thereby providing guidance for the treatment of carbon-limited high-strength ammonium wastewater.},
}

@article {pmid42946178,
year = {2026},
author = {Li, JT and Zhang, SM and Jiang, X and Liu, DL and Wang, ZG and Zhao, HX},
title = {Exploration of the therapeutic mechanisms of nuciferine in polyendocrine metabolic ovarian syndrome treatment based on multi-omics approaches.},
journal = {Genomics},
volume = {},
number = {},
pages = {111333},
doi = {10.1016/j.ygeno.2026.111333},
pmid = {42946178},
issn = {1089-8646},
abstract = {Polyendocrine metabolic ovarian syndrome (PMOS) is one of the most common reproductive endocrine and metabolic diseases affecting women's health. Here, we investigated the effect of nuciferine (NUC) on PMOS in vivo experiments. For transcriptome sequencing analysis and verification results, NUC mainly affected PI3K-AKT and MAPK pathways in liver tissue and affected PI3K-AKT and NF-κB pathway in adipose tissue, respectively. Molecular dynamics simulations indicated that the binding of PI3K to NUC is more effective. Meanwhile.Indole-3-acetic acid and Tryptamine were the key production of intestinal flora regulated by NUC after integrating metagenomics and non-targeted metabolomics analysis. The study confirmed the efficacy of NUC in DHEA - induced PMOS mice. PI3K might be the key target protein and Indole-3-acetic acid and Tryptamine were the key production regulated by NUC in PMOS treatment.},
}

@article {pmid42946188,
year = {2026},
author = {Liu, W and Song, B and Chen, Q and Du, M and Xu, N and Huang, R and Wei, H and Bai, H and Zhang, S},
title = {Meta-omic insight into the community-level tolerance of the activated sludge to limited-dose ionizing radiation (LimDIR).},
journal = {Environmental research},
volume = {},
number = {},
pages = {126020},
doi = {10.1016/j.envres.2026.126020},
pmid = {42946188},
issn = {1096-0953},
abstract = {Ionizing radiation is a promising advanced oxidation process for wastewater treatment, yet the community-level tolerance mechanisms of conventional activated sludge (CAS) under limited-dose ionizing radiation (LimDIR, 2-50 Gy) remain poorly characterized. To address this knowledge gap, we investigated such tolerance mechanisms by integrating batch experiments, 16S rRNA profiling, metagenomics, metatranscriptomics, and metagenome-assembled genome (MAG)-resolved analyses of glucose-fed communities receiving a single acute X-ray dose. Under LimDIR, the CAS community maintained NH4[+]-N removal despite transient inhibition at 2-15 Gy and recovery at higher doses, and progressively enhanced carbon removal (from 64.5% to 71.6%, R[2] = 0.85 with dose), while community diversity and the dominant phylogenetic framework were preserved even though genus-level composition shifted. In contrast, transcriptional profiles responded sensitively to irradiation, indicating that resilience was mainly driven by functional regulation rather than compositional turnover. Mechanistically, the dose-dependent increase in repair transcripts was carried by RecA-mediated homologous recombination together with the SOS/translesion damage-tolerance set, and enzymatic antioxidant systems constituted the major defense against oxidative stress. Community-level tolerance was further supported by quorum sensing, two-component systems, biofilm/extracellular polymeric substance (EPS)-related protection, and syntrophic carbon and nitrogen metabolism. MAG-resolved analysis suggested a core-partner cooperative tolerance model. In this model, self-protective core taxa encoded integrated DNA repair, antioxidant defense, and stress-responsive regulatory functions, whereas partner populations supplied essential structural components, including lipopolysaccharide biosynthesis, and metabolic complementarity required for community-level stability. Functional redundancy across taxa further buffered irradiation stress and sustained process performance. These findings indicate LimDIR tolerance in activated sludge as a cooperative, multilayer community property and provide a mechanistic basis for the resilience of biological wastewater treatment under irradiation stress.},
}

@article {pmid42946190,
year = {2026},
author = {Chen, H and Chai, Z and Song, C and Zheng, Y and Chen, J and Zheng, M},
title = {Revitalizing simultaneous nitrification, endogenous denitrification and phosphorus removal under carbon starvation: Redox mediator-modulated electron transfer and metabolic coordination.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126032},
doi = {10.1016/j.envres.2026.126032},
pmid = {42946190},
issn = {1096-0953},
abstract = {The simultaneous nitrification, endogenous denitrification and phosphorus removal (SNEDPR) process provides a resource-efficient paradigm for synergistic nutrient removal. However, its efficacy can be severely constrained by limited electron-donor availability and inefficient intracellular electron transfer under low carbon-to-nitrogen (C/N) ratios. Herein, we demonstrate that anthraquinone-2-sulfonate (AQS) serves as an effective redox mediator to alleviate these electron-transfer limitations. Under severe carbon-limited conditions, with an influent C/N ratio of 3.24±0.11, supplementation with 0.3 mmol/L AQS successfully restored the deteriorated system, recovering total inorganic nitrogen (TIN) removal efficiency to 96.57±0.87% while sustaining robust phosphorus removal (96.47±2.68%). Batch kinetic assays showed that AQS increased electron transfer system activity (ETSA) by over 100%, accompanied by enhanced nitrification-related activity, endogenous denitrification and phosphorus uptake. Integrated metagenomic and metatranscriptomic analyses further revealed transcriptional responses consistent with an electron-shuttling role of AQS, including enhanced ETC-associated electron-transfer potential and increased transcription of downstream denitrification enzymes. ATP synthase-related transcription was also enhanced, indicating an increased potential for PMF-coupled cellular energy conservation. Consequently, increased transcription was observed for key functional genes involved in nitrification (amoABC, nxrAB), denitrification (narGHI, napAB, nirKS, nosZ), and polyphosphate synthesis (ppk). Furthermore, AQS-amended operation was associated with microbial community succession toward a more specialized consortium, in which comammox, Thauera and Candidatus Accumulibacter clade ⅡC were associated with nitrification, endogenous denitrification, and denitrifying phosphorus removal, respectively. Although practical translation will require effective retention or recovery of soluble AQS, these findings demonstrate the potential of AQS-enhanced SNEDPR under carbon-limited conditions and provide multi-omics evidence linking improved nutrient removal with increased electron-transfer activity and coordinated microbial metabolic responses.},
}

@article {pmid42946193,
year = {2026},
author = {Lu, P and Chen, A and Feng, Y and He, S and Han, G and Hu, S},
title = {Microbial-Mediated Degradation of Aflatoxin B1 in Agricultural Soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126028},
doi = {10.1016/j.envres.2026.126028},
pmid = {42946193},
issn = {1096-0953},
abstract = {Aflatoxin B1 (AFB1) is commonly present in agricultural soil and poses severe threats to soil ecosystems due to its high toxicity, yet its environmental fate and microbial-mediated degradation mechanisms remain insufficiently studied. In this study, the environmental behavior of AFB1 in an agricultural soil was investigated. Metagenomic analysis showed that exposure to a higher concentration of AFB1 (5.0 mg kg[-1]) altered soil bacterial community structure and reduced community diversity. After 30 days of incubation, AFB1 was slowly removed from natural soil microcosms but persisted in sterilized soil microcosms, indicating that indigenous soil microorganisms make a major contribution to AFB1 dissipation. Exposure to high-concentration AFB1 significantly enriched the genus Nocardioides, and a novel AFB1-degrading strain, Nocardioides sp. N13 (phylum Actinomycetota), was isolated from the agricultural soil. Strain N13 harbors three genes encoding putative F420H2-dependent reductase (FDR) homologs, which are hypothesized to be involved in the initial degradation of AFB1. Bioinformatics analysis revealed that putative FDR homolog-carrying bacteria are mostly assigned to the phylum Actinomycetota and are widely distributed across diverse soil environments worldwide. These findings provide a theoretical basis and potential microbial resources for mitigating AFB1 contamination in soil ecosystems.},
}

@article {pmid42946251,
year = {2026},
author = {Charles, DW and Alkabab, Y and Sharma, D and Adekunle, RO and Catalano, J and Colven, R and Curry, SR and Dorman, SE and Meissner, EG and Mills, A and Patterson, L and Teixeria, CS and Tyler, RS and Salgado, CD and Harris, CE},
title = {Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing in Adult Immunocompromised Patients: A Real-World Cohort Study.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2026.10.011},
pmid = {42946251},
issn = {1538-2990},
abstract = {BACKGROUND: Plasma metagenomic next generation sequencing (mNGS) enables noninvasive pathogen detection independent of organism viability. Although analytic performance has been described, the real-world clinical impact in immunocompromised hosts remains incompletely defined.

METHODS: We conducted a retrospective cohort study of immunocompromised adults undergoing plasma mNGS testing from January 2022 through November 2024 at the Medical University of South Carolina. Immunocompromised conditions included solid organ transplantation, hematopoietic stem cell transplantation, active hematologic malignancy, HIV, or biologic immunosuppressants. Clinical impact was adjudicated by infectious disease physicians as positive, negative, or neutral. Positive results were classified as definite, probable, possible, or unlikely infectious based on clinical correlation and concordance with conventional microbiologic testing (CMT).

RESULTS: Ninety-eight patients were included (median age 60 years [range 18-76]; 63% male), including solid organ transplant (31%), hematopoietic stem cell transplant (8%), HIV (13%), active malignancy (42%), corticosteroids (3%), and biologic therapy (10%). At testing, 85% were receiving antimicrobials and 88% were hospitalized. Plasma mNGS was positive in 62% of cases, with CMT concordance in 30%. Thirty-two percent of tests had positive clinical impact, identifying unrecognized infection or antimicrobial optimization. Sixty-six percent had no treatment impact and 2% had potential negative impact. More than half of discordant positives were deemed possible or unlikely infections. False-negative cases included invasive mold and nontuberculous mycobacterial infections.

CONCLUSIONS: In this antimicrobial-exposed immunocompromised cohort, plasma mNGS frequently detected organisms but less often influenced clinical management. Discordant positives were common, and false negatives occurred in selected syndromes, supporting cautious interpretation and stewardship-guided use.},
}

@article {pmid42946473,
year = {2026},
author = {Pradhan, M and Molinaro, A and Ginanni Corradini, S and Silecchia, G and Ferri, F and Capoccia, D and Lv, B and Wu, H and Huber-Schönauer, U and Völkerer, A and Mischitelli, M and Parlati, L and Bergström, G and Datz, C and Leonetti, F and Tilg, H and Tremaroli, V and Bäckhed, F},
title = {Gut microbiome profiles associated with simple liver steatosis in MASLD.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337572},
pmid = {42946473},
issn = {1468-3288},
}

@article {pmid42946695,
year = {2026},
author = {Dahal, A and Chang, WC and Grashel, B and Morgan, D and Spagna, D and Kim, DH and Sachdeva, S and Phelan, KJ and Satish, L and Biagini, JM and Haslam, DB and Ollberding, NJ and Khurana Hershey, GK},
title = {Longitudinal Skin Bacterial Cluster Associated With Protection Against Allergic Co-Morbidity in Pediatric Atopic Dermatitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70554},
pmid = {42946695},
issn = {1398-9995},
support = {U19AI070235//National Institute of Allergy and Infectious Diseases/ ; F30AI181481//National Institute of Allergy and Infectious Diseases/ ; T32GM149200/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is an inflammatory skin condition that often portends the development of allergic comorbidities. Despite evidence supporting the role of the skin microbiome in AD, its temporal patterns and associations with risk or protection for allergic co-morbidity remain unclear. Our objective is to characterize core species of the pediatric AD bacterial microbiome, assess microbial networks and clusters, and identify global microbial changes relevant to AD and the atopic march.

METHODS: We performed metagenomic shotgun sequencing on 353 non-lesional skin samples from children in the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort across 5 annual visits. We assessed taxonomic composition and analyzed longitudinal skin microbial patterns with progression to allergic co-morbidities.

RESULTS: We identified 436 distinct species. Shannon diversity and richness declined with age, and socioeconomic factors explained the variance in species composition. Staphylococcus aureus (SA) was more abundant in severe AD. Cluster 5, comprised of typically gut-associated microbes, was more abundant in non-sensitized children who did not develop allergic co-morbidities over time.

CONCLUSIONS: Our analyses revealed key patterns in core taxa, diversity and abundance of the skin microbiome over time in early life and highlighted previously unexplored factors such as socioeconomic status as key contributors to the variability in species composition. Abundance of SA confers risk, while gut-associated microbes may offer protection, influencing the clinical trajectory of AD and the atopic march. Thus, these results provide a novel and comprehensive understanding of the temporal dynamics of the skin microbiota in pediatric AD.},
}

@article {pmid42946708,
year = {2026},
author = {Wang, Y and Kim, H and Malmuthuge, N and Zhou, M and Chen, Y and Alexander, TW and Timsit, E and Yao, J and Liang, G and Guan, LL},
title = {Early-life bovine respiratory virome analysis reveals phage-driven adaptation and cross-host evolutionary signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946708},
issn = {2041-1723},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Bacteriophages/genetics/physiology ; Phylogeny ; Humans ; Genome, Viral ; *Respiratory System/virology ; Metagenomics ; Respiratory Tract Infections/virology/veterinary ; Evolution, Molecular ; },
abstract = {Past outbreaks of zoonotic viral infections highlight the importance of understanding respiratory virome ecology. As major food-producing animals with frequent human contact, cattle represent a critical host at the human-animal interface; however, the early-life establishment of their respiratory virome and its evolutionary connections to viruses from other hosts remain underexplored. Here, we longitudinally profile the upper respiratory tract (URT) virome of beef calves from birth to weaning using an optimized viral enrichment procedure and metagenomic workflow. Viral communities exhibited increased richness and turnover, reflecting ecological structuring during early life. Temperate phages dominate the URT phage community and share virulence- and mobility-associated genes with bacterial hosts, likely contributing to host adaptation and colonization persistence. Vertebrate-associated viruses emerge after the first week of life. Targeted reassembly from bovine URT viromes recovers near-complete betacoronavirus-like (CoV-D180) and adenovirus-like (AdV-D56) genomes positioned phylogenetically between bovine and human viral lineages. Competitive mapping of bovine-derived CoV-D180 and AdV-D56 to human respiratory metatranscriptomic datasets reveals genome-specific, regionally structured coverage patterns distinct from reference viruses, supporting shared sequence features in conserved genomic regions across host-associated viral lineages. Collectively, these findings reveal early-life assembly dynamics of the bovine respiratory virome and highlight cross-host signatures in a One Health framework.},
}

Animals
Cattle
*Virome/genetics
*Bacteriophages/genetics/physiology
Phylogeny
Humans
Genome, Viral
*Respiratory System/virology
Metagenomics
Respiratory Tract Infections/virology/veterinary
Evolution, Molecular

@article {pmid42946746,
year = {2026},
author = {McLatchie, S and Palestini, S and Woodhead, A and Gutierrez, T and Walsh, DA},
title = {Evidence of an acetone carboxylation pathway in photoheterotrophic bacteria from the Arctic Ocean.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946746},
issn = {2041-1723},
mesh = {Arctic Regions ; *Acetone/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Seawater/microbiology ; Oceans and Seas ; Metagenome ; Rhodopsins, Microbial/genetics ; Genome, Bacterial ; Carbon Dioxide/metabolism ; *Gammaproteobacteria/genetics/metabolism ; Gene Transfer, Horizontal ; Heterotrophic Processes ; Carbon Cycle ; },
abstract = {Carboxylases are among the most important enzymes in nature as they catalyze the fixation of inorganic carbon (CO2), a central step in the global carbon cycle. In addition to their well-known function in autotrophic CO2 fixation, many carboxylases play a role in the heterotrophic assimilation of organic compounds. In this study, we provide genomic evidence for an assimilatory carboxylation pathway involved in acetone degradation in photoheterotrophic bacteria from metagenomes collected along a latitudinal transect of the Arctic Ocean. This curious metabolism was linked to a single population of Gammaproteobacteria (Porticoccus arcticus). P. arcticus has a streamlined genome compared to Porticoccus relatives but has maintained a complete acetone carboxylation pathway while acquiring multiple proteorhodopsin genes by lateral gene transfer. Arctic Ocean metatranscriptomes revealed the acetone carboxylase and rhodopsins genes were among the most highly expressed P. arcticus genes in oligotrophic Arctic surface waters. P. arcticus sequences were consistently detected, and often abundant (up to 9%), in a multiyear Arctic Ocean 16S rRNA time-series, supporting its ecological significance in Arctic marine systems. Overall, this work reports a metabolic module (acetone carboxylation) in the ocean that may allow photoheterotrophic bacteria to enhance their biosynthetic capacity via CO2 assimilation.},
}

Arctic Regions
*Acetone/metabolism
RNA, Ribosomal, 16S/genetics
Phylogeny
Seawater/microbiology
Oceans and Seas
Metagenome
Rhodopsins, Microbial/genetics
Genome, Bacterial
Carbon Dioxide/metabolism
*Gammaproteobacteria/genetics/metabolism
Gene Transfer, Horizontal
Heterotrophic Processes
Carbon Cycle

@article {pmid42946988,
year = {2026},
author = {Tataka, Y and Kawashima, H and Nanri, H and Watanabe, D and Watanabe, K and Yamaguchi, M and Kunisawa, J and Miyachi, M},
title = {Standardization of shotgun metagenomics parameters for pks-positive enterobacteria detection in human fecal samples: Receiver operating characteristic analysis using polymerase chain reaction as reference standard.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42946988},
issn = {1471-2180},
support = {JP16ck0106243h0001//Development of Innovative Research on Cancer Therapeutics from the Japan Agency for Medical Research and Development/ ; JP16K00944//Grant-in-Aid for Scientific Research C/ ; 201709002 B//Health and Labor Sciences Research Grant/ ; },
mesh = {Humans ; *Feces/microbiology ; *Polymerase Chain Reaction/standards/methods ; *Metagenomics/methods/standards ; *Enterobacteriaceae/genetics/isolation & purification/enzymology ; *Polyketide Synthases/genetics ; ROC Curve ; Shotgun Sequencing ; Female ; Adult ; Male ; Reference Standards ; Middle Aged ; Peptides/genetics ; Japan ; Polyketides/metabolism ; Aged ; },
abstract = {BACKGROUND: Enterobacteria harboring the polyketide synthase (pks) island (clbA-clbS), which encodes colibactin (pks[+] enterobacteria), is a putative risk factor for colorectal cancer. Polymerase chain reaction (PCR) is the current standard for detection. Primer-independent shotgun metagenomic sequencing (SMS) is increasingly used; however, thresholds and analysis parameters for identifying pks[+] enterobacteria remain unstandardized. This study aimed to evaluate how accurately SMS can reproduce PCR-defined pks[+] status and identify practical cutoffs by analyzing fecal samples from 223 healthy adults in a Japanese cohort.

RESULTS: PCR identified 60/223 (26.9%) participants as pks⁺. SMS detected at least one clb gene in 85/223 (38.1%) at ≥ 90% identity; 49 of these agreed with PCR positives. Among the single-gene rules, clbB yielded the best discrimination (area under the curve (AUC) = 0.826) across 70-90% identity. The total-read rule across 19 clb genes performed best overall (AUC = 0.838), with higher AUCs above the 60% threshold (all p ≤ 0.045). The rule requiring detection of at least eight clb genes was inferior (AUC = 0.734-0.773). Detection performance depended on gene length; longer clb genes (> 1,500 amino acids) achieved higher accuracy (AUC ≥ 0.800).

CONCLUSIONS: Optimized SMS can reproduce PCR-based detection of pks⁺ enterobacteria in feces with high accuracy. clbB and a cluster-level rule aggregating reads across clbA-clbS are effective, although tightening the sequence-identity threshold did not consistently improve performance. The standardized criteria proposed here enable cross-study comparability and may accelerate epidemiologic assessment of pks⁺ enterobacteria and its clinical translation for colorectal cancer prevention.},
}

Humans
*Feces/microbiology
*Polymerase Chain Reaction/standards/methods
*Metagenomics/methods/standards
*Enterobacteriaceae/genetics/isolation & purification/enzymology
*Polyketide Synthases/genetics
ROC Curve
Shotgun Sequencing
Female
Adult
Male
Reference Standards
Middle Aged
Peptides/genetics
Japan
Polyketides/metabolism
Aged

@article {pmid42947177,
year = {2026},
author = {Zhang, X and Yin, D and Liu, P and Song, J and Fang, Z and Liu, J},
title = {Improving silage fermentation of distilled grain waste-based spent mushroom substrate using indigenous lactic acid bacteria: metagenomic insights.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {19},
number = {1},
pages = {},
pmid = {42947177},
issn = {2731-3654},
support = {32370133//National Natural Science Foundation of China/ ; 32470122//National Natural Science Foundation of China/ ; 2508085Y011//Natural Science Foundation of Anhui Province/ ; },
abstract = {BACKGROUND: Rising global mushroom production calls for recycling spent mushroom substrate (SMS). However, its high moisture content, susceptibility to spoilage, and low abundance of indigenous lactic acid bacteria (LAB) limit its use as silage. In this study, an effective silage inoculation strategy was developed to transform SMS derived from composted distilled grain waste (DGW) and colonized by Pleurotus ostreatus.

RESULTS: Three indigenous lactic acid bacteria, including Limosilactobacillus fermentum L2, Weissella paramesenteroides W1, and Pediococcus acidilactici P1, were isolated and selected for their rapid growth and acidification capacity, and applied individually or in combination at different stages of fungal colonization. Compared with a commercial inoculant, all indigenous lactic acid bacteria (LAB) treatments, especially a combination of L. fermentum L2 and P. acidilactici P1, significantly enhanced silage fermentation, as evidenced by lower pH (4.04-4.73), 31-fold and 1.87-fold increases in lactic acid and acetic acid production, respectively, improved crude protein retention, and preserved dry matter contents. KEGG enrichment analysis demonstrated that carbon metabolic flux was markedly redirected toward lactic acid fermentation, while pathways related to protein degradation and biosafety were significantly suppressed in LAB-treated SMS silage. Weighted metabolic analysis revealed that LAB contributed most to fermentative processes, thereby enriching Pediococcus, Weissella, and Lactobacillus, whereas the contributions of non-LAB and potentially harmful microorganisms were substantially reduced.

CONCLUSION: These results indicate that indigenous LAB enhance the ensiling efficiency of SMS by driving functional reallocation and pathway-level dominance, thereby improving fermentation efficiency, stability, and nutritional quality, highlighting their potential for promoting SMS silage as a high-quality ruminant feed resource.},
}

@article {pmid42947248,
year = {2026},
author = {Wagner, J and Rajan, D and Field, SF and Betteridge, E and Bellis, K and Knoll, M and Ng, D and Teixeira, D and Blane, B and Akram, A and de Sousa, C and Brennan, J and Aggarwal, D and MacIntyre-Cockett, G and Chaudron, SE and Grayson, N and Hyatt, B and Wong, A and Galvin, A and Huang, YL and Jackson, D and Forbes, M and Schwach, F and Frick-Kretschmer, A and Figueroa, K and Lassalle, F and Roberts-Sengier, W and Lignes, A and Novaes, F and Fatima, S and Howe, K and Stott, S and Bonsall, D and Harrison, EM},
title = {Benchmarking and optimisation of bait-capture metagenomics for sequencing of respiratory viruses at scale.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42947248},
issn = {1756-994X},
support = {220540/Z/20/A//Wellcome/ ; Quinquennial Review 2021-2026'//Wellcome Sanger Institute/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Genome, Viral ; Benchmarking ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Reproducibility of Results ; Workflow ; },
abstract = {BACKGROUND: Sequencing respiratory virus genomes is essential for public health surveillance and research. Although shotgun metagenomics is pathogen agnostic, its sensitivity is limited by abundant off-target host nucleic acids. Hybridization bait capture overcomes this limitation by selectively enriching viral sequences prior to sequencing.

METHODS: We evaluated three respiratory viral bait capture workflows (veSEQ, RVI-seq, and Illumina) to compare their performance and assess their suitability for scalable respiratory virus sequencing. Synthetic RNA controls and clinical samples containing SARS-CoV-2, influenza A, influenza B, human parainfluenza virus, and respiratory syncytial virus (RSV) were analysed.

RESULTS: All three workflows demonstrated high efficiency, reproducibility and broadly comparable performance across respiratory viruses. Complete viral genomes were consistently recovered from samples containing 10,000 viral copies, while viral reads remained detectable at substantially lower viral loads, including approximately 100 copies. Workflow optimisation reduced reagent costs and enabled laboratory automation without compromising sequencing sensitivity.

CONCLUSION: Hybridization bait capture provides an effective and scalable approach for respiratory virus genome sequencing. Cost reductions and automation can be implemented without compromising performance, supporting its use in routine genomic surveillance and public health preparedness.},
}

*Metagenomics/methods
Humans
*Genome, Viral
Benchmarking
High-Throughput Nucleotide Sequencing/methods
SARS-CoV-2/genetics
Reproducibility of Results
Workflow

@article {pmid42947262,
year = {2026},
author = {Baxter, N and Plata, G and Bown, L and Shields, J and Augspurger, N and Kumar, A and Susanti, D},
title = {Bacillus probiotic blend modulates ileal microbiome to improve growth performance and prevent necrotic enteritis in broiler chickens.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42947262},
issn = {2524-4671},
abstract = {The intensification of poultry production has led to an increased prevalence of necrotic enteritis (NE), a costly disease caused by Clostridium perfringens, traditionally managed through antibiotic use. However, concerns over antibiotic resistance have driven the search for alternative solutions. This study evaluates the efficacy of a three-strain Bacillus probiotic blend as an alternative for preventing NE in broiler chickens. The three Bacillus strains, Bacillus subtilis ATCC PTA126786, B. velezensis ATCC PTA127064, and B. velezensis ATCC PTA 127065, were selected based on their probiotic attributes, especially their ability to inhibit the growth of C. perfringens and other poultry pathogens. Our results from in vivo experiments showed that dietary supplementation with the probiotic blend significantly reduced NE-associated mortality and improved growth performance metrics such as average daily gain and feed conversion ratio. Metagenomic analyses of ileal contents of chickens supplemented with the Bacillus blend revealed a significant reduction in the abundances of C. perfringens, Enterococcus cecorum, and Eimeria acervulina following NE challenge, despite modest changes in overall microbiome composition. Importantly, the observed probiotic efficacy was strongly associated with the Bacillus strains colonization in the gut, as measured by the Bacillus genome recovery in ileal content samples. These findings highlight the potential of Bacillus-based probiotics as an effective alternative to antibiotics in poultry production, contributing to improved animal health and sustainability.},
}

@article {pmid42947834,
year = {2026},
author = {Quan, R and Wang, C and Li, W and Jiang, K and Huang, K},
title = {Case Report: Delayed diagnosis of adult-onset Still's disease after sepsis-like acute liver failure with macrophage activation syndrome.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1941213},
pmid = {42947834},
issn = {2296-858X},
abstract = {BACKGROUND: Adult-onset Still's disease (AOSD) is a rare systemic autoinflammatory disease characterized by heterogeneous and nonspecific clinical manifestations. It often requires differentiation from infectious diseases, malignancies, and other rheumatic autoimmune disorders, making early diagnosis challenging. Acute liver failure (ALF) is a rare but severe complication of AOSD. AOSD may also be complicated by macrophage activation syndrome (MAS), a severe hyperinflammatory condition that can cause multiorgan dysfunction and mimic sepsis, further complicating diagnosis and management.

CASE PRESENTATION: We report a 35-year-old woman with AOSD complicated by macrophage activation syndrome who initially presented with acute liver failure. Multiple pathogens were detected by metagenomic next-generation sequencing (mNGS), leading to an initial misdiagnosis of sepsis. Over the following two years, the patient experienced recurrent episodes of fever, rash, arthralgia, and liver dysfunction. After comprehensive evaluation, the diagnosis of AOSD was established according to the Yamaguchi criteria, and MAS was diagnosed based on the HLH-2004 criteria and HScore. The patient achieved clinical remission after high-dose glucocorticoid therapy and remained stable during follow-up.

CONCLUSIONS: This case highlights that AOSD complicated by MAS should be considered in patients with unexplained fever and acute liver failure, particularly those with hyperferritinemia, rash, and multisystem involvement. Even in the presence of evidence suggestive of infection, clinicians should remain vigilant for AOSD with MAS to avoid misdiagnosis and delayed treatment.},
}

@article {pmid42947847,
year = {2026},
author = {Zhao, R and Liang, LJ and Lu, SF and Yao, R and Cheng, T},
title = {Case Report: Paralytic rabies masquerading as traumatic spinal cord injury: a diagnostic pitfall in trauma surgery.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1954968},
pmid = {42947847},
issn = {2296-858X},
abstract = {Rabies is a uniformly fatal zoonotic encephalitis. Its paralytic form, which accounts for approximately 20% of cases, frequently resembles acute spinal cord injury (SCI). When there is a coincident history of trauma, diagnostic anchoring may wrongly attribute neurological decline to the injury, thereby delaying the correct diagnosis. We describe the case of a 26-year-old man who developed progressive, ascending paralysis of the lower limbs 10 days after a 3-m fall. At a secondary hospital, he was clinically diagnosed with traumatic SCI without spinal MRI. On transfer, reassessment revealed a fox bite 4 months earlier and features of the hydrophobia variant (a sensation of water "entering the brain" during swallowing). Cerebrospinal fluid metagenomic next-generation sequencing (mNGS) detected Rabies lyssavirus within 48 h, showing 100% sequence identity to Chinese isolates spanning the N and L genes. This finding was subsequently confirmed by the Sichuan Provincial Center for Disease Control and Prevention (CDC) using standard reference testing on peripheral blood. The patient subsequently died of autonomic and respiratory failure. This case highlights how recent trauma can obscure a fatal infectious cause. A clinical diagnosis of SCI made without neuroimaging should be regarded as provisional, and mNGS can provide an unbiased, rapid means of resolving diagnostically challenging neurological presentations.},
}

@article {pmid42947889,
year = {2026},
author = {Tauekelova, A and Katkenov, N and Kozhakhmetov, S and Jarmukhanov, Z and Vinogradova, E and Abdrakhmanov, A and Sailybayeva, A and Bekbossynova, M and Kushugulova, A},
title = {Gut microbiome taxonomic and functional capacity alterations in CHD and HFpEF.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875692},
pmid = {42947889},
issn = {1664-302X},
abstract = {The gut microbiome is known to modulate metabolic health, yet its role in coronary heart disease (CHD) and heart failure with preserved ejection fraction (HFpEF) remains unclear. In the present study, we profiled the gut microbiome of 234 participants using shotgun metagenomic sequencing across controls (n = 43), individuals with low-risk atherosclerosis (LRAS, n = 23), and patients with CHD + HFpEF (n = 168). Species richness was significantly increased in CHD + HFpEF, with no disruption in taxonomic evenness. LRAS did not diverge significantly in alpha metrics. In contrast, beta diversity analysis demonstrated significant divergence of both LRAS and CHD + HFpEF taxonomic structure from controls, with the greatest divergence in CHD + HFpEF, particularly in older patients. Notably, all differences were attenuated when comparing obese controls and disease groups. However, significant heterogeneity in multivariate dispersion was observed, and a contribution of differences in variation cannot be excluded. Further differential analysis, adjusting for age, BMI, sex, and glucose and lipid profiles, revealed significant associations between specific taxa and CHD + HFpEF, including depletion of the saccharolytic fermenter Bifidobacterium and enrichment of taxa linked to proteolytic or inflammatory metabolism (notably Prevotella and Bilophila), regardless of age and BMI. Subsequent analysis of inferred functional features indicated increased potential for L-citrulline, L-glutamate, L-lysine, and pyrimidine metabolism in CHD + HFpEF. Collectively, the present analysis suggests that CHD + HFpEF is associated with distinct compositional and functional shifts in the gut microbiome. Further longitudinal and interventional research is required to determine which of these microbial features contribute to disease progression and to better characterize underlying mechanisms.},
}

@article {pmid42930732,
year = {2026},
author = {Tanida, K and Degel-Broßmann, N and Robitaille, A and Heim, D and Glatzel, M and Blümke, P and Aepfelbacher, M and Lütgehetmann, M and Christner, M and Grundhoff, A and Fischer, N},
title = {Disseminated Mucor indicus Infection in a Heart Transplant Recipient: Complementary Conventional and Sequencing-Based Diagnostic Approaches.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {42930732},
issn = {2309-608X},
support = {SFB 1648/1 (2024) - 512741711//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Background: Mucormycosis is a rapidly progressive and often fatal invasive fungal infection in immunocompromised patients. Diagnosis remains challenging because microscopy and culture have limited sensitivity, while targeted molecular assays may fail to detect uncommon Mucorales species. Case Presentation: We report a fatal case of disseminated Mucor indicus infection with pulmonary and cerebral involvement in a heart transplant recipient receiving immunosuppressive therapy and posaconazole prophylaxis. Initial microscopy of bronchial secretions demonstrated broad pauciseptate hyphae consistent with Mucorales, whereas targeted PCR assays remained negative. Species identification was subsequently achieved by culture, MALDI-TOF mass spectrometry, and internal transcribed spacer (ITS) sequencing. Following neurological deterioration, brain biopsy confirmed cerebral involvement histopathologically, and ITS sequencing detected M. indicus. Comparative DNA- and RNA-based metagenomic sequencing identified Mucorales sequences, although read abundance remained unexpectedly low despite extensive histopathological fungal burden. Nevertheless, independent mapping of metagenomic reads against databases comprising all genomic viral and fungal reference sequences readily identified Mucor indicus as the sole pathogen receiving significant scores. Conclusions: This case illustrates that targeted Mucorales PCR may fail to detect an uncommon species despite evidence of invasive fungal infection. Microscopy, culture, histopathology, ITS sequencing, and comprehensive metagenomic analyses provided complementary evidence for disseminated Mucor indicus infection. Integrated diagnostics combining histopathology, culture, and complementary molecular methods remain essential for accurate diagnosis of invasive mucormycosis.},
}

@article {pmid42930741,
year = {2026},
author = {Wang, H and Che, Y and Liu, H and Yu, X and Liu, B and Shu, F and Zhou, J and Wu, M},
title = {Arbuscular Mycorrhizal Fungi Inoculation Promotes Growth and Alleviates Fusarium tricinctum-Induced Growth Inhibition in Quercus variabilis Seedlings.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {42930741},
issn = {2309-608X},
support = {No. 42430702//National Natural Science Foundation of China/ ; },
abstract = {Quercus variabilis is a key species for reforestation in East Asia, yet the mechanisms by which arbuscular mycorrhizal fungi (AMF) influence seedling growth and responses to soil-borne fungal challenge remain incompletely understood. This study combined physiological and metagenomic approaches to address this gap. Among seven rhizosphere fungal isolates, Fusarium tricinctum (F15) exerted the strongest growth-inhibitory effect on Q. variabilis seedlings and was therefore selected for subsequent experiments. Inoculation with the AMF Rhizophagus intraradices significantly promoted seedling growth (p < 0.05), increasing root length by 4.94% relative to the uninoculated control and increasing ground diameter and aboveground fresh weight by 28.57% and 117.07%, respectively, relative to F15-treated seedlings. AMF inoculation also significantly altered substrate nutrient status (p < 0.05), particularly nitrogen, phosphorus, and potassium, and enhanced the activity of antioxidant enzymes, including peroxidase and catalase (p < 0.05). Metagenomic analysis revealed that AMF significantly reshaped rhizosphere microbial community composition and bacterial α-diversity (p < 0.05), enriching beneficial taxa such as Mesorhizobium. Functional profiling showed differences in predicted microbial functional profiles between AMF-inoculated and F15-treated groups. Together, these results indicate that AMF enhances seedling growth and mitigates the negative effects associated with F15 challenge, potentially through altered substrate nutrient dynamics, enhanced antioxidant capacity, and modulation of the rhizosphere microbial community.},
}

@article {pmid42931080,
year = {2026},
author = {Hudu, SA and Morad, EA and Alhazimi, GM and Othman, RQA and Elboraei, YAE and Jimoh, AO},
title = {Hidden Microbiome of Mining Environments: Implications for Occupational Health, Bioaerosol Exposure, and Antimicrobial Resistance.},
journal = {Journal of xenobiotics},
volume = {16},
number = {6},
pages = {},
pmid = {42931080},
issn = {2039-4713},
support = {NBU-CRP-2026-3770.//Northern Border University/ ; },
abstract = {Mining environments are extreme subsurface ecosystems characterized by elevated concentrations of metals and minerals, limited light, and high particulate loads. Occupational health research in mining has traditionally emphasized physical and chemical hazards, whereas biological exposures remain less well-characterized. This narrative review synthesizes evidence on mining-associated microbial communities, bioaerosols, occupational exposure, respiratory health, and antimicrobial resistance (AMR). The literature search covered PubMed/MEDLINE, Scopus, and Web of Science from database inception through August 2026. Evidence from coal, uranium, metal mining, acid mine drainage, and mine dust environments indicates that geochemical conditions and mining activities shape microbial communities. Drilling, blasting, excavation, and ore transport can aerosolize microbial cells, spores, and dust-associated microbial components, creating plausible inhalation pathways. Metal-rich environments may also favor persistence and co-selection of metal- and antibiotic-resistance determinants within environmental microbial communities. Metagenomic sequencing and environmental DNA approaches have expanded detection of microbial diversity, functional genes, and environmental resistomes. However, environmental detection does not establish microbial viability, effective worker exposure, transmission, or disease causation. Future research should integrate standardized environmental and personal microbial exposure measurements with respirable dust and chemical monitoring, longitudinal occupational epidemiology, and functional validation of resistance determinants to determine the actual occupational-health significance of mining-associated microbiomes.},
}

@article {pmid42931176,
year = {2026},
author = {Bommineni, V and Edison, LK and Kariyawasam, S},
title = {Current Status and Future Trends in Campylobacter Detection and Quantification Across the Food Production Continuum.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931176},
issn = {2076-0817},
support = {//University of Florida/ ; },
mesh = {*Food Microbiology/methods ; Animals ; *Campylobacter Infections/microbiology/diagnosis ; *Campylobacter/isolation & purification/genetics ; Humans ; Foodborne Diseases/microbiology ; Campylobacter jejuni/isolation & purification/genetics ; Poultry/microbiology ; },
abstract = {Campylobacter spp., particularly Campylobacter jejuni and Campylobacter coli, remain the leading bacterial causes of foodborne gastroenteritis worldwide, with poultry serving as the dominant reservoir and additional transmission routes involving livestock, raw milk, water, fresh produce, and food-processing environments. Accurate detection and quantification are essential for risk assessment, process hygiene monitoring, outbreak investigation, and One Health surveillance; however, reliable measurement is complicated by the organism's fastidious microaerophilic growth requirements, stress sensitivity, low or uneven distribution in complex matrices, and ability to enter viable but non-culturable (VBNC) states. This review examines current and emerging approaches for Campylobacter detection and quantification across the food production continuum, including pre-harvest, harvest and processing, post-harvest, and retail, as well as consumer-level settings. Conventional culture, colony-count enumeration, most probable number (MPN) methods, and immunological assays are compared with molecular approaches, including polymerase chain reaction (PCR), qPCR, digital PCR, viability PCR, whole-genome sequencing, metagenomics, biosensors, microfluidics, and artificial intelligence-assisted surveillance. Regulatory and standardization frameworks, including the International Organization of Standards (ISO), Food and Drug Administration (FDA), United States Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS), and European Union (EU) process hygiene criteria are discussed, together with One Health surveillance systems. Overall, future Campylobacter monitoring will require integrated, matrix-specific strategies that combine standardized culture-based enumeration, viability-informed molecular quantification, genomic source attribution, and harmonized metadata to support more rapid, accurate, and risk-based food-safety decision-making.},
}

*Food Microbiology/methods
Animals
*Campylobacter Infections/microbiology/diagnosis
*Campylobacter/isolation & purification/genetics
Humans
Foodborne Diseases/microbiology
Campylobacter jejuni/isolation & purification/genetics
Poultry/microbiology

@article {pmid42931196,
year = {2026},
author = {Chen, J and Zou, Q and Pan, B and Zhang, Y},
title = {Genomic Surveillance of Respiratory Pathogens: From Molecular Detection to Precision Infection Control.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931196},
issn = {2076-0817},
support = {32270528//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/prevention & control/microbiology/epidemiology ; *Genomics/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Diagnostic Techniques/methods ; Artificial Intelligence ; },
abstract = {Respiratory pathogens remain a major global public health concern due to factors including their genetic diversity, dynamic transmission patterns, and increasing antimicrobial resistance. Conventional molecular diagnostics, particularly polymerase chain reaction (PCR)-based assays, remain essential for rapid and scalable pathogen detection but provide limited information on pathogen evolution, transmission, and resistance mechanisms. Advances in whole-genome sequencing (WGS), targeted sequencing, and metagenomic next-generation sequencing (mNGS) have expanded respiratory pathogen surveillance from targeted detection toward higher-resolution genomic characterization. However, no single technology can adequately address all surveillance objectives. Instead, molecular diagnostics, genomic sequencing, epidemiological investigation, and clinical assessment provide complementary information that can be integrated according to the pathogen, clinical context, and specific public health question. This review examines the evolution of respiratory pathogen surveillance and emphasizes an integrated framework in which different technologies are selected and combined to support pathogen characterization, transmission investigation, antimicrobial resistance surveillance, and preventive decision-making. We further discuss emerging applications of artificial intelligence (AI) for integrating genomic, epidemiological, and clinical data, with potential roles in genomic interpretation, early risk assessment, and precision infection control. Although AI-enhanced surveillance remains largely at the research and validation stage, advances in data integration, model development, and computational infrastructure may enable more predictive and actionable surveillance systems. Overall, the future of respiratory pathogen surveillance will depend not simply on adopting more advanced technologies, but on integrating complementary detection and analytical approaches to transform pathogen detection into actionable evidence for public health decision-making.},
}

Humans
*Respiratory Tract Infections/diagnosis/prevention & control/microbiology/epidemiology
*Genomics/methods
Metagenomics/methods
High-Throughput Nucleotide Sequencing
Molecular Diagnostic Techniques/methods
Artificial Intelligence

@article {pmid42931227,
year = {2026},
author = {Liu, Q and Jiang, Y},
title = {Diagnosis of Extrapulmonary Tuberculosis at the Interface of Pathogen Detection and Host Response: Molecular, Microbiological, and Histopathological Advances.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931227},
issn = {2076-0817},
support = {2025SWGKY391//the Preventive Medicine Association of Hubei Province/ ; WF2025Y08//Wuhan Pulmonary Hospital/ ; },
mesh = {Humans ; *Tuberculosis, Extrapulmonary/diagnosis ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; Biomarkers ; *Host-Pathogen Interactions ; },
abstract = {Extrapulmonary tuberculosis (EPTB) accounts for approximately 16% of notified tuberculosis (TB) cases worldwide and disproportionately affects children and immunocompromised populations. Paucibacillary disease, anatomically diverse sites, and nonspecific presentations make EPTB one of the most persistent diagnostic challenges in TB control. This review integrates microbiological, molecular, sequencing-based, and histopathological approaches to EPTB diagnosis within the context of site-specific immunopathology, including granuloma biology and the microenvironment of caseous necrosis. Comparative evidence is synthesized across osteoarticular, lymph node, pleural, central nervous system, and disseminated EPTB, focusing on Xpert MTB/RIF and Ultra, targeted and metagenomic next-generation sequencing (mNGS), and emerging host-response biomarkers and AI-assisted histopathology. Pragmatic, tiered diagnostic algorithms are proposed for resource-limited settings, where most EPTB occurs, and unresolved gaps in current international guidance are identified. Aligning diagnostic modality choice with anatomical site, specimen quality, pathological subtype, and laboratory capacity can shorten the time to EPTB diagnosis and inform host-directed diagnostic strategies.},
}

Humans
*Tuberculosis, Extrapulmonary/diagnosis
*Mycobacterium tuberculosis/genetics/isolation & purification
Molecular Diagnostic Techniques/methods
High-Throughput Nucleotide Sequencing
Biomarkers
*Host-Pathogen Interactions

@article {pmid42931636,
year = {2026},
author = {Wang, Y and Yu, W and Kanda, K and Iwata, H and Guo, J},
title = {In Ovo Exposure to Phenanthrene Promotes Antimicrobial Resistance Genes and Hemolysin Virulence Factor in Guts of Chicken Embryos.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931636},
issn = {2305-6304},
support = {42571089//National Natural Science Foundation of China/ ; 2026JC-YXQN-119//Natural Science Basic Research Program of Shaanxi/ ; },
abstract = {Antimicrobial resistance genes (ARGs) are increasingly recognized as emerging environmental contaminants that threaten ecological integrity and animal health. Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants that accumulate in the environment and have been detected in wild bird eggs. Although PAHs have been shown to accelerate ARG dissemination in environmental matrices, their influence on ARG dynamics in birds is unclear. Therefore, it is hypothesized that exposure to elevated levels of PAHs promotes the propagation and enrichment of ARGs in the avian gut. In this study, chicken embryos at Hamburger-Hamilton Stage 1 (HHS 1) were exposed in ovo to phenanthrene (PHE; 1, 100, and 400 nmol/g egg), and the toxic effects were evaluated. High PHE exposure significantly reduced embryonic tarsus length by 14.81% and increased the liver somatic index (LSI) by 26.97%. Functional annotation based on the Virulence Factor Database (VFDB) showed that the relative abundance of hemolysin, a microbial virulence factor associated with gastrointestinal microorganisms, was significantly elevated in the high-PHE group. In a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes involved in nucleotide excision repair (NER) and basal transcription factor (BTF) pathways showed significantly lower relative abundance following high-dose exposure. Additionally, ARGs related to polymyxin and pleuromutilin resistance were significantly enriched in the high-exposure group. Partial least squares path modeling (PLS-PM) indicated that ARG enrichment was jointly shaped by multiple factors. PHE may be directly associated with ARG proliferation or may act indirectly through mobile genetic elements (MGEs), whereas bacterial community abundance might be linked to the potential dissemination of ARGs given its significant positive association with MGEs. Collectively, these findings provide correlative evidence that PHE exposure is associated with increased ARG abundance in avian organisms and highlight the need for an integrated evaluation of PAH-associated hazards to avian health.},
}

@article {pmid42931645,
year = {2026},
author = {Song, F and Bao, S and Chen, C and Xu, M},
title = {Viruses in Soil: A Review of Methods, Distribution and Ecological Functions.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931645},
issn = {2305-6304},
support = {I2023004//Shanghai Science and Technology Development Foundation/ ; },
abstract = {Viruses are the most abundant and active biological organisms in soil ecosystems. However, their spatial distribution and ecological functions remain inadequately addressed owing to a lack of systematic analysis and the complexity of the soil matrix. Therefore, this review systematically summarizes current knowledge of soil viruses through an examination of research methods, spatiotemporal distribution, and ecological functions. Our review indicates that current progress of soil viruses remains constrained by technological inconsistencies and difficulties in viral isolation techniques within complex soil matrices. Therefore, viral distribution analyses are largely limited to small-scale sections of agricultural land, forest, pastureland, and grassland. There is insufficient exploration of viral distribution across large-scale geographic areas and desert soil environments, as well as RNA virus diversity. The characteristics of soil viral communities are primarily influenced by environmental factors such as temperature, moisture, and pH. Overall, we conclude that soil viruses are pivotal drivers of microbial community dynamics and biogeochemical cycling, although our comprehensive understanding is severely bottlenecked by complex soil matrices and inconsistent viral isolation methodologies. Future research should focus on methodological innovations such as long-read sequencing and single-cell approaches to decipher virus-host interaction networks and their ecological roles across large-scale and extreme environments.},
}

@article {pmid42931687,
year = {2026},
author = {Huang, X and Li, Q and Feng, M and Liu, C and Shi, H and Wang, D},
title = {Microbial-Clay Mineral Interactions: Mechanisms and Applications in Environmental Remediation.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931687},
issn = {2305-6304},
support = {2026GXNSFBA00640164//Guangxi Science and Technology Department/ ; Guike AD25069074//Guangxi Science and Technology Department/ ; 42367061//National Natural Science Foundation of China/ ; //Bagui Youth Top Talent Program of Guangxi/ ; },
abstract = {Microbial-clay mineral interactions play a pivotal role in environmental remediation, biogeochemical cycling, and the long-term evolution of the Earth's systems. This review critically synthesizes the fundamental mechanisms, reactive pathways, and environmental implications of microbial-clay mineral interactions. Clay minerals, owing to their large specific surface area, high cation exchange capacity, and tunable surface charge, are shown to sustain microbial metabolism by offering physical shelter and serving as sources of essential nutrients. Concurrently, microorganisms mediate the dissolution, structural alteration, and neoformation of clay phases via proton production, electron transfer reactions, and genetic regulatory networks, thereby establishing a dynamic synergistic relationship. In environmental remediation, clay-microorganism complexes have been demonstrated to promote heavy metal stabilization. They concurrently expedite the breakdown of organic contaminants, including polycyclic aromatic hydrocarbons (PAHs). Nevertheless, major knowledge gaps persist, especially concerning the multiscale complexity of interfacial behaviors and still-elusive molecular-scale interaction mechanisms. Finally, several priority directions for the future are proposed, including the integration of metagenomics and molecular modeling, the design of biomarker-based monitoring tools, and the scalable translation of bench-scale discoveries and laboratory insights into field-scale remediation technologies. Collectively, this work advances fundamental knowledge of key microbe-mineral biogeochemical processes and provides a scientific basis for the development of sustainable, nature-based environmental remediation strategies.},
}

@article {pmid42933050,
year = {2026},
author = {He, X and Zhou, J and Long, S and Liu, H and Zou, G and Song, G},
title = {Nocardia terpenica bacteremia confirmed by blood culture in a patient with granulocytopenia and Aspergillus fumigatus coinfection: a first case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {117},
number = {1},
pages = {117708},
doi = {10.1016/j.diagmicrobio.2026.117708},
pmid = {42933050},
issn = {1879-0070},
abstract = {BACKGROUND: Nocardia terpenica is a rare environmental actinomycete without prior report of human bloodstream infection. In immunocompromised hosts, it often causes mixed infections, complicating diagnosis and treatment.

CASE PRESENTATION: We report the first bacteremia case of N. terpenica in an adult with severe granulocytopenia after B-ALL induction chemotherapy. Blood culture (positive at 5.9 days) revealed branched Gram-positive rods; species was confirmed by MALDI‑TOF and whole‑genome sequencing (WGS). Plasma mNGS also detected Aspergillus fumigatus, and chest CT showed halo/air‑crescent signs, establishing concurrent invasive pulmonary aspergillosis. The patient cleared infection after combined antibiotics (trimethoprim‑sulfamethoxazole, voriconazole, imipenem/cilastatin, vancomycin) and completed subsequent chemotherapy.

CONCLUSION: We report the first case of N. terpenica bacteremia, highlighting that this species can cause bloodstream infection in severely immunocompromised hosts. Prolonged culture incubation and molecular diagnostics (WGS and mNGS) are essential for timely diagnosis and optimal management.},
}

@article {pmid42933349,
year = {2026},
author = {Qin, H and Zhang, S and Xia, F and Tan, Q and Wan, H and Cai, Y},
title = {Seasonally shifting methane-control regimes across urban rivers and urban wetland rivers in the GBA, China, revealed by environmental, isotopic, and microbial evidence.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131239},
doi = {10.1016/j.jenvman.2026.131239},
pmid = {42933349},
issn = {1095-8630},
abstract = {Urban rivers (UR) and urban wetland rivers (WR) are increasingly recognized as CH4 sources, yet the processes underlying differences between these aquatic habitats remain poorly resolved. We investigated excess CH4 concentration (ΔCH4), estimated diffusive flux, environmental conditions, stable carbon isotopes, and sediment microbial functional potential in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), China. CH4 dynamics exhibited a clear seasonal shift between contrasting spatial patterns. UR showed an amplified CH4 state during the first two seasons, the wetland outlet (WO) in wet season 1 and than both WR and WO in dry season 1. In UR, ΔCH4 decreased with dissolved oxygen (β = -0.194, p = 0.020) and increased with total nitrogen (β = 0.272, p = 0.003), indicating strong nutrient-redox control on CH4 accumulation. Stable-isotope signatures overlapped broadly among potential production and oxidation processes, while WR displayed more [13]C-depleted CH4 than UR during wet season 1 despite lower ΔCH4, indicating that source signatures did not translate directly into net CH4 accumulation. Consistently, mcr and CO2-reducing methanogenesis genes and methanogenic taxa were relatively enriched in early UR seasons, whereas pmo-family genes and methane-oxidizing taxa were distributed more broadly across WR and WO. Together, these complementary lines of evidence reveal a seasonally reversible transition from nutrient-redox-driven CH4 amplification in urban rivers to more complex wetland-associated regulation involving carbon supply, redox heterogeneity, and methane-oxidation potential.},
}

@article {pmid42933698,
year = {2026},
author = {Qiao, Z and Wei, Z and Yuan, M and Wei, L and Hu, M and Song, K and Bi, Z and Qin, X and Yin, X},
title = {Start‑up and functional performance assessment of electron-shuttling-driven microalgal-anammox process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136132},
doi = {10.1016/j.biortech.2026.136132},
pmid = {42933698},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process has received extensive attention because of its low energy consumption and high nitrogen removal efficiency. Nevertheless, its long start-up period limits practical application. In this study, a microalgae-bacteria symbiotic system (ABSS) based on Chlorella vulgaris (C. vulgaris) was established to investigate its effects on anammox start-up and nitrogen and phosphorus removal. The introduction of C. vulgaris shortened the start-up time from 68 to 46 days, corresponding to a 32 % reduction. After 210 days of operation, the nitrogen removal rate (NRR) and phosphorus removal rate (PRR) in the microalgae-bacteria symbiotic reactor (RAM) were 21 % and 25 % higher than those in the control reactor (RA), respectively. The concentration of extracellular polymeric substances (EPS) derived from C. vulgaris, as quantified via total organic carbon measurement, was 297.73 ± 8.55 mg/L. Spectroscopic analyses suggested the presence of humic-like substances and quinone-related structures in the EPS, indicating a potential role in electron transfer. At 100 mg/L, EPS increased hydrazine dehydrogenase (HDH) activity by 49 % relative to the control group. After CoQ extraction, EPS restored HDH activity more effectively than exogenous coenzyme Q (CoQ). Metagenomic analysis showed higher abundances of genes associated with photosynthesis, carbon fixation, and nitrogen metabolism. These findings imply that EPS-mediated electron transfer and strengthened HDH activity may have contributed to the establishment of anammox activity and the shortened start-up period. Overall, this study highlights microalgal integration as a potential strategy for accelerating anammox startup and improving simultaneous nitrogen and phosphorus removal.},
}

@article {pmid42934169,
year = {2026},
author = {Chasapi, IN and Aplakidou, E and Chasapi, MN and Lamari, E and Galaras, A and Diplari, S and Iliopoulos, I and Emiris, IZ and Georgakopoulos-Soares, I and Patalano, S and Stravopodis, DJ and Karatzas, E and Baltoumas, FA and Kyrpides, NC and Pavlopoulos, GA},
title = {ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1067},
pmid = {42934169},
issn = {1362-4962},
support = {23592-EMISSION//Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation/ ; //Penn State College of Medicine and the University of Texas at Austin/ ; //US Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//US Department of Energy Office of Science user facilities/ ; 7832-YGIAMEL//Postdoctoral Researcher/ ; //HEAL-Link/ ; },
abstract = {Metagenomic studies of arthropod-associated microbiomes have generated vast amounts of sequence data, yet the functional and structural organization of these proteins remains largely unexplored. Here, we present ArthroVerse, the first comprehensive database of protein families derived from arthropod-associated metagenomes. Non-redundant protein families were generated after rigorous filtering, deduplication, and clustering. The protein families were further annotated with microbial taxonomy, host associations, protein structural information, and carbohydrate-active enzymes predictions. The resulting dataset integrates both metagenomic and reference genome-derived proteins, enabling systematic exploration of functional diversity, evolutionary relationships, and host-microbe interactions in insect microbiomes. ArthroVerse provides a valuable resource for the study of microbial ecology and arthropod physiology, offering unprecedented insight into the protein landscape of insect-associated microbial communities. ArthroVerse is publicly accessible at https://envofams.org/arthroverse/.},
}

@article {pmid42934259,
year = {2026},
author = {Serra Moncadas, L and Ruscheweyh, HJ and Woodhouse, J and Salcher, MM and Okazaki, Y and Ngugi, DK and Pester, M and Posch, T and Ghai, R and Grossart, HP and Sunagawa, S and Pernthaler, J and Andrei, AS},
title = {A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42934259},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_182489//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; *Fresh Water/microbiology ; *Biodiversity ; *Eukaryota/genetics/classification ; Metagenome ; },
abstract = {Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis. Consequently, regional‑to‑global gradients in richness, turnover, and phylogenetic structure remain poorly resolved. Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories. From 3,400 metagenomes spanning 362 lakes on seven continents, we reconstruct ~20,000 mitochondrial metagenome-assembled genomes (mitoMAGs), densely populating previously sparse branches of the eukaryotic tree-notably SAR (Stramenopiles-Alveolata-Rhizaria), Cryptophyceae, and Haptista. An empirically calibrated 98.1% mitoMAG‑identity threshold delineates species and tethers community profiles to an evolutionary backbone. On this backbone, coverage‑standardized inventories recover canonical ecological patterns: mesotrophic richness peaks, surface-layer expansion of phylogenetic breadth, and spring maxima with the strongest surface-deep coupling at vernal mixing; supporting the framework. Treating mitoMAGs as primer‑free barcodes yields a single, species‑level, phylogeny‑aware currency that renders richness, evenness, and phylogenetic breadth directly comparable across datasets, depths, seasons, and regions. By placing microbial eukaryotes on an analytical footing comparable to prokaryotes, the resulting atlas brings their diversity into reach and lays the groundwork for future high-throughput, species-aware monitoring and ecological forecasting.},
}

Phylogeny
*Genome, Mitochondrial/genetics
*Fresh Water/microbiology
*Biodiversity
*Eukaryota/genetics/classification
Metagenome

@article {pmid42934712,
year = {2026},
author = {Gu, C and Zhang, R and Rao, YZ and Zhang, X and Zhou, Z and Liu, Y and Dong, X and Wang, L and Wang, Y and Hua, ZS and Krupovic, M and Li, M},
title = {Expansion of the Asgard archaeal virome and defensome provides insights into virus-host interactions.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934712},
issn = {2049-2618},
mesh = {*Archaeal Viruses/genetics/classification/physiology/isolation & purification ; *Archaea/virology/genetics/classification ; *Virome/genetics ; Metagenomics/methods ; Genome, Viral ; Phylogeny ; *Host Microbial Interactions ; Host-Pathogen Interactions ; },
abstract = {BACKGROUND: Asgard archaea, broadly considered as a group of archaea that exhibit the closest evolutionary relationship with eukaryotes, encode diverse defense systems and are infected by distinct viruses. However, the diversity of Asgard archaeal viruses and their interactions with the hosts remain poorly explored.

RESULTS: Here, using CRISPR spacer-protospacer matching, we predict 23 viruses associated with Asgard archaea from various habitats. Apart from clusters with known viruses, we report three previously undescribed groups of Asgard viruses with predicted head-tailed virions of the realm Duplodnaviria and filamentous virions characteristic of the archaea-specific realm Adnaviria. Mapping of metagenomic reads to viral and host genomes suggested that most Asgard viruses display relatively low virus-to-host ratios, typically below 10. In addition, we considerably expanded the known defensome of Asgard archaea, among others, detecting putative PARIS and Prometheus defense systems. Finally, the diversity of anti-defense proteins and putative archaeal type IV pilins encoded by some Asgard viruses provide additional insights into the interactions between Asgard archaea and their viruses.

CONCLUSIONS: Overall, this work sheds new light on the Asgard archaeal virome and defensome, and virus-host interactions. Video Abstract.},
}

*Archaeal Viruses/genetics/classification/physiology/isolation & purification
*Archaea/virology/genetics/classification
*Virome/genetics
Metagenomics/methods
Genome, Viral
Phylogeny
*Host Microbial Interactions
Host-Pathogen Interactions

@article {pmid42934726,
year = {2026},
author = {Auguste, M and Bosi, E and Saad, J and Oliveri, C and Doni, L and Marchese, A and Travers, MA and Toulza, E and Boulo, V and Courtay, G and Petton, B and Koechlin, H and Montagnani, C and Di Cesare, A and Corno, G and Andree, KB and Gairin, I and Furones, D and Broquard, C and Wegner, KM and Destoumieux-Garzón, D and Vezzulli, L},
title = {The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934726},
issn = {2049-2618},
mesh = {Animals ; *Metagenomics/methods ; Europe ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Ostreidae/microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health threat, and the environment is increasingly recognised as a key reservoir of antibiotic resistance genes (ARGs). In marine ecosystems, filter-feeding organisms such as oysters are sentinel species that reflect the microbiological diversity of their environment. Here, we investigated the ARG content of the Pacific oyster Magallana gigas across four European coastal sites, contrasting anthropogenically impacted aquaculture sites (Bay of Brest, Ebro Delta, Thau lagoon) with natural oyster reefs (Sylt island). ARGs sequencing was enriched using a targeted probe-and-capture metagenomic approach employing 37,826 RNA baits covering over 2000 ARG sequences. Moreover, a novel bioinformatic pipeline ARGifier was specifically designed for sensitive, high-resolution detection and classification of ARGs in metagenomic samples dominated by host DNA.

RESULTS: This strategy was able to overcome limitations of cultivation-based methods and whole metagenomic sequencing, enabling the detection of more than 33,000 ARG sequences in the oyster resistome spanning over 450 genes distributed over 23 resistance classes. Reads assigned to ARGs represented 0.23% of all raw reads and 25.02% of host-depleted reads. Accordingly, comparison of targeted metagenomics and pool-seq analysis of cultured isolates (culturomics) in specific pathogen-free oysters revealed that metagenomics captured dominant, community-wide resistance determinants, whereas culturomics recovered a broader diversity of ARGs due to their presence in genomes of cultivable strains. The oyster resistome across the four farming sites was dominated by multidrug efflux systems associated with intrinsic and housekeeping-related mechanisms, suggesting an environmentally shaped resistance profile. Clinically relevant ARGs, including extended-spectrum Beta-Lactamase, carbapenem, colistin, and vancomycin resistance genes, were detected in low abundance at all sites, with higher enrichment in anthropogenically impacted areas. In addition, several ARGs were associated with plasmids, indicating mobilization potential. Taxonomic analysis revealed that a limited subset of bacteria, particularly Betaproteobacteria and Actinomycetes, carried a disproportionately high number of ARGs despite their low relative abundance in the oyster microbiome.

CONCLUSIONS: Overall, this study delivers a comprehensive inventory of ecologically and clinically relevant ARGs in European coastal environments, positioning farmed and wild oysters as sentinel organisms for monitoring antimicrobial resistance in coastal waters. Our findings highlight the circulation of ARGs within coastal marine ecosystems, which may act as reservoirs and potential sources of mobilisable antimicrobial resistance. Video Abstract.},
}

Animals
*Metagenomics/methods
Europe
*Bacteria/genetics/classification/drug effects/isolation & purification
*Ostreidae/microbiology
Metagenome
Anti-Bacterial Agents/pharmacology
Microbiota
Sequence Analysis, DNA

@article {pmid42934727,
year = {2026},
author = {Liu, Y and Wu, X and Guo, Y and Mei, W and Gao, R and Wang, F and Chen, C and Wang, L and Hao, Y and Wu, T and Yao, X},
title = {Multi-omics analysis reveals that sleep deprivation exacerbates intestinal barrier injury via the microbiota-dependent taurodeoxycholic acid/group 3 innate lymphoid/IL-22 axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42934727},
issn = {1479-5876},
support = {82403215//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Sleep Deprivation/microbiology/immunology/pathology ; Interleukin-22 ; *Interleukins/metabolism ; *Multiomics ; *Intestinal Barrier Function ; *Lymphocytes/metabolism ; *Immunity, Innate ; Mice, Inbred C57BL ; Male ; *Intestines/pathology ; Fecal Microbiota Transplantation ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {BACKGROUND: Clinical studies demonstrated a correlation between sleep dysfunction and intestinal diseases. However, the detailed interactions and underlying mechanisms linking sleep disruption to intestinal microenvironment remain poorly understood.

METHODS: We employed the Curling Prevention by Water (CPW) paradigm to establish a mouse model of sleep deprivation (SD) for durations ranging from 0 to 96 h. The dynamic changes in the intestinal microenvironment were systematically profiled using multi-omics approaches, including metagenomic sequencing, untargeted metabolomics and RNA sequencing. The causal role of microbial dysbiosis and the underlying mechanisms were further investigated using germ-free mice, fecal microbiota transplantation (FMT), flow cytometry, and targeted intervention.

RESULTS: The intestinal microenvironment was highly sensitive to SD. Distinct microbial communities and metabolite profiles were observed among brief SD (< 24 h of SD), prolonged SD (24-96 h of SD) and control. Brief SD triggered a self-regulatory response of the gut microbiota, characterized by an increase in certain beneficial bacteria (e.g., Parabacteroides goldsteinii). In contrast, prolonged SD shaped a pro-inflammatory microbial structure, characterized by reduced Akkermansia muciniphila and enriched Pseudomonadota. Multi-omics analysis revealed that SD significantly inhibited microbial bile acid metabolism, particularly taurodeoxycholic acid (TDCA), and impaired intestinal barrier function while suppressing the intestinal immune response to bacteria antigens. Mechanistically, SD exacerbated intestinal barrier damage by inhibiting the TDCA/group 3 innate lymphoid cells (ILC3)/IL-22 axis. Supplementation with TDCA effectively restored ILC3 function, IL-22 production, and barrier integrity in SD mice. Furthermore, FMT from patients with sleep dysfunction significantly disturbed intestinal microenvironment and increased serum cortisol by regulating gut microbiota and inhibiting TDCA/ILC3/IL-22 axis.

CONCLUSION: This study dynamically delineates how SD disrupts intestinal homeostasis by reshaping the gut microbiota and suppressing the TDCA/ILC3/IL-22 axis. These findings provide novel mechanistic insights and identify potential therapeutic targets for sleep dysfunction-associated intestinal complications.},
}

Animals
*Sleep Deprivation/microbiology/immunology/pathology
Interleukin-22
*Interleukins/metabolism
*Multiomics
*Intestinal Barrier Function
*Lymphocytes/metabolism
*Immunity, Innate
Mice, Inbred C57BL
Male
*Intestines/pathology
Fecal Microbiota Transplantation
Mice
*Gastrointestinal Microbiome
*Microbiota

@article {pmid42935434,
year = {2026},
author = {Chen, J and Jiang, YL and Lü, J and Ma, Y and Yang, X and Shen, C and Guo, FL and Yang, ZL},
title = {[Effects of Different Treatment Methods for Printing and Dyeing Sulfate Wastewater on Microbial Structure and Sulfur Cycle Functional Genes].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {10},
pages = {7341-7353},
doi = {10.13227/j.hjkx.202510110},
pmid = {42935434},
issn = {0250-3301},
mesh = {*Wastewater/chemistry ; *Sulfur/metabolism ; *Waste Disposal, Fluid/methods ; *Coloring Agents/isolation & purification ; *Sulfates/isolation & purification/metabolism/chemistry ; Industrial Waste ; Bacteria/genetics/metabolism ; Printing ; Wetlands ; Water Pollutants, Chemical ; },
abstract = {The advantages of Xinjiang raw cotton resources have gradually transformed into manufacturing advantages dominated by textile printing and dyeing， while the high water consumption of the textile printing and dyeing industry conflicts sharply with the water shortage in Xinjiang. The time for comprehensive utilization after the treatment of printing and dyeing wastewater in Xinjiang meets the standards is relatively short， and there is a lack of research support on whether the discharge and utilization will have an impact on the desert ecosystem. This study takes a printing and dyeing wastewater treatment system in an industrial park in Alar City， Xinjiang as the research object and comprehensively analyzes the characteristics and related driving factors of physical and chemical factors of sediment， microbial community， functional structure， sulfur cycle functional genes in drainage outlet （PSK）， constructed wetland （RGSD）， and oxidation pond （YHT）. After the printing and dyeing wastewater was treated by RGSD and YHT， the Na[+]， Cl[-]， SO4[2-]， and electrical conductivity in the water increased significantly. PSK had higher contents of TN， SOC， SO4[2-]， and TDS in sediment， and RGSD had higher contents of Ca[2+]， SO4[2-]， TDS， and TP in sediment， while TN and SOC decreased significantly. YHT had higher contents of Na[+] and Cl[-]， while Ca[2+] and SO4[2-] decreased significantly. The microbial community in sediment was dominated by bacteria， and its α and beta diversity varied significantly among different treatment units， with RGSD having the lowest microbial diversity. Sulfur cycle functional genes analyses showed that assimilatory sulfate reduction was the dominant pathway， dissimilatory sulfate reduction genes were the highest in RGSD， and sulfur oxidation genes were the most abundant at PSK. Structural equation and Mantel analysis indicated that nutrients in sediment promoted microbial diversity and assimilatory sulfate reduction process， while ion concentration had an inhibitory effect on them， and TP， TDS， and SO4[2-] were the key factors driving the variation of microbial community structure. Different ions had different effects on the sulfur metabolic pathway. TN and SOC inhibited dissimilatory sulfate reduction while promoting assimilatory sulfate reduction and sulfur oxidation. Cl[-]， Na[+]， K[+]， and Mg[2+] ions inhibited sulfur oxidation and assimilatory sulfate reduction processes. This study reveals the microbial sulfur metabolism synergy mechanism in different treatment methods of sulfate printing and dyeing wastewater from the perspectives of microbial ecology and functional genes， providing a theoretical basis for the effluent comprehensive utilization of printing and dyeing wastewater treatment and prevention and control of black and odorous water pollution in the Xinjiang Region in the future.},
}

*Wastewater/chemistry
*Sulfur/metabolism
*Waste Disposal, Fluid/methods
*Coloring Agents/isolation & purification
*Sulfates/isolation & purification/metabolism/chemistry
Industrial Waste
Bacteria/genetics/metabolism
Printing
Wetlands
Water Pollutants, Chemical

@article {pmid42935761,
year = {2026},
author = {Whitman, BT and Karimianghadim, R and Auch, B and Liachko, I and , and Monaghan, TM and Pakpour, S and Kao, D},
title = {Metabolic network restoration, not donor microbial engraftment, associates with resolution of recurrent Clostridioides difficile infection.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117907},
pmid = {42935761},
issn = {2589-0042},
abstract = {Fecal microbiota transplantation (FMT) effectively prevents recurrent Clostridioides difficile infection (rCDI). However, the mechanisms underpinning FMT efficacy are incompletely understood. We used proximity-ligation metagenomics, metaproteomics, and metabolomics to profile dynamic changes in rCDI. We analyzed samples collected from the first 7 responders during a clinical trial comparing two donor-based treatments (lyophilized FMT [LFMT] or lyophilized sterile fecal filtrate [LSFF], free of intact microorganisms) to prevent rCDI. LSFF is enriched in Caudoviricetes, lipids, fatty acids, and human and extracellular bacterial proteins compared with LFMT. LFMT recipients had donor microbial engraftment, while LSFF recipients achieved only partial microbial community recovery without donor's contribution. Our multi-omics analyses identified a functional convergence following both treatments, shifting away from oxidative and antibiotic stress survival pathways toward enhanced carbon-nitrogen utilization pathways, suggesting that FMT mechanisms may involve metabolic reprogramming and host-microbial amino acid co-metabolism. Our findings provide important hypothesis-generating insights that warrant further validation.},
}

@article {pmid42935865,
year = {2026},
author = {Abdel Shafi, IR and El Bassiouni, SO and Abdeltawab, MSA},
title = {Living within: endosymbiosis in parasites of medical importance-profits, expenses, and implications for host-parasite interactions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1956183},
pmid = {42935865},
issn = {2235-2988},
mesh = {*Symbiosis ; Humans ; Animals ; *Host-Parasite Interactions ; *Parasites/microbiology/virology/physiology ; Bacteria ; },
abstract = {Endosymbiosis is a biological relationship, where one organism lives within the body of another. The concept of endosymbiosis was first introduced relevant to the origin and development of organelles in eukaryotes. Later, microorganisms were reported to be associated with different eukaryotes including arthropods, parasitic helminths, and protozoa; subsequently, their role in parasite biology and parasite-human host interactions has been minded. Within this context, filaria-Wolbachia, Leishmania-Leishmania RNA virus (LRV), and Trichomonas-Trichomonas vaginalis virus (TVV) are extensively studied models that demonstrate how endosymbionts can directly drive immunomodulation in human host and worsen the clinical outcome, whereas Acanthamoeba stands out as a reservoir of an array of microorganisms including pathogenic bacteria, and a training hub for bacterial virulence evolution. Despite the progress achieved in understanding these models, the depth of characterization of endosymbionts across parasite taxa is markedly uneven. Disclosing the world of microorganisms living within parasites, especially with the advanced metagenomic analysis, constitutes an emerging field of research of immense scientific significance for parasitology, microbiology, and host-parasite interactions.},
}

*Symbiosis
Humans
Animals
*Host-Parasite Interactions
*Parasites/microbiology/virology/physiology
Bacteria

@article {pmid42936323,
year = {2026},
author = {Li, Y and Fan, M and Hu, Y and Yang, Y and Li, W and Zhang, W and Wang, Y},
title = {Cerebrospinal fluid metagenomic next-generation sequencing for culture-negative anaerobic central nervous system infection involving Prevotella oris: attribution challenges in low-biomass specimens.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896093},
pmid = {42936323},
issn = {1664-3224},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Prevotella/genetics/isolation & purification ; *Bacteroidaceae Infections/diagnosis/cerebrospinal fluid/microbiology ; DNA, Bacterial/genetics ; },
abstract = {Anaerobic central nervous system (CNS) infections are uncommon but diagnostically difficult because fastidious organisms may be suppressed by empirical antimicrobial therapy and conventional cultures may remain negative. Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) can recover microbial nucleic acids in this setting, but low microbial biomass creates a central attribution problem: a detected organism may represent active infection, introduced commensal DNA, laboratory background, or bioinformatic misclassification. This narrative Mini Review uses Prevotella oris as a representative oral anaerobe to examine that problem. We synthesize evidence on low-biomass CSF specimen processing and sequencing strategies, including nanopore sequencing, whole-genome amplification, and targeted approaches, alongside contamination control, sequence-level and taxonomic credibility, host-response immunology, neuroimaging and source concordance, antimicrobial timing, and discordant clinical scenarios. We then organize these established principles into an expert-informed two-step pathway that separates technical signal credibility from clinical attribution and explicitly preserves an indeterminate state when evidence conflicts. P. oris is positioned as a useful model of the plausible contaminant paradox rather than as a pathogen with a unique CNS phenotype. We also outline syndrome-based management, source control, and treatment-duration principles. The framework is conceptual and non-validated; its purpose is transparent reasoning and reporting, not diagnostic scoring or probability estimation.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Prevotella/genetics/isolation & purification
*Bacteroidaceae Infections/diagnosis/cerebrospinal fluid/microbiology
DNA, Bacterial/genetics

@article {pmid42937190,
year = {2026},
author = {Quinger, F and Klein, N and Steinhoff-Wagner, J and Camarinha-Silva, A and Rodehutscord, M and Seifert, J},
title = {Field Pea Variants affect Nutrient Digestibility and Gut Microbiome in Pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag346},
pmid = {42937190},
issn = {1525-3163},
abstract = {The digestibility of nutrients in different field pea variants in pigs can vary due to characteristics such as anti-nutritional factors. Undigested nutrients can be fermented in the hindgut, and their amount and composition likely affect microbial composition. This study compared a spring field pea variant (SP) with two winter field pea variants (WP1, WP2) with higher trypsin inhibitor activity and a tannic spring forage pea variant (SFP) in terms of nutrient digestibility and effects on the gut microbiome in growing pigs. Four diets containing 40% of one of the four field pea variants were formulated and randomly assigned to 8 ileally cannulated barrows according to a 4 × 4 double Latin square design with the blocking factors animal and period. The experiment consisted of 4 periods, each lasting 11 days. Ileal digesta and feces were collected for 2 days each to determine nutrient digestibility. On the last day of every period, ileal digesta and feces were sampled and analyzed for digestive enzyme activity, metagenomics, metaproteomics, and metabolomics. The data was integrated using DIABLO. The winter field pea variants decreased the prececal digestibility of 16 amino acids (P ≤ 0.032) and increased the activity of carboxypeptidase A (P = 0.002). Pigs fed the SFP showed decreased hindgut disappearance of total dietary fiber (P < 0.001) and concentrations of acetate, propionate, and butyrate in the feces (P ≤ 0.026). More differentially abundant taxa in metagenomic and metaproteomic data were detected in the feces than in ileal digesta among field pea variants. The SFP increased the abundance of host proteins related to innate immune response in ileal digesta and feces (adjusted P ≤ 0.047). Integration of the acquired data layers revealed a negative association of ileal amino acid concentrations with the abundance of Prevotella and proteins related to starch degradation and propionate production in the ileal digesta for winter field pea variants. For SFP, reduced hindgut disappearance of total dietary fiber was associated with a reduction of proteins from Ruminococcus. In conclusion, field pea variants can affect the ileal and fecal microbiome in pigs, potentially due to anti-nutritional factors that either indirectly influence the microbiome by reducing nutrient digestibility or directly affect individual microbial taxa.},
}

@article {pmid42937301,
year = {2026},
author = {Moyo-Heath, B and Chigome, G and Mushamba, R and Onyeaghala, C and Bailey, SF},
title = {Metagenome sequences of unintended bacterial communities from a Pseudomonas fluorescens experimental evolution study.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085326},
doi = {10.1128/mra.00853-26},
pmid = {42937301},
issn = {2576-098X},
abstract = {We report 16 metagenome sequences from unintended contaminant communities that invaded an evolution experiment initiated with Pseudomonas fluorescens SBW25. Low-diversity bacterial assemblies from center and edge locations across eight populations in contrasting uniform or heterogeneous glucose agar plate environments feature four primary genera: Pseudomonas, Chryseobacterium, Delftia, and Moraxella.},
}

@article {pmid42937321,
year = {2026},
author = {Yagupsky, P},
title = {Diagnosing pediatric skeletal system infections: you are as good as your lab.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0050826},
doi = {10.1128/jcm.00508-26},
pmid = {42937321},
issn = {1098-660X},
abstract = {Pediatric skeletal system infections are medical emergencies that may cause severe acute complications and long-term orthopedic disabilities. Because the clinical presentation of septic arthritis and osteomyelitis may mimic non-infectious conditions, early identification of the causative agent and determination of its antibiotic susceptibility profile are cornerstones of patient management. The etiology of childhood skeletal system infections has changed over time, reflecting the implementation of conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae, as well as the development of sensitive molecular detection tests. These novel laboratory methods, coupled with rapid pathogen identification by MALDI-TOF technology, have reduced the fraction of "culture-negative" infections and shortened the turnaround time for pathogen identification from days to hours. However, even today, a substantial fraction of bone and joint infections remains microbiologically unconfirmed. Metagenomic next-generation sequencing holds great promise, but its high cost, the need for technical expertise, and the detection of commensal organisms of dubious significance severely limit its routine use. On the other hand, metagenomic next-generation sequencing has not expanded the list of known pediatric skeletal system pathogens, suggesting that underutilization of current diagnostic methodologies, rather than reduced sensitivity, drives suboptimal diagnosis.},
}

@article {pmid42937368,
year = {2026},
author = {Mishra, S and Mutnuri, S},
title = {Metagenomic and thermodynamic mapping of Ny-Ålesund, Arctic microbiota: harnessing low temperature biohydrogen production.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145126},
doi = {10.1128/spectrum.01451-26},
pmid = {42937368},
issn = {2165-0497},
abstract = {Biohydrogen produced by psychrophilic dark fermentation has lower energy requirements than conventional methods. In this study, kinetic, thermodynamic, and functional metagenomic analyses were conducted to determine the profiles of microbial consortia from Ny-Ålesund, Svalbard, incubated at 4°C and 20°C in the presence or absence of the methanogenic inhibitor 2-bromoethanesulfonate. Biogas potential values derived from volumetric analyses indicated that pure biohydrogen (>95.6%) was produced, while also confirming the presence of these consortia adapted to operate with lag phases of 4-7 days and exhibiting temperature sensitivity coefficients (Q10) <2.0 at 4°C. While thermodynamic analysis indicated that methanogenic inhibition theoretically disrupted syntrophic electron transfer and yielded a higher activation energy, both anaerobically fermentative acetic and butyric acid pathways remained exergonic. Community succession was observed in functional metagenomic analyses, marked by the enrichment of fermentative genera (Clostridium, Enterobacter, and Klebsiella) harboring the genetic potential for the pyruvate:ferredoxin oxidoreductase (PFOR) and formate hydrogenlyase (FHL) pathways. Metagenomic enrichment for the genes encoding cold-shock defense (cspA, dnaK) and putative electron-bifurcating complexes (rnf, ech) highlights the combined genetic potential to sustain viability and overcome thermodynamic limits at all incubation temperatures. Overall, the biochemical characteristics of native Arctic consortia provide evidence of their potential to serve as viable biocatalysts for biohydrogen production, currently under laboratory batch conditions at low temperatures.IMPORTANCEBiohydrogen production is a potentially sustainable energy source that offers new options for generating carbon-neutral renewable energy. Traditionally, biohydrogen production methods require substantial, continuous heating energy input. This publication describes the examination of the "underutilized" biohydrogen production potential of microbial communities in the Arctic region (Ny-Ålesund, Svalbard) that have separately evolved genetic adaptations necessary to maintain metabolic functions at sub-zero temperatures. Psychrophilic dark-fermentation experiments, combined with thermodynamic modeling and metagenomic analyses, show how unique cold-adapted microorganisms can produce high-purity biohydrogen gas at extreme ambient temperatures under laboratory batch conditions, highlighting a fundamental baseline that could inform future efforts to reduce the energy footprint of biofuel production. While long-term reactor stability and scalability remain to be validated, this work bridges the divide between observational Arctic microbiology and foundational green energy research, demonstrating that the discovery of extreme microbial environments holds promise for developing low-energy biological processes.},
}

@article {pmid42937679,
year = {2026},
author = {Ran, J and Qiu, G and Jin, J and Zhang, P and Hu, H and Liu, Y and Liu, X and Li, C and Xi, Y},
title = {Clinicopathologic Features of Stress-Associated Sudden Death in Three Captive Crested Ibis (Nipponia nippon).},
journal = {Avian diseases},
volume = {70},
number = {3},
pages = {349-358},
doi = {10.1637/aviandiseases-D-26-00005},
pmid = {42937679},
issn = {1938-4351},
mesh = {Animals ; *Death, Sudden/veterinary/etiology ; *Stress, Physiological ; *Birds ; *Bird Diseases/pathology/etiology ; Female ; Male ; Endangered Species ; Animals, Zoo ; Corticosterone/analysis ; },
abstract = {The endangered crested ibis (Nipponia nippon), once reduced to just seven individuals in the wild worldwide in 1981, has rebounded to more than 10,000 through intensive conservation. Yet the species remains highly vulnerable to acute environmental disturbance, with stress-induced sudden death (SISD) posing persistent challenges for captive management and reintroduction programs. We investigated three SISD cases, integrating behavioral context with necropsy and histopathology in all cases, and computed tomography/magnetic resonance imaging neuroimaging and metagenomic pathogen screening in a subset. Major organs showed no diagnostic lesions, with only mild, nonspecific digestive tract changes. Neuroimaging identified localized subdural hemorrhage without diffuse parenchymal damage. Metagenomic screening detected no high-pathogenicity avian viruses, fungi, or parasites and only trace environmental bacteria. Using published datasets, we also compared baseline corticosterone (CORT) from feathers and blood across five avian species; crested ibis occupied the lower end of baseline CORT distributions, consistent with reduced endocrine buffering capacity. These observations suggest that peracute death may occur in association with acute disturbance even in the absence of overt infectious or major degenerative lesions, with panic flight and collision trauma likely contributing to the terminal events. Framing SISD as a failure of physiological tolerance thresholds highlights actionable management: minimizing startle stimuli, reducing predator cues and human disturbance during sensitive periods, carefully staging transfers to new enclosures, managing group dynamics to limit social transmission of stress, designing for safe flight, and early-warning monitoring. Taken as case-based evidence, this work may help refine captive husbandry and reintroduction protocols aimed at improving survival and long-term population resilience.},
}

Animals
*Death, Sudden/veterinary/etiology
*Stress, Physiological
*Birds
*Bird Diseases/pathology/etiology
Female
Male
Endangered Species
Animals, Zoo
Corticosterone/analysis

@article {pmid42937876,
year = {2026},
author = {Hioki, Y and Klapper, M and Ibrahim, A and Hübner, A and Steinacker, M and Willing, K and Nachawati, R and Hildebrandt, D and Reimer, L and Zimmermann, A and Mantke, J and Sato, M and Warinner, C and Stallforth, P},
title = {Reconstruction of a 30,000-Year-Old Biosynthetic Gene Cluster Reveals Lasso Peptides Formed by a Highly Tolerant Cyclase.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {38},
pages = {40629-40635},
pmid = {42937876},
issn = {1520-5126},
support = {NA//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; JP24KJ1884//Japan Society for the Promotion of Science/ ; NA//Astellas Foundation for Research on Metabolic Disorders/ ; },
mesh = {*Multigene Family ; *Peptides/chemistry/genetics/metabolism ; Humans ; *Actinomyces/genetics/enzymology ; Amino Acid Sequence ; Phylogeny ; },
abstract = {Microbial metagenomes preserved in prehistoric dental calculus samples provide access to past bacterial biodiversity and evolutionary dynamics across archeological time scales. Consequently, this sequence space represents a largely unexplored resource for natural product discovery. Phylogeny-guided genome mining of human dental calculus metagenomes spanning recent times to the Middle and Upper Paleolithic revealed a distinct lasso cyclase lineage associated with oral Actinomyces species. Heterologous expression of a biosynthetic gene cluster reconstructed from an approximately 30,000-year-old sample yielded two lasso peptides, palassoptides A1 and A2. Structure analyses established a canonical class II lasso topology with an eight-residue macrolactam ring. Notably, both palassoptides feature an unprecedented amino acid composition for lasso peptides. Mutational analysis of the PalA2 precursor further showed that PalC accepts all possible substitutions at core position 1 except for Pro, revealing the broadest respective tolerance reported for a lasso cyclase to date. Homologous gene clusters with highly conserved yet variable precursor sequences are widespread among modern oral Actinomyces, indicating long-term preservation of this biosynthetic lineage within the human oral microbiome. The two palassoptides exhibited combination-dependent antibacterial activity against selected Gram-positive bacteria. These findings demonstrate that ancient metagenomes can reveal chemically uncharacterized natural products and expand the known structural diversity of natural products.},
}

*Multigene Family
*Peptides/chemistry/genetics/metabolism
Humans
*Actinomyces/genetics/enzymology
Amino Acid Sequence
Phylogeny

@article {pmid42938079,
year = {2026},
author = {Pallasdies, L and Barber, H and Lee, M and Burchill, L and Ho, HNN and Stewart, AWE and Nastasovici, A and Sanne-Wander, H and Rathnayake, DT and Hofferek, V and Jebeli, L and McDaniels, TA and McConville, MJ and Field, RA and Pidot, S and Scott, NE and Jin, Y and Williams, SJ},
title = {A Bacterial Pathway for Homotaurine Catabolism via Sulfopropanoate.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {37},
pages = {39900-39910},
doi = {10.1021/jacs.6c10662},
pmid = {42938079},
issn = {1520-5126},
support = {NA//Australian Government/ ; 218568/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MX31850//Diamond Light Source/ ; NA//Australian Government/ ; 218568/Z/19/Z//Royal Society/ ; NA//University of Manchester/ ; DP210100362//Department of Education and Training/ ; DP230102668//Department of Education and Training/ ; DP240100126//Department of Education and Training/ ; FT200100270//Department of Education and Training/ ; GNT2018980//Australian Government/ ; GNT2021638//Australian Government/ ; NA//Australian Academy of Science/ ; NA//University of Melbourne/ ; },
mesh = {*Taurine/metabolism/analogs & derivatives/chemistry ; Models, Molecular ; },
abstract = {Small aminoorganosulfonates are reservoirs of carbon, nitrogen, and sulfur in marine and host-associated ecosystems. Homotaurine, a C3-aminoorganosulfonate produced by marine algae and present in algal-derived foods, is comparatively well documented, but its complete microbial catabolism has remained unresolved. Here we identify a complete bacterial pathway for homotaurine catabolism in Caballeronia jiangsuensis strain McCoy, isolated by metabolic enrichment from soil by growth on homotaurine. Growth, proteomic, metabolomic, biochemical, structural, and heterologous-expression analyses show that homotaurine is imported and oxidatively deaminated to sulfopropanoate, then converted to sulfolactate through E-sulfoacrylate by SpuABCD and SpuIJ, enzymes related to succinate dehydrogenase and fumarase. Sulfolactate is cleaved by redundant SuyAB sulfolyases to release pyruvate and sulfite, which is oxidized and excreted as sulfate, completing biomineralization. Crystal structures of the HtaA homotaurine-binding protein and SuyAB2 sulfolyase reveal ligand recognition and provide a structural framework for sulfolactate cleavage. Hidden Markov model searches and Tara Oceans and human gut metagenomes show that the core sulfopropanoate-to-sulfolactate module is widespread in marine Proteobacteria, especially Roseobacter-lineage bacteria, and occurs more narrowly in human gut-associated sulfur-metabolizing taxa such as Bilophila wadsworthia. This pathway connects algal, dietary, and xenobiotic C3-aminoorganosulfonates to microbial carbon, nitrogen, and sulfur cycling, and identifies sulfopropanoate turnover as a conserved module in organosulfonate metabolism.},
}

*Taurine/metabolism/analogs & derivatives/chemistry
Models, Molecular

@article {pmid42938125,
year = {2026},
author = {Andonov, V and Velchov, V and Nikolov, Y and Cherkezov, N and Tenev, D and Dimitrov, M and Tsenkov, T and Dimitrov, N},
title = {From Measured Accuracy to Patient Outcome: Navigation in Total Hip Arthroplasty and Molecular Diagnosis of Periprosthetic Joint Infection: A Narrative Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938125},
issn = {2075-4418},
abstract = {Background: Total hip arthroplasty (THA) and the diagnosis of periprosthetic joint infection (PJI) have each acquired a technology that measures with high precision: intraoperative navigation, which reports component position to within a few degrees, and molecular methods, which identify the infecting organism and the host response at genomic resolution. Objective: To establish whether the measured accuracy has been shown to reach the patient as a clinical outcome. Methods: This is a narrative review, reported according to SANRA. MEDLINE, Scopus, and Web of Science databases were searched from inception to 31 August 2026. English-language studies in humans were eligible if they reported positional or diagnostic accuracy, a patient-level clinical or economic outcome after THA or after treatment of PJI or osteomyelitis, or a factor modifying the relation between the two. Animal, in vitro, and cadaveric studies, conference abstracts, and reports without extractable data were excluded. Forty studies were included. No pooled estimate was calculated, and no new statistical analysis was performed. Results: Navigation reduced positional outliers consistently, but in two matched claims-based cohorts of patients with morbid obesity (4499 and 5835 patients), it was not associated with lower rates of PJI, dislocation, periprosthetic fracture, mechanical loosening, or revision within two years. Candidate immunogenetic variants in osteomyelitis have never been tested against a treatment decision. Metagenomic sequencing was no more accurate than culture (sensitivity 63.2% versus 68.4%; specificity 80.0% versus 95.0%) except after antibiotic exposure. Reported infection rates and test accuracy both change with the case definition applied. Conclusions: In both settings, the limiting factor is the design of the studies linking measurement to outcome rather than the precision of the measurement.},
}

@article {pmid42938214,
year = {2026},
author = {Bratosin, F and Branea, HS and Hogea, E},
title = {Plasma and Serum Metagenomic Sequencing of Microbial Cell-Free Nucleic Acids for Suspected Central Nervous System Infection: A Systematic Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938214},
issn = {2075-4418},
abstract = {Background/Objectives: Untargeted metagenomic sequencing of microbial cell-free DNA or RNA in plasma or serum offers pathogen detection without lumbar puncture or biopsy, but its value in suspected central nervous system (CNS) infection is uncertain. We reviewed diagnostic yield, agreement with CNS-site testing, clinical impact, and failure modes. Methods: PubMed/MEDLINE was searched with seven documented strings (inception to 2 September 2026), supplemented by citation and web searching. Eligible reports were primary human studies of untargeted plasma or serum metagenomic sequencing with a separable result in patients with suspected or confirmed infectious CNS syndromes. Selection, extraction, and design-specific risk-of-bias appraisal followed PRISMA 2020 and were performed independently by two authors with disagreements resolved by discussion; the search was restricted to PubMed/MEDLINE and no protocol was registered. Synthesis was narrative because designs and reference standards were incompatible. Results: Of 190 reports assessed, 69 studies were included (18 denominator-based cohorts, 8 small series, 43 case reports; 51 from the United States). Positive CNS-specific clinical impact in commercial assay cohorts ranged from 0 of 24 adult to 5 of 24 pediatric meningoencephalitis tests. Among 51 case-level reports, the plasma or serum result was concordant with CNS-site testing in 28, positive when CNS-site testing was negative in 5, unconfirmed in 12, and negative or missed the pathogen in 6. All five plasma-only detections came from single case reports, which contributed to no yield or agreement denominator; excluding the four abstract-level case reports moved no proportion by more than 1.3 percentage points. RNA viruses, low-burden focal mould disease, and chromosomally integrated HHV-6 were recurrent sources of false-negative or misleading results. Conclusions: Plasma or serum metagenomic sequencing is a useful adjunct in selected difficult CNS infections, particularly disseminated, fungal, amoebic, or fastidious bacterial disease, but it does not replace CNS-site diagnostics.},
}

@article {pmid42938241,
year = {2026},
author = {Zhang, B and Zhang, Y and Wu, Y and Gao, Y and Li, X and Wu, H and Li, Y and Song, N},
title = {Application Value and Cognitive Challenges of PET/CT in the Diagnosis and Treatment of Visceral Leishmaniasis: A Retrospective Single-Center Case Series and Literature Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938241},
issn = {2075-4418},
abstract = {Background and Clinical Significance: The role of [18]F-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) in visceral leishmaniasis (VL) remains undefined. We sought to characterize the PET/CT features of VL and assess its diagnostic and therapeutic value. Case Presentation: Four VL patients undergoing PET/CT at our hospital (2022-2025) were retrospectively analyzed as a single-center case series, combined with a literature review of published VL PET/CT cases up to December 2025. Three of the four cases exhibited increased [18]F-fluorodeoxyglucose ([18]F-FDG) uptake in the spleen, bone marrow, and lymph nodes, with additional tonsillar uptake in one case and hepatic uptake in another; one case presented with isolated lymph node uptake. In three cases, initial bone marrow smears were negative for amastigotes, and PET/CT was performed for fever of unknown origin (FUO). One case was diagnosed within one week via metagenomic next-generation sequencing (mNGS) prompted by PET/CT and epidemiological history. In the other two, VL was not suspected; they received chemotherapy/corticosteroids for presumed hemophagocytic syndrome (HPS) or connective tissue disease, and the time from symptom onset to VL diagnosis ranged from 2.5 to 4.5 months. The fourth case, confirmed by bone marrow smear, underwent PET/CT for suboptimal treatment response to exclude other diseases. Among 99 published VL cases undergoing PET/CT, indications were documented in 35, with FUO representing 83%. Initial bone marrow smears were negative in 69% of 64 evaluable cases. Of the 88 cases with evaluable PET/CT findings, 5 showed no abnormal FDG uptake. The predominant pattern was increased [18]F-FDG uptake in the reticuloendothelial system (RES), most frequently involving the spleen (73/88, 83%), bone marrow (44/88, 50%), lymph nodes (29/88, 33%), and liver (15/88, 17%); other sites (lungs/pleura, colon, tonsils) were rarely involved. Accompanying enlargement of the spleen or liver was seen in approximately 50% of cases. The most common involvement patterns were combined splenic and bone marrow (23/88, 26%) and isolated splenic (20/88, 23%). Conclusions: PET/CT can provide diagnostic clues for VL, screen for comorbidities, and guide biopsy. Typical PET/CT findings-increased RES uptake without significant other organ involvement-reflect the parasite's RES tropism. However, these findings mimic lymphoma, HPS, hematological disorders, and connective tissue diseases, risking misdiagnosis. Thus, VL should be promptly excluded in such patients using epidemiological history and etiological testing before considering alternative diagnoses.},
}

@article {pmid42938719,
year = {2026},
author = {Schroeder, TH and Eliwi Alsaffan, M and Bondarenko, A and Dervishi, A},
title = {Integrating Plasma mNGS into ICU Antimicrobial Stewardship: A Four-Phase Framework.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938719},
issn = {2079-6382},
abstract = {Background: Plasma metagenomic next-generation sequencing (mNGS) may complement conventional microbiology in critically ill patients, yet its contribution to antimicrobial stewardship in the intensive care unit (ICU) remains unclear. Methods: In this retrospective, single-center observational study, we analyzed 243 paired mNGS-blood culture episodes from 180 ICU patients. We applied a four-phase stewardship framework that integrated clinical severity, biomarker kinetics, blood culture results, mNGS findings, and clinical assessment. Treatment adaptations were classified as escalation, de-escalation, discontinuation, or no change. Multivariable regression identified factors associated with stewardship modification and mortality. Results: Active treatment adaptation occurred in 121 of 243 episodes (49.8%), comprising 61 escalations, 39 de-escalations, and 21 discontinuations. mNGS positivity was independently associated with treatment modification (OR 2.66, 95% CI 1.23-5.75; p = 0.014), whereas blood culture positivity showed an inverse association (OR 0.45, 95% CI 0.20-1.04; p = 0.062). Mortality was primarily linked to physiologic severity and host-response markers, particularly SAPS II and procalcitonin. In-hospital survival did not differ between patients who received stewardship-guided adaptation and those in whom empirical antibiotic therapy was maintained (HR 1.02, 95% CI 0.57-1.81; log-rank p = 0.951). Conclusions: Microbiological findings, particularly mNGS, were associated with antimicrobial treatment adaptation but not independently with mortality. Because mNGS was embedded within a multimodal diagnostic and clinical pathway, its independent contribution cannot be fully separated from concurrent microbiological, biomarker, and clinical information. These findings should be regarded as exploratory and require prospective multicenter validation.},
}

@article {pmid42938727,
year = {2026},
author = {Vulpie, S and Ceachir, P and Craciun, AM and Varan, I and Magiar, O and Dugăeșescu, D and Muntean, D and Licker, M},
title = {Carbapenemases in Gram-Negative Bacilli: Classification, Detection, Therapeutic Options, and Resistance to Novel Antimicrobials.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938727},
issn = {2079-6382},
abstract = {Carbapenem-resistant Gram-negative bacilli (CR-GNB), particularly Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii, remain a major clinical challenge and serious threat to modern medicine, with carbapenemase production representing a particular clinical and epidemiological concern. This structured narrative review integrates three clinically linked areas: the evolution and classification of clinically important carbapenemases; phenotypic and molecular methods for their detection and characterization; and the organism- and enzyme-specific activity of recently introduced antimicrobial agents and β-lactam-β-lactamase inhibitor combinations, including ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, imipenem-cilastatin-relebactam, cefiderocol, plazomicin, eravacycline, cefepime-enmetazobactam, sulbactam-durlobactam (FDA 2023), aztreonam-avibactam (EMA 2024; FDA 2025), and cefepime-zidebactam (FDA 2026). Particular emphasis is placed on baseline, experimentally selected and treatment-emergent resistance mechanisms and their clinical implications. Although these agents have substantially expanded the therapeutic armamentarium against CR-GNB, important gaps persist, particularly for metallo-β-lactamase-producing organisms, carbapenem-resistant A. baumannii, and metallo-β-lactamase-producing P. aeruginosa. Their activity may be compromised by pre-existing resistance determinants, target alterations, permeability defects, efflux-pump overexpression, β-lactamase evolution or overproduction, and combinations of these mechanisms, while treatment-emergent resistance threatens long-term effectiveness. By linking laboratory carbapenemase detection with a comparative, mechanism-based assessment of antimicrobial activity, resistance determinants, and clinical limitations, this review provides a practical framework for mechanism-directed therapy and antimicrobial stewardship and identifies priorities for future research, including improved direct inhibition of metallo-β-lactamases, more reliable therapeutic options for CR-GNB, prospective studies stratified by resistance mechanisms, strengthened epidemiological surveillance and infection-prevention strategies, and continued therapeutic innovation.},
}

@article {pmid42938781,
year = {2026},
author = {Shuvo, MSH and Ju-Young, W and Jo, S and Ahmed, I and Aziz, MT and Atashi, A and Raihan, MA and Yeji, P and Hyunhee, C and Kim, T and Yu, H and Bae, H and Kim, S and Seo, H and Song, HY},
title = {Hospital Drain Microbiomes as Distinct Microbial Signatures Within Urban Wastewater Networks in the Han River Watershed.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938781},
issn = {2079-6382},
support = {RS-2023-00219563//Ministry of Science and ICT/ ; P0027492//Korea Institute for Advancement of Technology/ ; NA//Korea Bio Associations/ ; NA//Soonchunhyang University/ ; },
abstract = {Background: Hospital drainage systems represent an important interface between healthcare facilities and urban wastewater networks and may contribute distinct microbial inputs to downstream aquatic environments. This issue is particularly relevant in Seoul, Republic of Korea, where urban wastewater discharges into receiving waters within the Han River watershed. Methods: In this study, we characterized hospital drain microbiomes to evaluate their microbial and environmental signatures, using residential drains as a non-clinical comparison. Results: Hospital drains exhibited a distinct taxonomic profile, with greater relative abundances of Bacteroidota and Firmicutes and several genera of environmental or potential public health relevance, including Mycobacterium, Legionella, and Pseudomonas. Although microbial richness was comparable between the two environments, Simpson diversity was significantly lower in hospital drains, indicating reduced community evenness. Bray-Curtis and Jaccard analyses showed clear separation between hospital and residential microbial communities, and hierarchical clustering further supported environment-associated community structuring. LEfSe analysis identified distinct hospital-associated taxonomic biomarkers, and predicted functional profiling revealed substantial metabolic differentiation, with 19 of the 25 most significantly differentiated pathways enriched in hospital samples. Conclusions: These microbial and functional differences underscore the ecological uniqueness of hospital drains and support their inclusion in future wastewater-based microbial surveillance strategies. Collectively, these findings establish hospital drains as distinct microbial ecosystems within urban wastewater networks and provide a baseline for future studies examining the persistence of hospital-associated microbial signatures within the Han River watershed.},
}

@article {pmid42939021,
year = {2026},
author = {Vieira, MS and Dias, RS and Lima, HS and Sousa, MP and Silva, CCD and Paula, SO},
title = {Influence of a Bacteriophage Cocktail as a Biocontrol Strategy on Sulfate-Reducing Bacteria in a Pilot-Scale System.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {42939021},
issn = {2306-5354},
support = {00000//Petrobras (Brazil)/ ; 00000//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 0000//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Sulfate-reducing bacteria (SRB) play crucial roles in microbiologically induced corrosion (MIC), especially in anaerobic environments where the production of hydrogen sulfide (H2S) and biofilm formation accelerate metal degradation. Conventional treatments, such as THPS-based biocides, while effective, face limitations relating to the development of resistance and poor biofilm penetration. In this study, we evaluated the use of a non-specific bacteriophage cocktail as a biological control strategy against a mixed SRB culture (AP) biofilm and related corrosion, utilizing a pilot-scale system with AISI 1020 carbon steel coupons. Over 38 days, we monitored H2S production, optical density, and ATP concentrations, along with the surface characterization of steel coupons through scanning electron microscopy (SEM) and profilometry. Metagenomic sequencing revealed changes in microbial community composition, including reductions in sulfate consumers and shifts in dominant taxa. SEM and profilometric analyses showed disrupted and less aggressive biofilms on treated surfaces, often exhibiting filamentous structures. Diversity indices indicated the modulation of microbial richness and composition over time. These findings demonstrate the potential of bacteriophage cocktails to reshape complex microbial communities and reduce MIC, providing a sustainable alternative to chemical biocides in large-scale industrial settings.},
}

@article {pmid42939184,
year = {2026},
author = {Ho, ST and Chen, MJ},
title = {From Microbiome Associations to Deployable Precision Probiotics in Animals: A Critical Narrative Review and Proposed Causal Evidence Framework for Next-Generation Probiotic Development.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939184},
issn = {2076-2615},
support = {NSTC 115-2313-B-002-006-MY3//National Science and Technology Council/ ; },
abstract = {Next-generation probiotics (NGPs) are promoted as precision tools for animal health, yet the term is often applied to uncommon taxa before causality, safety and target-species efficacy are established. This critical narrative review reframes animal NGPs as a development pathway rather than a taxonomic category. A structured PubMed search was last run on 14 September 2026 with a publication date cutoff of 1 September 2026 and was supplemented by citation tracing and targeted searches of authoritative sources. From the screened literature, 45 representative and conceptually informative sources were purposively selected for the final narrative synthesis; the review was not intended to provide systematic or exhaustive coverage. The detailed synthesis focused on terrestrial farm and companion animals, whereas equine, rabbit and aquaculture studies were treated as boundary evidence. We evaluate how strain-resolved metagenomics, culturomics, metatranscriptomics, metaproteomics, metabolomics, host transcriptomics, machine learning, metabolic modeling and perturbation systems can move discovery beyond association. Studies across animal sectors show many biomarkers but limited causal validation, strain tracking, formulation data, multisite trials and ecological safety assessment. We propose an author-developed conceptual framework comprising a cumulative evidence ladder, from reproducible associations to field-ready deployment, and the ANIMAL-NGP reporting checklist (Animal endotype, Native ecological fit, Identity and genomic safety, Mechanism, Administration and manufacturing, and Longitudinal validation). These tools are intended to align claims with evidence and require prospective application and external validation. Multi-omics should therefore function as an evidence-navigation system, not as a substitute for causality.},
}

@article {pmid42939670,
year = {2026},
author = {Dawson, ZD and Martin, T and Ji, E and Lee, KE and Chen, X and Zhou, X and St Jean, S and Li, Y and Ma, J},
title = {PAD2 Deficiency Reveals Sex-Divergent Colonic Homeostasis, β-Catenin Remodeling, and Antibiotic-Sensitive Phenotypes.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939670},
issn = {2218-273X},
support = {R01AG071676/AG/NIA NIH HHS/United States ; R01AG072430/AG/NIA NIH HHS/United States ; R01EY036243/EY/NEI NIH HHS/United States ; R01HL157215//National Heart Lung and Blood Institute/ ; },
mesh = {Animals ; *beta Catenin/metabolism ; Female ; Male ; Mice ; Colitis/chemically induced/metabolism/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; Homeostasis/drug effects ; *Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism ; Mice, Knockout ; *Colon/metabolism/pathology/drug effects ; Phenotype ; Intestinal Mucosa/metabolism ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Peptidylarginine deiminase 2 (PAD2) catalyzes protein citrullination and is implicated in inflammatory bowel disease and colorectal cancer. However, its role in regulating the intestinal epithelium and the influence of biological sex and the microbiome remain poorly defined. This study investigated the relationships among PAD2 deficiency, sex-divergent epithelial states, β-catenin regulation, and the intestinal microbiome. Global PAD2 knockout and wild-type littermate mice of both sexes were characterized under basal conditions and following dextran sodium sulfate-induced colitis. Intestinal epithelial phenotypes were assessed by histology, immunofluorescence, immunoblotting, quantitative RT-PCR, and immunoprecipitation. Gut microbial communities were evaluated by shotgun metagenomics, while broad-spectrum antibiotic treatment, fecal protein immunoblotting, and recombinant human PAD2 exposure in vitro were used to examine relationships among antibiotic-sensitive factors, β-catenin regulation, and epithelial phenotypes. PAD2 deficiency was associated with distinct epithelial states in male and female colons before injury. Male KO mice displayed increased β-catenin phosphorylation and increased susceptibility to DSS colitis, whereas female KO mice demonstrated increased total β-catenin abundance and preservation of structural epithelial features following injury. Female KO microbiota exhibited genotype-associated differences in microbial community composition by exploratory Bray-Curtis PERMANOVA. Broad-spectrum antibiotic treatment altered the female epithelial phenotype, reduced active β-catenin, and progressively depleted luminal PAD2-immunoreactive proteins. Exogenous recombinant human PAD2 increased epithelial protein citrullination and altered active β-catenin abundance in HT29 cells. Collectively, these findings demonstrate both sex-specific and sex-divergent colonic phenotypes while supporting a framework connecting PAD2 biology, epithelial architecture, and the microbial environment during intestinal maintenance and injury.},
}

Animals
*beta Catenin/metabolism
Female
Male
Mice
Colitis/chemically induced/metabolism/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
Homeostasis/drug effects
*Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism
Mice, Knockout
*Colon/metabolism/pathology/drug effects
Phenotype
Intestinal Mucosa/metabolism
Dextran Sulfate
Gastrointestinal Microbiome/drug effects

@article {pmid42939710,
year = {2026},
author = {Ascari, F and Baldelli, L and Scicchitano, D and Pellegrini, C and Ravaioli, F and De Fanti, S and Esposito, E and Porru, E and Di Laudo, F and Lodi, R and Bacalini, MG and Candela, M and Provini, F and Fiori, J and Interino, N},
title = {Exploratory Metabolomic and Metagenomic Profiling of Fecal Samples in Isolated REM Sleep Behavior Disorder.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939710},
issn = {2218-273X},
support = {//Ministero della Salute/ ; 2024.0058//Fondazione Del monte di Bologna e di Ravenna/ ; },
mesh = {Humans ; *REM Sleep Behavior Disorder/metabolism/microbiology/genetics ; *Feces/chemistry/microbiology ; *Metabolomics/methods ; Female ; Male ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; *Metagenomics/methods ; Multiomics ; Gastrointestinal Microbiome ; Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Isolated REM sleep behavior disorder (iRBD) is among the most reliable prodromal markers of α-synucleinopathies. Under the body-first (gut-first) model of α-synuclein pathology, in which pathology may originate in the enteric nervous system and ascend to the brain, the gut is a biologically plausible compartment in which early and accessible molecular alterations might be detectable; however, the fecal metabolome remains poorly investigated in this population. In this exploratory, cross-sectional study of 21 iRBD patients and 15 healthy controls, we characterized fecal samples through an integrated multi-omics framework. The fecal metabolome was profiled on two complementary mass spectrometry platforms: HS-SPME GC-EI-high-resolution MS, used for both untargeted volatilomics and targeted quantification of linear and branched short-chain fatty acids, and untargeted LC-MS/MS for the non-volatile fraction. Gut microbial community composition was characterized on the same material by 16S rRNA gene sequencing, and the metabolomic and microbial layers were combined by DIABLO multi-omics integration. Linear short-chain fatty acids were preserved, whereas branched-chain fatty acids were selectively increased in iRBD, indicating a shift toward proteolytic fermentation. Volatile indole was reduced, while p-cresol and 2-octanone were increased, paralleled at the LC-MS/MS level by attenuation of the tryptophan-indole axis, class-level bile acid depletion, and increased acylcarnitines. The microbiome was depleted of Blautia and Faecalibacterium and enriched in Oscillospirales. Integration resolved a coherent host-microbe signature that discriminated iRBD patients from controls within this discovery cohort (84.8% cross-validated accuracy). These cross-sectional findings characterize candidate fecal signatures associated with iRBD; given the exploratory design and the limited sample size, they are hypothesis-generating, and their value for predicting phenoconversion remains to be established in prospective studies.},
}

Humans
*REM Sleep Behavior Disorder/metabolism/microbiology/genetics
*Feces/chemistry/microbiology
*Metabolomics/methods
Female
Male
Cross-Sectional Studies
*Metabolome
Middle Aged
*Metagenomics/methods
Multiomics
Gastrointestinal Microbiome
Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42939852,
year = {2026},
author = {Kim, JW and Lee, YJ and Kim, K and Ko, SH},
title = {Interplay Between the Gut Microbiome and Oxidative Stress in Type 2 Diabetes.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939852},
issn = {2076-3921},
support = {No. RS-2024-00338024//National Research Foundation of Korea/ ; },
abstract = {Type 2 diabetes (T2D) develops when pancreatic beta cells progressively fail to compensate for insulin resistance in a host environment shaped by diet, adiposity, aging, medications, and genetics. Gut microbial dysbiosis and oxidative stress are often treated as parallel abnormalities; however, evidence increasingly supports a bidirectional microbiome-redox axis. Reduced butyrate production, altered bile-acid and amino-acid metabolism, intestinal barrier failure, and microbial products can promote mitochondrial dysfunction, NADPH oxidase activity, inflammation, and impaired insulin signaling. Conversely, hyperglycemia, lipotoxicity, inflammation, and reactive oxygen and nitrogen species remodel the intestinal habitat, favoring inflammation-adapted organisms and reinforcing dysbiosis. This review synthesizes evidence linking this circuit to insulin-responsive tissues, pancreatic islets, regulated cell death, and diabetic complications and critically examines dietary, microbiome-directed, antioxidant, glucose-lowering, and metabolic-surgical interventions. Human evidence is strongest for reproducible functional shifts, medication-microbiome interactions, and modest benefits of selected dietary and biotic interventions, whereas redox mediation and durable clinical efficacy remain heterogeneous. Future studies should integrate longitudinal metagenomics, metabolomics, validated redox biomarkers, strain-level and spatial sampling, and causal designs to identify patients with T2D most likely to benefit from microbiome-redox precision therapy.},
}

@article {pmid42940926,
year = {2026},
author = {Kuprin, A and Baklanova, V and Rechits, A},
title = {First Shotgun Metagenomic Characterization of the Gut Microbiome of the Endangered Longhorn Beetle Callipogon relictus (Coleoptera: Cerambycidae).},
journal = {Insects},
volume = {17},
number = {10},
pages = {},
pmid = {42940926},
issn = {2075-4450},
abstract = {The gut microbiome of Callipogon relictus, a rare member of the family Cerambycidae, was characterized for the first time using shotgun metagenomic sequencing. The aim of this study was to compare the taxonomic diversity and structure of the gut microbial communities in larvae and adults. Bacteria dominated the metagenomic profiles, accounting for 92.47% of the taxonomic composition in adults and 85.31% in larvae. Proteobacteria predominated in the bacterial component of both pooled profiles, accounting for 87.88% and 89.43%, respectively. The pooled adult profile had the highest relative abundances of Gammaproteobacteria and Enterobacterales, whereas the pooled larval profile had higher relative abundances of Alphaproteobacteria and Rickettsiales. In the pooled samples analyzed, 155 bacterial and 69 fungal genera were detected in the larval profile, compared with 85 and 17 genera, respectively, in the adult profile; the fungal component accounted for 10.46% of the larval profile and 0.18% of the adult profile. The two profiles shared 77 bacterial, 17 fungal, and 15 protist genera. The virus-like/retroelement sequence fraction was dominated by sequences related to Errantivirus, a member of the family Metaviridae. Because Metaviridae comprise LTR retrotransposons, this signal was interpreted as endogenous retroelement DNA rather than evidence of a free-virus gut virome. These results provide a preliminary description of a shared bacterial core accompanied by differences between the pooled profiles in lower-rank bacterial composition and in the structure of the fungal and protist components of the C. relictus microbiome.},
}

@article {pmid42940937,
year = {2026},
author = {Zulian, L and Peruzzo, A and Bertola, M and Scopel, G and Albertin, E and Martinello, M and Manzinello, C and Moressa, A and Petrin, S and Gallocchio, F and Dacasto, M and Pauletto, M and Mutinelli, F and Bordin, F and Granato, A},
title = {Honey Bees as Bioindicators of Environmental PFASs Contamination and Potential Effects on Gut-Microbial Communities.},
journal = {Insects},
volume = {17},
number = {10},
pages = {},
pmid = {42940937},
issn = {2075-4450},
support = {IZS VE 06/23 RC//Ministry of Health/ ; },
abstract = {Honey bees are valuable bioindicators of environmental contamination due to their wide foraging range and exposure to diverse biotic and abiotic stressors. This study evaluates the use of honey bees as bioindicators for detecting per- and polyfluoroalkyl substances (PFASs) in areas with varying levels of exposure risk (high-, intermediate-, and low-), as well as their potential effects on gut-microbial communities. Analytical chemistry to detect PFASs and pesticide residues were combined with molecular and metagenomic analyses to identify common honey bee pathogens and characterize gut-microbial communities. Short-chain PFASs were predominated over long-chain compounds, particularly in high-risk areas, while pesticide residues occurred in only a few apiaries. Molecular analyses revealed several widespread pathogens, while metagenomics showed a stable gut microbiome mainly composed of the genera Lactobacillus, Bartonella, Bombilactobacillus, Snodgrassella, Gilliamella, Bifidobacterium, and Gluconacetobacter. However, microbial-community composition differed significantly between apiaries with high- versus low-risk PFAS exposure. These results support honey bees as effective bioindicators for environmental PFAS monitoring and suggest that PFAS exposure may be associated with alterations in their gut-microbial communities. Further research is needed to elucidate the impact of PFASs on honey bee toxicity, gut-microbiota composition, and overall health.},
}

@article {pmid42941196,
year = {2026},
author = {Pizzocaro, E and Soverini, M and Salvagno, GL and Lotfollahzadeh, A and Santacroce, B and Bruno, G and Frigerio, I and Di Renzo, L and Castagnetti, A and Butturini, G},
title = {Gut Microbiome Compositional and Functional Signatures Associated with Chemotherapy Response in Pancreatic Ductal Adenocarcinoma: An Exploratory Cohort Study.},
journal = {Metabolites},
volume = {16},
number = {10},
pages = {},
pmid = {42941196},
issn = {2218-1989},
support = {NA//Fondazione Unipancreas ETS/ ; },
abstract = {Background/Objectives: The gut microbiome modulates chemotherapy efficacy in pancreatic ductal adenocarcinoma (PDAC), yet its relationship with the clinically relevant endpoint of post-chemotherapy surgical eligibility remains poorly characterised. We explored whether baseline gut microbiome composition and metagenomically predicted metabolic function differ between chemotherapy responders and non-responders in PDAC. Methods: In this prospective single-centre exploratory cohort study, faecal samples were collected from 15 patients with non-immediately resectable PDAC at diagnosis, before chemotherapy. Whole-genome shotgun metagenomics was performed, and microbial functional capacity was inferred through an assembly-based pipeline. Patients were classified as responders (achieved surgical eligibility, n = 6) or non-responders (n = 9). Results: At baseline, responders showed enrichment of Collinsella aerofaciens (p = 0.026) and Butyrivibrio fibrisolvens (p = 0.012), while non-responders were enriched in oral-origin bacteria (Streptococcus gordonii, Actinomyces spp., Rothia dentocariosa). Predicted butyrate showed the largest effect size difference between groups but did not reach significance (p = 0.179); responders also had broadly elevated predicted SCFAs and bile acids. However, chemotherapy regimen (mFOLFIRINOX in 5/6 responders vs. 2/9 non-responders; Fisher p = 0.041) and disease stage were unevenly distributed between groups. Conclusions: This exploratory study identifies the compositional and functional microbiome features distinguishing PDAC chemotherapy responders from non-responders. These associations are confounded by disease stage and regimen and require validation in larger, regimen-stratified cohorts before predictive or mechanistic claims can be made.},
}

@article {pmid42941936,
year = {2026},
author = {Vacaras, C and Vacaras, V and Nistor, C and Vesa, SC and Jucan, C and Furdui, IM and Strilciuc, S and Stefanescu, E and Chira, D and Rafila, A and Muresanu, DF},
title = {Limited Gut Microbiome Differences Between Relapsing-Remitting and Secondary Progressive Multiple Sclerosis: A Shotgun Metagenomic Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {20},
pages = {},
pmid = {42941936},
issn = {1422-0067},
support = {//Foundation for the Study of Nanoneurosciences and Neuroregeneration and by the Romanian Society of Microbiology./ ; },
mesh = {Humans ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; *Multiple Sclerosis, Chronic Progressive/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Biomarkers/blood ; Cross-Sectional Studies ; Shotgun Sequencing ; },
abstract = {The gut microbiome may contribute to multiple sclerosis (MS) pathophysiology, but its relationship with disease phenotype and progression remains unclear. To characterize taxonomic and functional gut microbiome differences between relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS) and their associations with neurological disability and circulating biomarkers. This cross-sectional study included 89 participants (30 healthy controls, 29 RRMS, and 30 SPMS). Shotgun metagenomic sequencing was used to assess microbial diversity, taxonomic profiles, and predefined short-chain fatty acid (SCFA)-related pathways, integrated with disability measures and serum GFAP, NfL, and S100B. SPMS participants were substantially older than those with RRMS (median 49.0 vs. 31.0 years), prompting age-adjusted analyses and an age-overlap sensitivity analysis. Alpha diversity and overall microbial community composition were similar across groups. SPMS showed greater interindividual microbial community dispersion than RRMS in the full cohort, with a similar direction and magnitude but attenuated statistical significance in the age-overlap sensitivity analysis. Exploratory taxonomic signals were not confirmed by FDR-controlled analyses. No robust phenotype-specific differences in predicted SCFA-related pathways or associations of taxonomic or functional features with disability or circulating biomarkers were identified. Greater microbial community dispersion in SPMS was observed in the full cohort, but this finding was attenuated in the age-overlap sensitivity analysis and should be considered preliminary. Overall, these findings do not support a distinct SPMS-associated gut microbiome signature, although potential phenotype-related differences cannot be excluded.},
}

Humans
*Multiple Sclerosis, Relapsing-Remitting/microbiology
*Multiple Sclerosis, Chronic Progressive/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Female
Male
Middle Aged
Adult
Biomarkers/blood
Cross-Sectional Studies
Shotgun Sequencing

@article {pmid42942211,
year = {2026},
author = {Zhao, Z and Luo, J and Zhao, Z and Liu, G and Feng, S and Chen, X and Cai, K and Song, Z},
title = {Effects of Arbuscular Mycorrhizal Fungi and Clay Minerals on Soil Nitrogen and Phosphorus Availability and Microbial Community Responses.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {10},
pages = {},
pmid = {42942211},
issn = {2075-1729},
support = {2023YFD2301500//National Key Research and Development Program of China/ ; },
abstract = {Efficient management of soil nitrogen and phosphorus availability is important for soil fertility and crop productivity, but the field responses of rhizosphere microbial communities to arbuscular mycorrhizal fungi (AMF) and clay-mineral amendments remain unclear. A wheat-field experiment compared four treatments: an untreated control (A), bentonite (B; 39 kg plot-1), sepiolite (C; 39 kg plot-1), and AMF inoculation (E; 2.25 kg inoculum plot-1; 120 spores g-1). Each treatment comprised six 4 × 7.5 m plots. Soil physicochemical properties were evaluated using all six plots, whereas rhizosphere microbial sequencing used three plots per treatment (plots 2, 4, and 6; n = 3). Treatment E showed higher mean alkali-hydrolyzable nitrogen (101.50 vs. 93.33 mg kg-1) and available phosphorus (56.00 vs. 20.98 mg kg-1) than the control, whereas treatment B showed a 32.8% higher mean available potassium. None of the bacterial or AMF alpha-diversity indices differed significantly among treatments. Taxonomic summaries showed descriptive variation among treatments, whereas principal component analysis (PCA) and analysis of similarities (ANOSIM) did not detect significant treatment-level separation of either the bacterial or AMF communities. Shotgun metagenomic annotation, rather than 16S-based functional inference, further showed descriptive differences in nitrogen- and phosphorus-related gene-abundance profiles and functional potential; Pseudomonadota and Actinomycetota accounted for substantial shares of several nutrient-cycling gene categories, while pstB showed comparatively pronounced numerical variation among treatments. These metagenomic profiles represent genetic functional potential and do not demonstrate transcript abundance or metabolic activity. Overall, AMF inoculation and clay-mineral amendments were associated with descriptive differences in nutrient availability, taxonomic profiles, and metagenomic functional potential in alkaline wheat farmland, but significant treatment-level separation of the overall bacterial and AMF communities was not detected.},
}

@article {pmid42942900,
year = {2026},
author = {Pătru, O and Luca, S and Păunescu, A and Enache, B and Văcărescu, C and Cozma, D and Crișan, S and Bena, A},
title = {The Gut Microbiome-Estrogen Axis in Menopause: Implications for Body Composition, Cardiometabolic Health and Nutrition.},
journal = {Nutrients},
volume = {18},
number = {20},
pages = {},
pmid = {42942900},
issn = {2072-6643},
mesh = {Humans ; *Menopause/physiology/metabolism ; Female ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/physiology ; *Body Composition/physiology ; *Nutritional Status ; Aging ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objectives: Menopause is associated with profound endocrine, metabolic, immune, and microbial changes that may contribute to accelerated biological aging and increased cardiometabolic risk. The gut microbiome represents a potential interface between estrogen biology, host metabolism, inflammation, and systemic organ function. This narrative review examines the role of menopause-associated gut microbiome remodeling in microbiome-mediated metabolic aging, focusing on the estrobolome, microbial metabolites, organ crosstalk, and microbiome-targeted interventions. Methods: Relevant literature was identified through searches of PubMed/MEDLINE, Scopus, and Web of Science, supplemented by reference-list screening. Human observational and clinical studies, mechanistic investigations, systematic reviews, meta-analyses, and relevant guidelines were critically evaluated and synthesized narratively. No formal meta-analysis was performed. Results: Menopause-associated changes in gut microbial composition and function may influence estrogen metabolism through the estrobolome and modify the production of short-chain fatty acids, lipopolysaccharides, trimethylamine N-oxide, and bile acid metabolites. These pathways may contribute to chronic low-grade inflammation, insulin resistance, endothelial dysfunction, dyslipidemia, hepatic metabolic dysfunction, adipose tissue inflammation, adverse changes in body composition, sarcopenia, neuroinflammation, and urogenital microbial instability. Dietary patterns, fermentable fiber, physical activity, probiotics, synbiotics, phytoestrogens, and menopausal hormone therapy may influence components of this network, although the strength of evidence remains variable. Current data do not support the use of microbiome characteristics to select or dose hormone therapy. Conclusions: The gut microbiome may act as a dynamic mediator linking estrogen decline with metabolic and systemic aging after menopause. However, causality, individual variability, and clinical translation remain insufficiently established. Longitudinal studies integrating shotgun metagenomics, metabolomics, hormone measurements, standardized hormone therapy exposure, and clinical outcomes are needed to determine whether microbiome-derived biomarkers can support risk stratification and personalized interventions for healthier aging in postmenopausal women.},
}

Humans
*Menopause/physiology/metabolism
Female
*Estrogens/metabolism
*Gastrointestinal Microbiome/physiology
*Body Composition/physiology
*Nutritional Status
Aging
Cardiometabolic Risk Factors

@article {pmid42943305,
year = {2026},
author = {Spathakis, M and Kolios, G and Paspaliaris, V and Dovrolis, N},
title = {Colorectal Cancer-Associated Microbiome Remodeling Implicates Host Microbial Metabolite-Receptor Axes.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {10},
pages = {},
pmid = {42943305},
issn = {1424-8247},
support = {//BioGut Technologies Inc./ ; },
abstract = {Background/Objectives: Colorectal neoplasia is accompanied by reproducible changes in the gut microbiome and fecal metabolome, but the receptor systems through which altered microbial metabolic outputs may interface with the host remain incompletely defined. We investigated whether disease-associated microbial functional remodeling converges on metabolite-sensing receptor axes that could prioritize mechanistic and pharmacological hypotheses across the adenoma-to-carcinoma sequence. Methods: We analyzed 1534 publicly available stool shotgun metagenomes from 11 colorectal neoplasia cohorts, including 624 controls, 209 adenomas and 701 colorectal cancers (CRCs). Study-adjusted species and unstratified MetaCyc pathway models were combined with stage-pattern classification and mapping of microbial pathways to predefined metabolite-receptor axes. Findings were examined in two independent fecal metabolomics datasets. Results: CRC was associated with 68 species and 249 unstratified pathways at false discovery rate q < 0.05. Among CRC-associated features, 17 species and 36 pathways were adenoma-concordant, whereas 37 species and 170 pathways were CRC-specific. Of 136 pathways mapped to seven receptor-linked ligand classes, 79 were FDR-supported. Nucleotide/purinergic metabolism contained 39 FDR-supported pathways, predominantly lower in CRC, whereas fatty-acid/short-chain fatty acid signaling contained 21 FDR-supported pathways, predominantly higher in CRC. Independent fecal metabolomics showed the strongest axis-level convergence for these two axes. Conclusions: Colorectal neoplasia is associated with reproducible microbial functional remodeling that can be organized into biologically defined metabolite-receptor axes. Fatty-acid/SCFA and nucleotide/purinergic pathways emerge as the leading candidates for prospective functional and pharmacological investigation. The analysis prioritizes testable host-microbiome signaling modules but does not establish metabolite flux, receptor activation or therapeutic efficacy.},
}

@article {pmid42943340,
year = {2026},
author = {Cheng, M and Zhang, M and Wang, W and Jia, X and Cong, B},
title = {Multi-Omics Analysis Identifies Gut-Associated Metabolic Signatures Associated with Metformin-Mediated Protection Against LPS-Induced Lung Injury.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {10},
pages = {},
pmid = {42943340},
issn = {1424-8247},
support = {30705010094//Hebei Medical University/ ; 2019-I2M-5-055//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; 82304360//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Lipopolysaccharide (LPS)-induced lung injury involves pulmonary inflammation, metabolic disturbance, and intestinal dysregulation. This study investigated whether metformin attenuates LPS-induced lung and colonic injury and characterized associated gut microbiota-metabolite changes. Methods: Male C57BL/6J mice were assigned to control (CON), LPS, metformin 200 mg/kg (MET 200 mg/kg), and metformin 400 mg/kg (MET 400 mg/kg) groups. Metformin was administered by gavage for 7 days before intranasal LPS challenge. Lung and colon injury were assessed by histology, immunostaining, ELISA, and RT-qPCR. Untargeted serum metabolomics, colonic-content metabolomics, and colonic-content shotgun metagenomics were performed in the CON, LPS, and MET 400 mg/kg groups. Differential-feature, pathway-enrichment, and exploratory Spearman correlation analyses were conducted. Results: Metformin reduced LPS-induced lung injury, inflammatory cytokine production, F4/80- and MPO-positive immune-cell infiltration, and colonic inflammatory and barrier-related abnormalities. Serum metabolomics identified 468 differential features in LPS versus CON and 286 in MET versus LPS, with 218 overlapping features. Colonic-content metabolomics identified 1000 and 554 differential features, respectively, with 328 overlapping features. Eight metabolites showed metformin-associated directional shifts toward control levels in both serum and colonic contents. Metagenomics showed metformin-associated remodeling of gut microbial composition and predicted gene-content functional potential. Exploratory integrated analyses linked metformin-responsive genera and shared metabolites with pulmonary inflammatory indicators. Conclusions: Metformin was associated with attenuated LPS-induced lung and colonic injury and coordinated gut-associated microbiota-metabolite remodeling. Because the study did not include a metformin-only group or causal perturbation experiments, these findings identify candidate associations rather than demonstrating a causal gut microbiota-metabolite-lung mechanism.},
}

@article {pmid42943366,
year = {2026},
author = {Moreira, J and Bettencourt, R},
title = {Deciphering Macroalgal Microbiomes: Metagenomic Insights, Ecological Roles and Bioprospecting Potential.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943366},
issn = {2076-2607},
support = {UID/05634/2025 (DOI: 10.54499/UID/05634/2025); UID/PRR/05634/2025 (DOI: 10.54499/UID/PRR/05634/2025); UID/PRR2/05634/2025 (DOI: 10.54499/UID/PRR2/05634/2025)//Fundação para a Ciência e Tecnologia/ ; PROSCIENTIA Incentive System-project M1.1.A/FUNC.UI&D/014/2025//Regional Directorate for Science, Innovation and Development of the Azores Government-PROSCIENTIA Incentive System/ ; ACORES-01-0145-FEDER-000138//European Regional Development Fund (ERDF)/ ; M3.1.b context emp/F/017/2024//Fundo Regional para a Ciência e Tecnologia/ ; },
abstract = {Macroalgae host complex microbial communities that influence surface colonization, development, nutrient transformation, carbohydrate turnover, environmental responses, and the production of potentially valuable metabolites. Advances in shotgun metagenomics and genome-resolved analysis have greatly expanded access to this functional diversity, but they have also increased the risk of conflating genomic potential with biological activity or host benefit. This narrative review evaluates the bacterial component of macroalgal microbiomes-the component for which mechanistic and experimentally validated evidence is most extensive-through a framework that separates what has been proven from what is merely predicted, distinguishing functional prediction from expression, biochemical activity, metabolite exchange, host response, and experimental causality. Particular attention is given to bacteria-dependent morphogenesis, metabolic complementarity, environmental acclimation, carbohydrate-active enzymes and polysaccharide-utilization loci, biosynthetic gene clusters, and the translational potential of seaweed-associated microorganisms. Comparative perspectives from microalgal and cyanobacterial systems are used to identify principles that generalize across algal microbiomes while emphasizing the distinctive spatial and chemical complexity of macroalgal surfaces. Invasive and bloom-forming macroalgae provide an additional ecological context in which microbial functional redundancy, recruitment flexibility, and dominant populations may shape whole-community profiles. An illustrative, hypothesis-generating taxon-attribution case study, based on single metagenomic datasets from Rugulopteryx okamurae and Sargassum sp. holobionts in the Azores, which confounds host identity with sampling location, time, and thallus condition, shows that the disproportionate genomic contribution of the genus Cobetia measurably alters the interpretation of a specific subset of community-level KEGG pathway contrasts, while the majority of pathway-level and taxon-specific signals discussed retain their direction after this taxon's exclusion and residual-community renormalization. Together, these analyses argue that macroalgal microbiome research should move beyond inventories of predicted functions toward explicit taxonomic attribution, experimental validation, and ecological context. Such integration will be essential for establishing which microbial functions are ecologically consequential and which can be translated reproducibly into biotechnology.},
}

@article {pmid42943375,
year = {2026},
author = {Anema, RF and Francis, FL and Smith, ZK and St-Pierre, B},
title = {Enrichment of Candidate Formate and Acetaldehyde-Producing Ruminal Bacteria in Response to Corn-Based Diets.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943375},
issn = {2076-2607},
support = {7010068, SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch/ ; },
abstract = {In ruminant production systems, feeding diets with easily digestible and energy-dense compounds during the finishing phase is a common strategy to ensure optimal growth and performance. As ruminal microbial communities are responsible for fermenting feed into nutrients that the animal host can absorb and use, concentrate-based diets favor specialists that can utilize starch, as well as other cross-feeding species that benefit from their metabolic activities and their end products. Currently, a gradual increase in the proportion of concentrate in rations remains the best strategy towards developing resilience to undesirable end products, thus mitigating their adverse effects on the host. In an effort to gain further insights into the mechanisms involved in the adaptation of ruminal microbial communities to starch-rich diets, we used a 16S rRNA gene-based approach to identify eight highly represented species-level Operational Taxonomic Units (OTUs) that were more abundant in the rumen of finishing lambs fed a whole corn-based diet for 56 (D56, n = 7) or 63 days (D63, n = 8) compared to samples collected from lambs on a forage diet (p < 0.05) that were harvested prior to the dietary transition (D0, n = 4). To assess their metabolic capabilities, a metagenomics-based approach was used for OTUs corresponding to uncharacterized bacterial species, while publicly available genomes were analyzed as a proxy for OTUs closely related to known bacterial species. As anticipated, the potential to hydrolyze starch and metabolize glucose into pyruvate was found in all datasets analyzed, but more diverse capabilities were observed for other functions, such as the types of end products synthesized. For instance, lactate was not the only undesirable microbial end product predicted, as the potential to generate formate, acetaldehyde and ethanol was also found across datasets. While the impact of these compounds on the rumen remains poorly explored, ongoing research on how they can affect gut health in humans indicates that they may have undesirable effects. Together, these and other results from this study provide further insight into how ruminal bacterial communities in finishing lambs adapt to starch-based ingredients and how they can in turn affect the ruminal environment.},
}

@article {pmid42943376,
year = {2026},
author = {Wang, Z and Cui, R and Tong, J and Liu, P and Huang, S and Gu, Y and Luo, G},
title = {Impact of Residual Glutaraldehyde-Didecyldimethylammonium Bromide on Fermentation Performance and Microbial Community in Ectopic Fermentation System.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943376},
issn = {2076-2607},
support = {32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//the Science and Technology Projects of Xizang Autonomous Region/ ; 2024ZHXC0005//the Sichuan Science and Technology Program/ ; 2026-YF05-00039-SN//the Chengdu Municipal Science and Technology Bureau Key R&D Support Program/ ; sccxtd-2026-08//the Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; ZYN2025261//the Fundamental Research Funds for the Central Universities of Southwest Minzu University/ ; },
abstract = {Ectopic fermentation systems (EFSs) are widely applied to treat livestock manure, yet residual disinfectants transferred from production areas into the manure collection system may compromise their performance, and the consequences of such continuous low-dose input remain unclear. Here, we aimed to determine whether long-term input of the widely used disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) impairs EFS operation, and to identify the changes in microbial communities and organic matter underlying these effects. Pig manure slurry containing 20 mg/kg GD was supplied continuously, and physicochemical parameters, enzyme activities, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and three-dimensional excitation-emission matrix (3D-EEM) spectra were monitored throughout the fermentation period. GD significantly reduced total nitrogen accumulation (p < 0.05) and suppressed lignocellulose-degrading enzyme activities during the late fermentation stage. Microbial richness declined significantly (Chao index, p < 0.05), accompanied by enrichment of thermotolerant taxa such as Thermobifida and Bacillus, while soluble microbial by-products decreased markedly. Unexpectedly, MGEs including intI1, intI2 and Tn916/1545 were less abundant under GD exposure, likely reflecting the overall inhibition of microbial growth. These findings demonstrate that GD residues exert cumulative adverse effects on EFS performance, and highlight the need to coordinate on-farm disinfection with downstream manure treatment.},
}

@article {pmid42943377,
year = {2026},
author = {Quiñonez Álvarez, CP and Berutti-Suárez, L and Mafla Andrade, SX},
title = {Association of Helicobacter pylori Infection with the Gastric Microbiota: A Scoping Review from a Molecular Diagnostic Perspective.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943377},
issn = {2076-2607},
abstract = {Helicobacter pylori infection remains globally one of the main causes of chronic gastritis, gastroduodenal ulcer disease, and gastric adenocarcinoma. Although the stomach has been considered an almost sterile environment, molecular techniques have revealed a complex and dynamic gastric microbiome whose composition may vary with H. pylori infection status. This review presents current knowledge on the impact of H. pylori on the composition, diversity, and functional implications of the gastric microbiome, focusing on studies applying molecular diagnostic techniques such as conventional PCR, quantitative real-time PCR (qPCR), 16S rRNA gene sequencing, and shotgun metagenomics. A systematic literature search was conducted between January and March 2025, including all eligible studies published from 2006 to 2025 following the PRISMA methodology for exploratory reviews. Thirty studies met the inclusion criteria and were integrated into the qualitative synthesis, which included primary studies, secondary sources, and methodological studies. The evidence suggests that H. pylori infection is generally associated with decreased alpha diversity and increased relative abundance of Proteobacteria (especially Helicobacter), along with decreased abundances of Firmicutes, Actinobacteria, and Bacteroidetes. Several studies have reported associations between virulence factors (e.g., CagA and VacA) and alterations in the gastric microenvironment, reflecting microbial and host-related changes relevant to chronic inflammation and gastric carcinogenesis. From a diagnostic perspective, qPCR and sequencing-based methods enable detection of H. pylori, evaluation of virulence- and resistance-associated targets, and broader taxonomic and functional analyses. However, significant methodological heterogeneity, particularly concerning sample types, DNA extraction, 16S hypervariable regions, and bioinformatics platforms, limits comparability between studies. These findings underscore the need for standardized molecular methods to improve understanding of interactions between H. pylori and the microbiome, as well as their clinical implications.},
}

@article {pmid42943391,
year = {2026},
author = {Chang, W and Ma, W and Du, J and He, W and Zhu, N},
title = {Warming and Nitrogen Addition Induce Asynchronous Taxonomic and Functional Responses and Reorganize Microbial C, N, P Cycling Potential in an Alpine Wetland on the Qinghai-Tibet Plateau.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943391},
issn = {2076-2607},
support = {32660405, 31860143//National Natural Science Foundation of China/ ; 26ZDFG001//Gansu Provincial Science and Technology Plan/ ; 2024RCXM82//the Priority Talent Project of Gansu Province/ ; 24ZYQA023//the Central Government Guide Local Science and Technology Development Funds/ ; 2021CYZC-15//the Gansu Provincial Department of Education Industrial Support Program Project/ ; 2026CXZX-793//the Innovation Star Project for Graduate Students in Universities in Gansu Province/ ; 26JDWA001//the innovation Platform Plan Program of Gansu Province/ ; },
abstract = {Climate warming and atmospheric nitrogen deposition are altering carbon (C), nitrogen (N), and phosphorus (P) cycling in alpine wetlands. However, how these drivers jointly reorganize microbial communities and their biogeochemical cycling potential remains poorly understood, particularly in cold, nutrient-limited alpine wetlands. We conducted a four-year field experiment combining open-top chamber warming and nitrogen addition. Soil physicochemical measurements were integrated with shotgun metagenomic sequencing to assess microbial community structure and the functional potential associated with C, N, and P cycling. The results showed that archaeal and bacterial community composition remained stable following warming and nitrogen addition, whereas fungal composition changed. Functional gene richness was positively correlated with archaeal and bacterial richness but was not correlated with fungal richness, indicating asynchronous responses between taxonomic-functional dimensions. Warming and nitrogen addition did not consistently increase the overall abundance of C, N, and P cycling functional genes. Instead, they induced pathway-specific responses: compensatory shifts among C fixation pathways, decreases in complex C degradation genes, increases in nitrification genes, and decreases in genes associated with P acquisition and homeostatic regulation. Soil moisture and enzyme activities were significantly correlated with C, N, and P cycling genes. These findings highlight domain-specific taxonomic responses and process-specific re-organization of microbial functional potential and emphasize the importance of hydro-thermal constraints when predicting alpine-wetland biogeochemical responses to future warming and increasing N inputs.},
}

@article {pmid42943393,
year = {2026},
author = {Senok, A and Verma, S and Shouqair, D and Alghafri, R and Moradigaravand, D and Nassar, R and Everett, D and Goering, R and Khan, M},
title = {Resolving Host-Associated Antimicrobial Resistance in Municipal Wastewater Using Hi-C Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943393},
issn = {2076-2607},
support = {AJF-NIH-1-MBRU//This work was funded by Grant# AJF-NIH-1-MBRU as part of the UAE-NIH Collaborative Research Initiative (UAE-NIH-CRI) which comprises four collaborating UAE institutes: Al Jalila Foundation, Mohammed Bin Rashid University of Medicine and Health Sciences, K/ ; },
abstract = {Conventional wastewater metagenomics enables population-level surveillance of antimicrobial resistance (AMR) but provides limited insight into the bacterial hosts, genomic context, and the mobility of resistance determinants. In this study, we applied high-throughput chromosome conformation capture (Hi-C) metagenomics, a proximity-ligation approach, to resolve host-associated AMR. Six influent wastewater samples collected from two municipal wastewater treatment plants over a four-month sampling period were investigated. Integrated shotgun metagenomic and Hi-C sequencing were used to reconstruct metagenome-assembled genomes (MAGs), plasmid bins, and viral bins, and to link AMR, stress-response, and virulence-associated genes to their bacterial hosts through Hi-C contacts. From 12,877 genome bins, 454 met quality thresholds (139 MAGs, 130 plasmid bins, 185 viral bins) spanning 70 bacterial and archaeal families. AMRFinderPlus identified 771 resistance and fitness-associated gene hits (517 AMR, 232 stress-response, 22 virulence-associated), dominated by macrolide-lincosamide-streptogramin B (n = 117), β-lactam (n = 114), and tetracycline (n = 96) determinants. Hi-C linked 490 gene hits to host families; Enterobacteriaceae had the highest number of host-assigned detections (n = 131), while Aeromonadaceae carried the broadest AMR repertoire (n = 102; 72% AMR). The host-plasmid network comprised 137 AMR-positive plasmid bins linked to 106 MAGs through 166 Hi-C-supported associations. Five plasmid contigs, including one harbouring blaCMY-4, were linked to MAGs from two distinct bacterial classes, suggestive of cross-lineage plasmid carriage. Viral AMR attribution was limited, with erm(B) as the sole resistance determinant identified on a viral contig. Hi-C metagenomics extends wastewater resistome profiling beyond gene inventories by resolving bacterial hosts, plasmid associations, and genomic context, strengthening the ecological interpretation of wastewater-based AMR surveillance.},
}

@article {pmid42943414,
year = {2026},
author = {Kimura, H and Kimura, R and Mizukoshi, F and Shikichi, A and Tsukagoshi, H and Tomita, H and Ryo, A},
title = {Molecular Public Health for Infectious Disease Prevention and Control.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943414},
issn = {2076-2607},
abstract = {Molecular technologies have transformed infectious disease surveillance, but their public health value depends on whether molecular signals can be converted into timely and effective action. Unlike molecular epidemiology, which primarily uses molecular variation to characterize distribution, relatedness, transmission, and evolution, molecular public health is defined here as an end-to-end operational framework that connects molecular evidence to population-level decisions, interventions, and evaluation. This narrative review integrates molecular detection, pathogen genomics, bioinformatics, metagenomics, wastewater and environmental surveillance, One Health monitoring, antimicrobial resistance genomics, multi-omics, and artificial intelligence. The framework progresses from detection and analytical interpretation to prediction, intervention, and feedback. Implementation maturity is heterogeneous: targeted PCR, short-read pathogen genomics, and bioinformatics-supported outbreak investigation are established in many defined use cases, whereas pathogen-agnostic metagenomics, multi-omics, and AI-enabled decision support remain more context dependent or emerging. Actionability is operationalized through analytical validity, epidemiological interpretability, sample-to-decision time relative to the intervention window, decision impact, and measurable post-intervention outcomes. Persistent barriers include sampling bias, uneven global capacity, incomplete metadata, insufficient standardization, governance concerns, and poorly defined trigger thresholds. The central criterion for the field should therefore be whether molecular information measurably improves prevention and control.},
}

@article {pmid42943417,
year = {2026},
author = {Pericàs, JM and Cañas, MA and Goenaga, MA and Nevado, C and Kestler, M and De La Villa, S and Muñoz, P and Blanes, R and Tasias, M and Escudero-Sánchez, R and Moreno-García, J and Alonso-Socas, MM and Rodríguez-Esteban, Á and Calderón-Parra, J and Diego-Yagüe, I and Boix-Palop, L and García-Álvarez, L and Gasch, O and Careta, O and Paredes, R and Luzko, IS and Garcia-De-La-Mària, C and Hernández-Meneses, M and Cuervo, G and Moreno, A and Arias, CA and Miró, JM and , },
title = {A Multicenter Prospective Protocol to Explore the Relationship Between Enterococcus faecalis Bloodstream Infections and Colorectal Neoplasms (EnteroColonus-GAMES Project).},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943417},
issn = {2076-2607},
support = {PI19/01898//Instituto de Salud Carlos III, Proyectos de Investigación en Salud/ ; 2017-26//Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)/ ; },
abstract = {Preliminary evidence suggests that patients with Enterococcus faecalis bacteremia and infective endocarditis, particularly those without an identifiable source, may have an increased prevalence of colorectal neoplasia. Whether systematic colonoscopy should be recommended in this population remains unresolved. EnteroColonus is a multicenter, prospective, observational matched cohort study that will recruit adults aged 50 years or older with E. faecalis bacteremia and/or infective endocarditis from 22 Spanish centers, together with asymptomatic controls undergoing colorectal cancer screening. Cases will be stratified into E. faecalis bacteremia/endocarditis of unknown origin (EFBEUO) and with suspected source (EFBESS). The original planned sample size initially was 414 participants: 276 cases and 138 matched controls. Under the amended protocol, the current confirmatory sample-size target is 165 participants (110 cases and 55 matched controls; 2:1 case-to-control allocation). Core procedures include colonoscopy, histopathology, clinical and microbiological phenotyping of colonic samples, fecal microbiome profiling by shotgun metagenomics, detection of E. faecalis genetic material in colorectal biopsy specimens using 16S sequencing and species-specific qPCR, and whole-genome, SNP, and phylogenetic analyses of clinical isolates. Secondary endpoints include microbiome profiles, biopsy positivity for E. faecalis, genomic traits of bloodstream isolates, mortality, relapse/recurrence, and development of a colorectal neoplasia risk score. This protocol is designed to clarify which patients with E. faecalis bloodstream infection might benefit from systematic colonoscopy evaluation and to explore host-microbe mechanisms underlying the observed association with colorectal neoplasia.},
}

@article {pmid42943445,
year = {2026},
author = {Wen, J and Huang, J and Liu, G and Liang, S and Zeng, L and Huang, R and Yu, N and Qin, G and Chen, Q and Yan, S},
title = {Taxonomic and Functional Profiles of the Gastrointestinal Microbiome Across Digestive Tract Segments in Growing Water Buffaloes.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943445},
issn = {2076-2607},
support = {2024YFD1301300//National Key Research and Development Program of China/ ; AA23026004//Guangxi Buffalo Breeding Key Technology R&D Talent Introduction Project/ ; AA22068099//uangxi Science and Technology Major Project/ ; },
abstract = {Gastrointestinal segments in ruminants differ in physiological environment and substrate availability. This study characterized taxonomic and gene-encoded functional profiles in 54 shotgun metagenomes from 30 growing male water buffaloes assigned to five dietary formulations. The dataset comprised 30 rumen-fluid samples, six per group, and 24 post-slaughter samples from six gastrointestinal sites in five animals. Comparisons among groups A-E yielded p = 0.9816 for final body weight, p = 0.9315 for overall average daily gain, and p = 0.2832 for rumen-fluid pH. Genus-level principal coordinate analysis (PCoA) used Bray-Curtis dissimilarities calculated from Hellinger-transformed relative abundances. In the 30 rumen-fluid samples, PERMANOVA yielded R[2] = 0.1554, pseudo-F = 1.1499, and p = 0.327. The cross-site profiles were described separately from the dietary-group comparison. Post-slaughter rumen contents had larger proportions of Bacteroidota than the other sampled sites, whereas Bacillota accounted for the largest proportions in the cecum and colon. Kyoto Encyclopedia of Genes and Genomes (KEGG) Level 2 profiles and carbohydrate-active enzyme (CAZyme) profiles described the distribution of annotated functions across sites. These data characterize taxonomic assignments and carbohydrate-utilization-related gene profiles from the rumen to the colon in growing water buffaloes.},
}

@article {pmid42943450,
year = {2026},
author = {Huang, JK and Wu, PH and Chen, ZF and Liu, PY and Chuang, YS and Kuo, MC and Chiu, YW and Hsu, PC and Kuo, TH and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with the Kynurenine Pathway in Tryptophan Metabolism in Patients Undergoing Hemodialysis.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943450},
issn = {2076-2607},
support = {MOST 111-2314-B-037-032-MY3 and MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology/ ; KMUH109-9R17, KMUH110-0R19, KMUH111-1R14, KMUH112-2R21 and KMUH113-3R18//Kaohsiung Medical University Hospital/ ; NHRIKMU-111-I003-2, NHRIKMU-113-I005, NYCUKMU-112-I006, KT112P012, KT113P006, NHRIKMU-114-I001 and S11209//Kaohsiung Medical University/ ; },
abstract = {Patients with chronic kidney disease (CKD) and hemodialysis (HD) often experience gut microbiota dysbiosis, which may influence tryptophan metabolism through the kynurenine pathway. We aimed to investigate the specific gut microbiota signatures associated with metabolites involved in the kynurenine pathway in HD patients. In this cross-sectional study, we analyzed serum metabolite concentrations and fecal shotgun metagenomic profiles from 85 patients receiving maintenance hemodialysis at Kaohsiung Medical University Hospital. Fecal samples were analyzed using shotgun metagenomic sequencing to characterize microbiome composition and functional pathways. We measured kynurenine pathway metabolites (kynurenine, kynurenic acid, nicotinuric acid, and trigonelline) by liquid chromatography tandem mass spectrometry and analyzed their associations with microbial species abundance and genomic metabolic modules (GMM). Several bacterial species displayed associations with kynurenine pathway metabolites. Ruminococcus gnavus and Eubacterium sp. CAG:180 demonstrated correlations with kynurenine and kynurenic acid levels, respectively; however, these associations did not persist after adjustment. Distinct levels of metabolites corresponded to distinct patterns of genomic metabolic modules. High kynurenine levels correlated with increased pathways for pectin and arginine degradation. Elevated nicotinuric acid levels were associated with enhanced pathways for anaerobic fatty acid beta-oxidation and propionate production. Trigonelline levels correlated with homocysteine metabolism and various amino acid degradation pathways. Specific microbial taxa and predicted functional modules were associated with circulating kynurenine- and niacin-related metabolites. These cross-sectional findings are hypothesis-generating and do not establish directionality, causality, or therapeutic efficacy. Interpretation is limited by the modest sample size and the absence of a non-hemodialysis control group.},
}

@article {pmid42943474,
year = {2026},
author = {Ghiba, MTA and Alsheikh-Hussain, A and Alzahrani, TE and Alhamdoosh, M and Alhetheel, AF and Hanif, A and Eifan, SA},
title = {Complementary Use of Shotgun Metagenomics and Multiplex PCR for Pathogen Detection on High-Touch Surfaces.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943474},
issn = {2076-2607},
support = {ORF-2026-797//King Saud University/ ; },
abstract = {Shotgun metagenomics is being increasingly promoted as a pathogen-agnostic alternative to targeted PCR for environmental surveillance, yet its practical value on dry, low-biomass, host-dominated surfaces remains uncertain. In a companion study, we reported QIAstat-Dx multiplex PCR screening of 55 pooled high-touch surface samples from Riyadh, identifying 19 positive pools (34.5%). Here, in a retrospective exploratory comparison, we use those previously reported PCR calls as the targeted comparator and ask what unenriched shotgun metagenomic sequencing adds. Ten archived pools, each with at least one PCR-detected viral target, were sequenced (Illumina NovaSeq X Plus, 2 × 150 bp). Human-mapped reads constituted a substantial fraction of every library (mean 59.1%; range 42.1-80.2%). Among 14 evaluable PCR-positive target events, metagenomics assigned at least one read pair to the corresponding target taxon in 10 (71.4%; exact 95% CI, 41.9-91.6%). Because the cohort was preselected for viral PCR positivity, this value represents positive agreement/taxonomic concordance within the selected cohort and not diagnostic sensitivity. At the same ≥1 read-pair threshold, target taxa were also assigned to 91 of 246 (37.0%) evaluable pool-by-target cells in which PCR was negative; raising the threshold to ≥10 read pairs reduced positive agreement to 35.7% while background assignment remained 24.8%. Of six target categories with PCR-positive events, only coronavirus 229E was assigned more read pairs in its PCR-positive pool than in any PCR-negative pool. Across all ten pools, the three respiratory RNA-virus taxa represented among the PCR-positive calls accounted for only 105 classified read pairs in total-including assignments in both PCR-positive and PCR-negative pool-target cells-equivalent to 0.12% of the viral fraction. Even the broadest viral reference coverage was limited, as adenovirus in HP10 reached 16.39% (23 distinct alignment spans), while SARS-CoV-2 in CP17 reached 8.83% (12 spans); these partial, discontinuous alignments did not support robust whole-genome consensus reconstruction or genome-wide variant or phylogenetic analysis. Metagenomics nevertheless provided a broader taxonomic context beyond the targeted panel. Under this retrospective unenriched workflow, target recovery was variable, no tested assignment threshold separated a PCR-positive target signal from the background assignment, and shotgun metagenomics added ecological context rather than providing a reliable replacement for targeted multiplex PCR in this dataset.},
}

@article {pmid42943483,
year = {2026},
author = {Pan, Z and Wang, Z and Zhao, S and Chen, G and Wu, D and Xia, Q},
title = {Escherichia marmotae Dominates the Global Distribution of cdtABC Carriers in the Human Gut.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943483},
issn = {2076-2607},
support = {ZR2023QC225//Shandong Academy of Sciences/ ; },
abstract = {The gut microbiota can influence colorectal cancer through microbial metabolism, immune regulation and direct damage to host DNA. Previous experimental studies have shown that cytolethal distending toxin (CDT) can damage host DNA and promote colorectal tumorigenesis in model systems. However, the distribution of bacteria carrying intact cdtABC systems in human gut populations remains poorly characterized. Here, we integrated systematic screening of 60,008 complete bacterial genomes with analyses of 12,238 human gut metagenomes from 45 countries. We identified 871 intact cdtABC loci in 783 genomes, revealing a taxonomically restricted but genetically diverse carrier landscape. Carriers were detected worldwide, but the population signal was strongly dominated by an Escherichia marmotae lineage, a pattern that remained robust across minimum abundance thresholds. Most carrier-detected samples contained a single carrier, indicating pronounced lineage dominance. After carrier species were removed from the taxonomic profiles, the surrounding microbiome consistently distinguished samples with and without carriers across studies. This community signal was strongest for E. marmotae but remained detectable for other carriers and involved reproducible associations with Escherichia, Faecalibacterium and other gut taxa. By connecting intact loci with carrier lineages, global gut distribution and microbial community context, our study extends CDT research beyond isolated bacterial strains. These findings provide a basis for prioritising cdtABC carriers for functional validation and evaluating their potential relevance to colorectal cancer.},
}

@article {pmid42943488,
year = {2026},
author = {Song, Y and Jia, Z},
title = {Comparative Genomics of Ecologically Differentiated Nitrososphaera-Related Ammonia-Oxidizing Archaea.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943488},
issn = {2076-2607},
support = {92251305//National Natural Science Foundation of China/ ; XDA28020203//Chinese Academy of Sciences/ ; },
abstract = {Soil acidification strongly influences the ecology of terrestrial ammonia-oxidizing archaea (AOA). Within this group, the Nitrososphaera-related alpha (NS-α) and delta (NS-δ) lineages exhibit pronounced pH-associated ecological differentiation. In the preceding microcosm experiment, NS-α populations showed greater persistence than NS-δ during ammonium-driven soil acidification, yet the genomic basis underlying this ecological differentiation remains poorly understood. In this study, metagenomic sequencing of one near-neutral baseline microcosm (pH 7.35) and one acidified microcosm (pH 4.73) was used to reconstruct 12 Nitrososphaera-affiliated metagenome-assembled genomes (MAGs), including 2 NS-α and 10 NS-δ MAGs. These genomes were compared using genome-based phylogenetic analysis, amoA phylogeny, average amino acid identity (AAI), average nucleotide identity (ANI), and KEGG functional annotation to investigate lineage-level genomic differentiation and candidate functional genomic features. Genome-based phylogenetic and whole-genome similarity analyses supported clear differentiation between NS-α and NS-δ, while also revealing substantial genomic heterogeneity within NS-δ. Functions related to nitrogen acquisition and regulation, respiratory energy metabolism, autotrophic carbon fixation, and oxidative-stress defense were broadly distributed across both lineages and showed no clear NS-α-specific pattern. In contrast, Mre11, HerA, NurA, and RadA were detected in both reconstructed NS-α MAGs. Comparison with representative NS-α reference genomes, including the neutrophilic Nitrososphaera viennensis EN76, further showed that this DNA-repair-related gene repertoire is not restricted to acidic environments and is more consistent with a broader NS-α-associated genomic feature. Na[+]/H[+] antiporters and Trk/Ktr-type K[+] transport systems were not detected within either reconstructed NS-α MAG, although MAG-level non-detection was not interpreted as definitive lineage-level absence. Overall, the results identify genomic differences between NS-α and NS-δ but do not establish a functional advantage under acidification. The potential physiological significance of the DNA-repair-related pattern therefore remains to be experimentally tested.},
}

@article {pmid42943547,
year = {2026},
author = {Branda, F and Maria, F and Alexiev, I and Demir, AB and Limon, Ö and Ceccarelli, G and Scarpa, F and Russo, A and Spoto, S and Ciccozzi, M},
title = {Surveillance, Detection and Therapeutic Innovation in Antimicrobial Resistance in the Age of Polycrisis: From Genomic and Digital Innovation to One Health Integration.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943547},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) surveillance is increasingly strained by interconnected global crises, i.e., pandemics, climate change, armed conflicts, population mobility, and health inequalities, that disrupt healthcare delivery, diagnostic capacity, and laboratory infrastructure. In parallel, artificial intelligence (AI), machine learning, whole-genome sequencing, metagenomics, and digital surveillance offer the potential to shift from reactive reporting to predictive intelligence that anticipates resistance threats, although current implementations remain sector-specific, retrospective, and project-funded. Environmental surveillance, particularly wastewater monitoring coupled with genomic epidemiology, provides early warnings at population and ecosystem levels. The future integration of AI across human, animal, and environmental sectors could enable unified One Health intelligence; no such integrated platform is currently operational. This review focuses primarily on bacterial AMR. It examines how global drivers strain surveillance, how genomic, metagenomic, digital, and AI-enabled technologies reshape AMR detection and prediction, and the emerging non-antibiotic therapeutic landscape, including bacteriophage therapy, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based antimicrobials, antimicrobial peptides, microbiota-directed interventions, nanomedicine, host-directed therapies, photodynamic therapy, and vaccines. It then explores how these innovations can be integrated within a One Health framework to support coordinated global preparedness. Addressing the AMR crisis will require not only technological innovation but also equitable implementation, interdisciplinary collaboration, and resilient systems.},
}

@article {pmid42943560,
year = {2026},
author = {Pappa, S and Tsioka, K and Sotiraki, S and Pervanidou, D and Papa, A},
title = {Detection and Genetic Analysis of Jingmen Tick Virus in Greece.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943560},
issn = {2076-2607},
support = {101102733//European Union/ ; 101132974//European Commission/ ; },
abstract = {Jingmen tick virus (JMTV) is an emerging, segmented RNA virus in the Flaviviridae family. Since its first identification in 2010 in China, JMTV has been detected in several parts of the world, primarily in ticks, but also in other arthropods, mammals, and even humans. The study included 400 adult ticks (333 Rhipicephalus bursa, 40 Ixodes ricinus and 27 Ixodes gibbosus) previously collected from livestock and the environment in various administrative regions of Greece. The ticks were grouped into 107 pools and screened for JMTV using an in-house real-time RT-PCR protocol. JMTV was detected in 41 (38.3%) tick pools (minimum infection rate 10.2%) in five of the seven regions tested. The virus positivity differed among tick species, hosts and regions. A single JMTV-positive R. bursa tick has been previously found co-infected with Aigai virus. Five positive pools with the highest viral load (Ct range 14.61-20.36) were subjected to metagenomic next-generation sequencing. Genetic analysis based on the complete coding sequences of all four RNA segments revealed that the sequences of the Greek strains cluster within JMTV Group 1, sharing 95.41% to 97.16% nucleotide identity with their closest relatives from Kosovo, Romania, and Türkiye. The results of the study confirm the wide distribution of JMTV in ticks in Greece, providing the first comprehensive genomic data for the virus in the country and highlighting the need for surveillance studies to assess any public health risk.},
}

@article {pmid42943562,
year = {2026},
author = {Hu, Y and Cheng, S and Fang, H and Lu, M},
title = {Short-Term Simulated NH4[+]/NO3[-] Inputs Reorganize Soil Microbial Communities and Modify N-Cycling Functional Potential in Temperate Forests.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943562},
issn = {2076-2607},
support = {32371725//National Natural Science Foundation of China/ ; 32501531//National Natural Science Foundation of China/ ; 20222-051244//"Unveiling the List of Hanging" and Technology Project of Jinggangshan Agricultural High-tech Industral Demonstration Zone/ ; XDA0440404//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA28130100//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 20244-018652//Ji'an City Science and Technology Plan Project/ ; 2024H-090166//Ji'an City Science and Technology Plan Project/ ; 20255-061606//Ji'an City Science and Technology Plan Project/ ; },
abstract = {Forest soil nitrogen (N) turnover and nitrous oxide (N2O) release are strongly influenced by atmospheric N deposition. Although the effects of individual inorganic N species on soil biogeochemistry are well documented, the consequences of changing their relative supply for N2O formation and the underlying microbial pathways remain less clear. We therefore examined soil N2O emissions, microbial communities, and N-transformation potential across a gradient of ammonium-to-nitrate (NH4[+]/NO3[-]) inputs in a temperate forest soil from Northeast China. Seven treatments covering NH4[+]/NO3[-] ratios from 1:5 to 5:1 were established. Soil physicochemical properties and N2O emissions were measured, while microbial taxonomic profiles and N-cycling genes were characterized by metagenomic sequencing. Altering the composition of inorganic N reorganized the microbial community, including the relative representation of archaeal, bacterial, and eukaryotic groups. N2O release was greatest when NH4[+] and NO3[-] were supplied in equal proportions, a pattern that may reflect a stronger contribution of nitrification-associated processes. Across the treatment gradient, the response of N2O emissions to inorganic N composition was nonlinear. By contrast, the 1:2.5 NH4[+]/NO3[-] treatment produced comparatively low N2O emissions and contained a greater representation of genes associated with N2O reduction, consistent with enhanced microbial potential for N2O consumption. Under the more nitrate-dominated 1:5 treatment, genes involved in dissimilatory nitrate reduction to ammonium (DNRA) were enriched, indicating a shift in the potential routes of nitrate transformation. Metagenomic data further revealed marked variation in genes linked to nitrification, denitrification, and biological N fixation. In comparison with these compositional and functional responses, microbial diversity changed relatively little, possibly because overlapping functions were distributed among different taxa under contrasting N inputs. Overall, the findings show that the balance between ammonium and nitrate can affect forest-soil N2O emissions by restructuring microbial assemblages and their potential to transform N. These responses emphasize the need to consider the composition, rather than only the amount, of N deposition when evaluating microbial regulation of ecosystem N cycling and greenhouse-gas release. Field studies are still needed to test the generality of these patterns and their relevance to N management.},
}

@article {pmid42943568,
year = {2026},
author = {Wang, Y and Li, J and Yang, X and Liu, F and Pei, G and Cui, M and Guo, Y and Jia, Y and Zhang, S and Bao, L and Cui, Y and Huang, Y},
title = {Soil Microbiome Signatures Associated with Epidemiological Heterogeneity Across Natural Plague Foci in Inner Mongolia, China.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943568},
issn = {2076-2607},
support = {2024YFC2310101//National Key Research and Development Program of China/ ; 2025ZD01900105//the National Science and Technology Major Project of China/ ; },
abstract = {Plague persistence relies on complex host-vector-environment interactions, yet the ecological contribution of soil microbiomes to natural foci remains poorly understood. We performed shotgun metagenomic sequencing of 143 soil samples across four distinct plague foci in Inner Mongolia, China, to characterize microbiome features associated with contrasting epidemiological states. Taxonomic, functional, and network analyses showed that the three active plague foci exhibited lower microbial diversity, simplified co-occurrence networks, and enrichment of specific taxa, particularly Streptomyces. Conversely, the quiescent Marmota sibirica focus harbored a more complex and interconnected microbial network with greater richness and exclusive detection of Yersinia bacteriophages, showing significant concordance with bacterial community structure. These patterns indicate distinct microbiome configurations associated with specific host and geographic settings, highlighting the need to disentangle host- and site-specific effects from broader epidemiological status. Compared with surface and deep soil, burrow-associated soil exhibited greater microbial differentiation and higher richness of bacteriophages, antimicrobial resistance genes, and virulence-associated genes, suggesting its potential as a sensitive environmental matrix for ecological monitoring. Overall, our findings identify distinct soil microbiome signatures-specifically taxonomic shifts, altered network complexity, exclusive Yersinia phage detection, and functional gene enrichment-associated with epidemiological heterogeneity across natural plague foci, providing a baseline for understanding ecological variation among endemic habitats.},
}

@article {pmid42943582,
year = {2026},
author = {Zhu, WJ and Zhang, Y and Mu, M and Pei, T and Wang, H and Liang, X and Tang, Y and Wang, C and Dai, Y and Wang, Z and Liu, Z and Yu, Z and Wang, T},
title = {Integrated Metagenomic and Metatranscriptomic Analysis Reveals Microbiome Differences Between Bisexual and Parthenogenetic Populations of Haemaphysalis longicornis.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943582},
issn = {2076-2607},
support = {32201274//National Natural Science Foundation of China/ ; BJK2023017//Science Research Project of the Hebei Education Department/ ; },
abstract = {The tick Haemaphysalis longicornis is an important vector of human and animal pathogens in East Asia that comprises both bisexual (Bis) and parthenogenetic (Par) populations. While previous studies have documented differences between these reproductive groups in genome ploidy, host transcription, and vector capacity, it remains unclear whether reproductive strategy is accompanied by systematic divergence in the tick-associated microbiome, including microbial community composition, transcriptional activities, and functional outputs. Here, we profiled laboratory-maintained Bis and Par populations using metagenomic (MG) and metatranscriptomic (MT) sequencing to integrate community composition, core taxa, functional potential, and RNA/DNA relative activity (RNA abundance normalized to corresponding DNA abundance). Par populations exhibited higher MG alpha diversity, whereas Bis populations showed higher MT alpha diversity, indicating a decoupling between the microbial DNA reservoir and the active RNA transcript community. MG functional analysis revealed that Par populations possessed a higher potential for environmental sensing, membrane transport, biofilm formation, porphyrin metabolism, and iron acquisition. Conversely, Bis populations exhibited enhanced potential in biotin metabolism, lipoic acid metabolism, and oxidative phosphorylation. MT analysis identified significant differences in a limited number of species and CAZy families, while selected KEGG pathways showed no significant variance, suggesting restricted rather than systemic transcriptional differentiation. By integrating DNA and RNA profiles, we classified 279 shared species into four activity states, revealing higher RNA/DNA relative activity ratios for thiamine metabolism in Par, and for biofilm formation, flagellar assembly, sulfur metabolism, and fatty acid degradation in Bis. Overall, Bis and Par populations exhibit distinct differences in their microbial reservoirs, transcript compositions, and relative transcriptional activities, providing critical microbiome insights into the symbiosis and vector adaptation associated with reproductive strategies in H. longicornis.},
}

@article {pmid42943597,
year = {2026},
author = {Atuahene, PY and Stevenson, B and Sang, Y},
title = {AI-Facilitated Discovery of Microbiome-Originated Antimicrobial Peptides: A Perspective on Combating Antibiotic Resistance Within Public Health and Food Safety Frameworks.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943597},
issn = {2076-2607},
support = {Evans-Allen-1013186//USDA NIFA/ ; 2020-67016-31347//NIFA AFRI/ ; 2025-38821-45500//NIFA AFRI/ ; },
abstract = {The escalating crisis of antimicrobial resistance (AMR) demands innovative therapeutic strategies beyond conventional antibiotics. Antimicrobial peptides (AMPs), particularly those originating from the human, animal, and environmental microbiome, represent a promising frontier within public health microbiology and microbial food safety. Recent advances in artificial intelligence (AI) and machine learning (ML) have revolutionized the discovery pipeline, enabling high-throughput mining of metagenomic data and de novo generation of novel peptide sequences. This perspective review synthesizes recent breakthroughs in AI-driven discovery of microbiome-originated AMPs, examines their preclinical efficacy against multidrug-resistant (MDR) pathogens under One Health and climate-sensitive frameworks and application in infectious disease treatment and discusses translational challenges including pharmacokinetics, toxicity, manufacturing scalability, and applications in food preservation and water safety. We argue that the convergence of microbiome science, deep learning, and synthetic biology positions AI-discovered AMPs as viable next-generation interventions against antibiotic resistance across human, animal, and environmental domains.},
}

@article {pmid42943600,
year = {2026},
author = {Kim, A and Moon, SB and Kim, JS and Kim, MS and Lee, Y and Kang, G and Kim, KH and Roh, H},
title = {Long-Read Metagenomics Reveals Temporal DNA Virome Dynamics and Recovers Sequences of a Major Viral Pathogen at a Sea-Cage Fish Farm.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943600},
issn = {2076-2607},
support = {//National Institute of Fisheries Science/ ; R2026058//Ministry of Oceans and Fisheries/ ; },
abstract = {Coastal sea-cage aquaculture environments support dynamic microbial communities, yet their viral components remain poorly characterized. This study profiled DNA viral-like reads recovered from total metagenomes of iron-flocculated seawater concentrates (operationally termed DNA virome) at a rock bream (Oplegnathus fasciatus) sea-cage farm off Geoje Island, Korea, at five time points between July 2024 and May 2025 using long-read Nanopore metagenomics. Multivariate analyses of DNA virome composition indicated temporal patterning in virome composition; samples collected within the cages tended to group together. The DNA virome was dominated overall by bacteriophages of abundant marine bacteria and by viruses infecting picoeukaryotic phytoplankton, and it showed marked temporal turnover during the investigated year: Micromonas-associated viruses became prominent in December, whereas Ostreococcus- and Bathycoccus-associated viruses increased during seasonal rewarming in May, suggesting that environmentally driven changes in microbial host communities may contribute to temporal virome turnover. Pelagibacter phage abundance was positively correlated with that of its potential host Pelagibacter ubique, and both Synechococcus T7-like virus and Synechococcus virus were positively correlated with Parasynechococcus marenigrum, associations that are consistent with, but do not demonstrate, taxon-specific virus-host relationships. Nanopore reads assigned to infectious spleen and kidney necrosis virus, now classified within the species Megalocytivirus pagrus 1, were recovered from samples collected in September 2024 (12,960 bp) and May 2025 (340 bp). Average nucleotide identity analysis indicated that the seawater-derived sequence was most closely related to red seabream iridovirus subtype II, the subtype predominant in Korean cultured marine fish. The seawater virome results and the bioinformatic pipelines developed in this study together may provide a non-invasive approach for tracking temporal virome dynamics and for environmental screening of viral pathogen DNA in sea-cage aquaculture.},
}

@article {pmid42943608,
year = {2026},
author = {Xie, M and Shang, H and Wang, F and Yang, J and Geer, N and Zhang, Q and Xu, X and Baolige, D},
title = {Exploratory Shotgun Metagenomic Analysis of the Fecal Microbiome and Antimicrobial-Resistance Potential in Simmental Calves with Different Diarrheal Statuses.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943608},
issn = {2076-2607},
support = {2025ZY0147//Central Government Guiding Local Science and Technology Development Fund Project/ ; 2025YFDZ0091//Inner Mongolia Autonomous Region Science and Technology Plan/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Project/ ; },
abstract = {Calf diarrhea is frequently accompanied by disruption of the gastrointestinal microbiota, but the relationships between clinical status and microbial community composition, gene-content functional potential, and antimicrobial-resistance-associated features remain incompletely characterized. This exploratory study aimed to characterize these features in calves with different diarrheal statuses using shotgun metagenomics. Six approximately 2-month-old Simmental calves from Chahar Right Middle Banner, Inner Mongolia, were included, comprising two healthy calves, two calves with mild diarrhea, and two calves with severe diarrhea. Read-based taxonomic profiling was complemented by gene-abundance-weighted taxonomic annotation, and microbial functional potential was characterized using eggNOG/COG, KEGG, and CAZy annotations, together with conservatively screened CARD-associated sequence-homology candidates. The two severe-diarrhea samples exhibited lower bacterial richness and Shannon diversity, although PCoA did not show clear separation according to clinical severity. These two samples showed high representation of Proteobacteria and Enterobacteriaceae-related taxa, particularly Escherichia-related assignments, together with lower representation of Ruminococcaceae, Faecalibacterium, and Prevotella. Gene-content profiles showed higher representation of selected functions related to transport, environmental sensing, motility, secretion, and bacterial cell-envelope processes, whereas several glycan- and complex-carbohydrate-associated functions showed lower representation. Selected CARD-associated candidates were also more abundant in the severe-diarrhea samples. Within this small exploratory cohort, the two severe-diarrhea samples therefore showed concordant taxonomic and gene-content differences; however, these observations should not be interpreted as a general severity-specific microbiome signature and require validation in larger longitudinal cohorts.},
}

@article {pmid42943609,
year = {2026},
author = {Naito, A and Kondratowicz, J and Hanger, S and Koulenti, D and Katsounas, A},
title = {Pneumocystis jirovecii Pneumonia in Critical Care: Evolving Host Populations, Diagnostic Uncertainty, and Management Controversies.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943609},
issn = {2076-2607},
abstract = {Pneumocystis jirovecii pneumonia (PCP) remains a major cause of acute respiratory failure in immunocompromised patients and is increasingly encountered in critical care outside the traditional human immunodeficiency virus (HIV) population. This narrative review examines the evolving epidemiology, diagnosis, management, prophylaxis, and prognosis of PCP in critically ill adults. The epidemiological landscape has shifted toward patients with haematological and solid malignancies, solid organ or haematopoietic stem-cell transplantation, autoimmune and inflammatory diseases, and exposure to corticosteroids or other immunosuppressive therapies. Emerging data also implicate states of immune dysregulation such as cirrhosis. Diagnosis remains challenging because Pneumocystis cannot be routinely cultured and molecular detection alone cannot reliably distinguish colonisation from active infection. Accordingly, respiratory polymerase chain reaction (PCR) results require interpretation alongside host factors, imaging, serum β-D-glucan, microscopy, and, increasingly, metagenomic sequencing. Trimethoprim-sulfamethoxazole remains first-line therapy. Lower-dose regimens may reduce toxicity while maintaining efficacy, but current evidence is largely retrospective and prospective trials are needed. The benefit of adjunctive corticosteroids in non-HIV PCP remains uncertain, with conflicting observational data and no definitive mortality benefit demonstrated in the first randomised trial. Echinocandins remain investigational adjuncts, whereas venovenous extracorporeal membrane oxygenation may provide rescue support in selected patients with refractory acute respiratory distress syndrome. Prophylaxis is effective but remains inconsistently applied in several at-risk groups. Mortality among intensive care unit (ICU) patients remains high, particularly in non-HIV PCP, and varies substantially according to underlying disease, immune phenotype, co-infection, and severity of respiratory failure. Improved risk stratification and adequately powered prospective studies are priorities.},
}

@article {pmid42943633,
year = {2026},
author = {Oshima, A and Sekiguchi, S and Uchikawa, S and Fujita, N and Yoshida, H and Yamada, S and Fujita, N and Shiwa, Y and Tsuji, A and Tanaka, N and Okada, S and Nishida, A},
title = {Shotgun Metagenomics Reveals Systemic Metabolic Pathways Promoting Organic Acid Production in Traditional Sunki Fermentation.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943633},
issn = {2076-2607},
abstract = {Salt-free lacto-fermentation is gaining attention owing to the global demand for sodium reduction. Sunki, a traditional unsalted Japanese turnip pickle, provides a unique ecological model. In this study, we investigated the microbial balance and systemic metabolic pathways that promote organic acid accumulation using shotgun metagenomics. We revealed that a high-quality sunki cluster exhibiting an abundant accumulation of organic acids (lactic acid 8.58 ± 2.42 g/L, acetic acid 2.70 ± 0.76 g/L, succinic acid 1.50 ± 0.52 g/L) and low pH (3.91 ± 0.15) was characterized by the co-dominance of specific lactic acid bacteria along with the foundational species Limosilactobacillus fermentum. This co-dominance enables the synergistic operation of both the homofermentative and heterofermentative pathways, whose functional potentials positively correlated with lactic acid (r = 0.50) and acetic acid (r = 0.48) concentrations, respectively, thereby achieving both effective preservation and flavor complexity. Furthermore, we propose a dual-pathway model for succinic acid production involving the reductive tricarboxylic acid cycle from malate and the γ-aminobutyric acid (GABA) shunt. Succinic acid positively correlated with the functional potential of the GABA shunt enzyme (puuE, r = 0.57) and negatively correlated with that of glutamate dehydrogenase (gdhA, r = -0.51), suggesting a metabolic switch redirecting glutamate flux toward the GABA shunt. This mechanism highlights an advanced ecological adaptation for pH homeostasis, emphasizing that a balanced co-dominance structure determines the quality of salt-free fermented foods.},
}

@article {pmid42943641,
year = {2026},
author = {Funada Barbosa, MR and Foro Ramos, EDS and Villanova, F and Silva, RLO and Zhang, W and Ferreira, NE and Tozetto-Mendoza, TR and Mendes-Correa, MC and Pandey, RP and Sato, MIZ and Leal, E and da Costa, AC},
title = {Molecular Characterization of Previous Unclassified Dicistroviruses in Water Reservoir in São Paulo, Brazil.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943641},
issn = {2076-2607},
abstract = {In this study, viral metagenomics was applied to identify viruses related to the Dicistroviridae family in freshwater samples collected from urban reservoirs of the state of São Paulo, Brazil. Through next-generation sequencing, five complete RNA genomes similar to Dicistroviridae were detected. These genomes range from 8.032 to 9.425 nucleotides in length, and each contains two open reading frames (ORFs) with conserved protein domains and internal ribosome entry sites (IRES) characteristic of Dicistroviridae. Phylogenetic and genetic identity analyses based on the amino acid sequences of the nonstructural (ORF1) and structural (ORF2) polyproteins suggest that these five genomes represent four putative novel species provisionally named Hydro virus 1 to Hydro virus 4. These findings enhance our understanding of the diversity and distribution of Dicistroviridae in aquatic environments.},
}

@article {pmid42943642,
year = {2026},
author = {Chen, S and Li, S and Li, Y and Zhang, Y and Duan, X and Xu, C and Qian, W and Si, H and Liu, H and Li, Z},
title = {Comparison of Fecal Microbiome of Wild Red Deer in Different Regions Reveals Geographic Differentiation.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943642},
issn = {2076-2607},
support = {20240101012JJ//Natural Science Foundation of Jilin provinces/ ; 2023YFD1302000//National Key Research and Development Program of China/ ; CARS-43//earmarked fund/ ; JLARS-2026-080204//Jilin Agricultural Research System/ ; },
abstract = {The gut microbiome plays critical roles in nutrient metabolism and host adaptation in ruminants, yet genome-level functional differences in the fecal microbiomes across geographic populations of wild red deer remain underexplored. Here, we integrated 16S rRNA gene sequencing and shotgun metagenomics to characterize the fecal microbiome of wild red deer populations in Inner Mongolia (NMG, n = 16) and Gansu Province (GS, n = 16), China. The NMG population exhibited significantly higher α-diversity and a distinct microbial community compared to GS (adjusted p < 0.05). NMG was enriched in Clostridium, Eubacterium, and Bacillus, while GS harbored higher abundances of Ruminococcus, Oscillospira, and Faecalibacterium (adjusted p < 0.05). Functional profiling revealed that the fecal microbiome in NMG showed greater functional potential associated with amino acid, pyruvate, and butanoate metabolism pathways, whereas the fecal microbiome in GS was enriched in the genetic potential of starch/sucrose metabolism, glycan degradation, and bile acid biotransformation (adjusted p < 0.05). CAZyme analysis demonstrated that GS was enriched in glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases, while NMG showed higher auxiliary activity family abundance (adjusted p < 0.05). Genome-resolved metagenomics recovered 456 species-level genome bins (SGBs), revealing that GS-enriched SGBs (Rikenellaceae, Oscillospirales CAG-272) contained CAZyme genes associated with pectin degradation, whereas NMG-enriched SGBs contained genes associated with lignin modification and chitin degradation. These findings demonstrate the significant differences in the fecal microbiomes between the two geographically distinct wild red deer populations.},
}

@article {pmid42943856,
year = {2026},
author = {Yao, P and Huang, J and Liu, W and Yuan, Q and Lv, J},
title = {Astragalus Polysaccharides Alleviate Inflammatory Damage in Murine Rheumatoid Arthritis by Modulating Th17/Treg Balance via the Gut-Joint Axis.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {20},
pages = {},
pmid = {42943856},
issn = {1420-3049},
support = {CSTB2022NSCQ-MSX0199//Natural Science Foundation of Chongqing/ ; 81903888//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Th17 Cells/drug effects/immunology/metabolism ; *T-Lymphocytes, Regulatory/drug effects/immunology/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism ; Mice ; *Astragalus Plant/chemistry ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; *Arthritis, Experimental/drug therapy/pathology/immunology ; *Joints/drug effects/pathology ; Inflammation/drug therapy ; Disease Models, Animal ; Male ; },
abstract = {Astragalus polysaccharides (APSs) have demonstrated protective effects in RA models; however, the underlying microbe-host crosstalk remains unclear. In this study, collagen-induced arthritis (CIA) was established in mice, followed by prophylactic and therapeutic APS administration. The following were then assessed: articular histopathology, splenic Th17/Treg frequencies via flow cytometry, serum and joint cytokine profiles via ELISA and immunohistochemistry, gut microbial metagenomes, and bone erosion via Safranin O-fast green staining. It was found that APS treatment significantly attenuated joint inflammation and bone destruction, rebalanced the Th17/Treg ratio, and reduced pro-inflammatory cytokines (TNF-α and IL-17) while elevating anti-inflammatory IL-10 both systemically and locally. Subsequently, fecal microbiota from APS-treated donor mice was transplanted via oral gavage into CIA recipient mice. APS reversed RA-associated gut dysbiosis by enriching Ligilactobacillus, Lactobacillus, Limosilactobacillus, and Bacteroides, and these microbial shifts closely paralleled diminished articular inflammation and preserved bone architecture. Collectively, these findings indicate that APS mitigates RA progression by reconfiguring the gut microbial ecosystem-favoring beneficial taxa while curbing pathobionts-thereby restoring intestinal homeostasis, normalizing the Th17/Treg axis, and suppressing systemic and articular inflammatory responses.},
}

Animals
*Th17 Cells/drug effects/immunology/metabolism
*T-Lymphocytes, Regulatory/drug effects/immunology/metabolism
*Polysaccharides/pharmacology/chemistry
*Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism
Mice
*Astragalus Plant/chemistry
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
*Arthritis, Experimental/drug therapy/pathology/immunology
*Joints/drug effects/pathology
Inflammation/drug therapy
Disease Models, Animal
Male

@article {pmid42944006,
year = {2026},
author = {Wyler, M and Darpel, K and Berset, R and Renzullo, S and Huber, H and Bauer, J and Peter-Egli, J and Bachofen, C and Kubacki, J},
title = {Identification, Isolation and Genomic Characterization of an Emerging Shamonda Virus Variant Associated with Bovine Disease in Switzerland.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944006},
issn = {1999-4915},
mesh = {Animals ; Cattle ; Switzerland/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Genome, Viral ; Phylogeny ; Disease Outbreaks/veterinary ; *Orthobunyavirus/genetics/isolation & purification/classification ; *Bunyaviridae Infections/veterinary/virology/epidemiology ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {In July 2026, an outbreak of a cattle illness characterized by high fever, diarrhea and reduced milk production, often affecting whole herds, was detected across several regions of northern Switzerland. To investigate the cause of the outbreak, a broad range of diagnostic methods was applied, including pathogen-specific RT-qPCRs, ELISA, serum neutralization test, virus isolation and metagenomic next-generation sequencing. A Shamonda virus (SHAV) was detected in samples from affected cattle, followed by successful virus isolation and complete genome sequencing of all three segments. Viral RNA was also detected in tissue samples from aborted calves, including the brain and spleen, supporting the need for further investigation of the virus in the context of reproductive disease. These findings document the first detection and molecular characterization of a SHAV in Switzerland and demonstrate its widespread circulation in cattle during the 2026 outbreak.},
}

Animals
Cattle
Switzerland/epidemiology
*Cattle Diseases/virology/epidemiology
*Genome, Viral
Phylogeny
Disease Outbreaks/veterinary
*Orthobunyavirus/genetics/isolation & purification/classification
*Bunyaviridae Infections/veterinary/virology/epidemiology
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing

@article {pmid42944039,
year = {2026},
author = {Socha, W and Krzysiak, MK and Moniuszko, E and Kulik, P and Tomana, J and Larska, M},
title = {Next-Generation Sequencing in Practical Wildlife Disease Investigation: Metagenomic Insights into European Bison and Gazelle Mortality and Morbidity Events.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944039},
issn = {1999-4915},
support = {101136346 EUPAHW//European Food Safety Authority/ ; },
mesh = {Animals ; *Bison/microbiology/virology ; *Metagenomics/methods ; *Animals, Wild/microbiology/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; *Animal Diseases/mortality/microbiology/epidemiology ; Metagenome ; Pasteurella multocida/genetics/isolation & purification ; *Ruminants/microbiology/virology ; },
abstract = {Wildlife disease investigations require diagnostic methods capable of detecting diverse and previously unrecognized pathogens. Metagenomic next-generation sequencing (mNGS) was applied to samples from three Dorcas gazelles (Gazella dorcas osiris) affected by sudden mortality and four European bison (Bison bonasus) with respiratory disease or necrotic balanoposthitis (NBP). No dominant bacterial species was detected in gazelles. In European bison, respiratory disease was associated with Pasteurella multocida, whereas NBP samples were dominated by Porphyromonas levii and other anaerobes. Dorcas gazelle samples contained mainly Retroviridae-related sequences of undetermined pathogenic significance. Parapoxvirus-related annotations were not confirmed by PCR, suggesting non-specific or host-related sequence similarity. Macavirus-related sequences were consistent with previous PCR findings and enabled reconstruction of an approximately 51.1 kb fragment of a divergent gammaherpesvirus genome. These findings demonstrate the value of mNGS for wildlife disease investigation and genomic surveillance, while emphasizing the need for independent validation of metagenomic taxonomic assignments.},
}

Animals
*Bison/microbiology/virology
*Metagenomics/methods
*Animals, Wild/microbiology/virology
*High-Throughput Nucleotide Sequencing
Phylogeny
*Animal Diseases/mortality/microbiology/epidemiology
Metagenome
Pasteurella multocida/genetics/isolation & purification
*Ruminants/microbiology/virology

@article {pmid42944051,
year = {2026},
author = {Ghidini, M and Sberna, G and Guerrera, LP and Maggi, F and Novazzi, F},
title = {The Gut Virome in Gastrointestinal Cancers: Mechanisms, Biomarkers, and Translational Opportunities.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944051},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Neoplasms/virology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Animals ; Bacteriophages ; Gastrointestinal Tract/virology ; Translational Research, Biomedical ; Biomarkers, Tumor ; Oncogenic Viruses ; Bacteria/virology ; },
abstract = {The gastrointestinal tract contains a dense multi-kingdom ecosystem in which bacteria, fungi, archaea, viruses, the mucosa, and the immune system interact. Although cancer microbiome research has focused mainly on bacteria, the gut virome dominated by bacteriophages may influence gastrointestinal carcinogenesis by reshaping bacterial communities, transferring functional genes, modulating inflammation, and altering treatment response. The strongest evidence comes from colorectal cancer, where multiple cohorts show altered phage diversity, temperate-phage enrichment, disrupted phage-bacteria networks, and reproducible stool-based diagnostic signals. Emerging studies in pancreatic cancer, esophageal adenocarcinoma, hepatocellular carcinoma, and precursor lesions suggest that virome disruption extends beyond colorectal cancer, although evidence remains uneven. Classic oncogenic viruses, including Epstein-Barr virus and hepatitis viruses, provide complementary examples of direct viral carcinogenesis in digestive organs. Anelloviruses are widespread in healthy individuals and are not established causes of cancer, but their abundance and composition may reflect immune status, inflammation, tissue injury, and altered host viral ecology. Virome-related interventions remain clinically immature: fecal microbiota transplantation has reached small phase I/II studies in gastrointestinal cancers, whereas phage, fecal-filtrate, and fecal virome approaches remain preclinical or non-oncology; direct oncolytic viruses have reached late-phase testing. Major barriers include viral dark matter, specimen and assay heterogeneity, disease-related confounding, limited external validation, and weak causal evidence. Standardized, mechanistically anchored, multi-kingdom studies are needed to establish clinical utility.},
}

Humans
*Gastrointestinal Neoplasms/virology/therapy
*Virome
*Gastrointestinal Microbiome
Animals
Bacteriophages
Gastrointestinal Tract/virology
Translational Research, Biomedical
Biomarkers, Tumor
Oncogenic Viruses
Bacteria/virology

@article {pmid42944114,
year = {2026},
author = {Ma, Q and Tharwat, M and Ullah, A and Liu, J and Alkheraif, AA and Khan, MZ},
title = {Integrating Host Transcriptomics and Metagenomics in the Periparturient Dairy Cow: From Molecular Signatures to Host-Microbiome Interfaces.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944114},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {The periparturient or transition period-roughly three weeks before to three weeks after calving-compresses the most severe metabolic, endocrine and immunological demands of the production cycle into a few weeks and accounts for most clinical disease and involuntary culling in dairy herds. Conventional surveillance relies on downstream indicators-non-esterified fatty acids, β-hydroxybutyrate, calcium and acute-phase proteins-that document failed adaptation without resolving its regulatory origins. Two omics platforms now close that gap. Transcriptomics shows that the liver, adipose tissue, mammary gland, endometrium, rumen epithelium and circulating leukocytes each execute a distinct, temporally ordered program organized around lipid mobilization, gluconeogenesis, endoplasmic reticulum stress, redox defense and inflammatory resolution, layered over a regulatory tier of non-coding RNAs. Metagenomics shows in parallel that rumen, hindgut, uterine, vaginal, teat-apex and colostrum communities are restructured by parturition and by the dietary shift into lactation, with reproducible dysbiotic signatures accompanying ketosis, fatty liver, metritis, endometritis and intramammary infection. Critically, the two layers are mechanistically coupled: microbial short-chain fatty acids, secondary bile acids, purine derivatives and amino acids reprogram hepatic and immune cell transcription, while host lipolysis, inflammation and mineral demand reshape community structure. This review synthesizes both groups of literature within a single framework, formalizes five host-microbiome interfaces supported by paired measurements and identifies the biomarker, nutritional and genetic-selection opportunities that emerge only when host and microbial evidence are read together.},
}

@article {pmid42944646,
year = {2026},
author = {Lynggaard, C and Bodawatta, KH and de Fraga, R and Martins, VCC and Aleixo, A and Tavares, VDC and Trevelin, LC and Gastauer, M and Bohmann, K},
title = {Active Filtration of Airborne eDNA for Vertebrate Surveys in Tropical Caves.},
journal = {Molecular ecology resources},
volume = {26},
number = {8},
pages = {},
doi = {10.1111/1755-0998.70218},
pmid = {42944646},
issn = {1755-0998},
support = {CF21-0411//Carlsbergfondet/ ; R100603.NNL.04//Instituto Tecnológico Vale/ ; R100603.CR.04//Instituto Tecnológico Vale/ ; VIL41390//Villum Fonden/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313429/2025-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 310865/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441201/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Caves ; Brazil ; *Vertebrates/classification/genetics ; *DNA, Environmental/genetics/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Extrachromosomal DNA ; *Filtration/methods ; Tropical Climate ; *Metagenomics/methods ; },
abstract = {Hidden from sunlight, caves are remarkable subterraneous ecosystems that host a wide range of animals, including unique species. Conventional cave biodiversity surveys can be physically challenging, disturb sensitive vertebrate communities, or require animal collection. Here we evaluate the use of metabarcoding of airborne environmental DNA (eDNA) as a non-invasive method for surveying cave vertebrates. We collected 55 samples by filtering air for 24 h at three light zones (outside, and in twilight and dark zones inside the cave) in three tropical caves in Amazonian Brazil. Using two metabarcoding primer sets targeting mammal and vertebrate DNA, we detected 123 wild vertebrate taxa encompassing mammals, birds, amphibians, and a reptile, of which 74 were identified to genus level. Genus richness in the twilight zone was significantly higher than outside the caves. Vertebrate diversity was also highest in the twilight zone, and community composition differed significantly between light zones and caves. Mammals and amphibians were mostly detected in the twilight and dark zones, whereas birds were more frequently detected outside the cave and in the twilight zone. While preliminary, our results show that caves with smaller entrances yielded more homogeneous communities in the twilight and dark zones. We detected eight of the 13 bat species and one of the four amphibian species recorded in previous surveys, while also detecting taxa not previously recorded in the caves, demonstrating complementarity with conventional surveys. As airborne eDNA requires minimal human presence in cave interiors, it reduces disturbance to sensitive fauna, lowers safety risks to surveyors, and offers a scalable method to complement conventional cave biodiversity surveys in tropical regions.},
}

Animals
*Caves
Brazil
*Vertebrates/classification/genetics
*DNA, Environmental/genetics/isolation & purification
*DNA Barcoding, Taxonomic/methods
Biodiversity
Extrachromosomal DNA
*Filtration/methods
Tropical Climate
*Metagenomics/methods

@article {pmid42786310,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Li, J and Guo, X and Xu, H and Wang, Y and Tang, H and Han, JJ},
title = {Multi-modality profiling identifies Neisseria flavescens as a central geroprotective oral commensal in humans.},
journal = {Nature aging},
volume = {6},
number = {10},
pages = {2202-2217},
pmid = {42786310},
issn = {2662-8465},
support = {32330017//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82361148130//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025YFA1805300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2024YFF0729200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2025YFC3409300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; L2604004//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; GZC20230084//China Postdoctoral Science Foundation/ ; },
mesh = {*Neisseria/physiology ; Humans ; *Aging/physiology ; Animals ; Mice ; Caenorhabditis elegans/physiology ; *Mouth/microbiology ; Multiomics ; Metagenome ; *Senotherapeutics ; Gastrointestinal Microbiome ; Biosynthetic Pathways ; Liver/metabolism ; Probiotics/administration & dosage ; Akkermansia/physiology ; Bifidobacterium/physiology ; Lactobacillaceae/physiology ; Random Allocation ; Male ; Mice, Inbred C57BL ; Tongue/microbiology ; },
abstract = {Aging is accompanied by progressive physiological decline, yet the microbiome determinants that modulate aging remain unclear. Here, we identify Neisseria flavescens (Nf) as an oral commensal associated with decelerated aging in humans. Using AURORA, a generative multi-modality framework, we developed multi-modality aging clocks, performed in silico screening for age-gap-reducing interventions and predicted Nf as a top hit. In silico perturbations linked increased Nf abundance to favorable physiological signatures, beneficial gut taxa and biosynthesis of beneficial metabolites. We isolated two Nf strains and validated their production of beneficial metabolites. Functional assays demonstrated that live Nf extended lifespan and healthspan in Caenorhabditis elegans. In aged mice, heat-killed Nf supplementation restored the serum metabolome, liver transcriptome and gut microbiome toward younger states. By establishing an AI-driven intervention discovery engine and identifying Nf as a geroprotective microorganism, these findings highlight the oral microbiome as an underestimated axis of systemic aging and a candidate for geroprotective interventions.},
}

*Neisseria/physiology
Humans
*Aging/physiology
Animals
Mice
Caenorhabditis elegans/physiology
*Mouth/microbiology
Multiomics
Metagenome
*Senotherapeutics
Gastrointestinal Microbiome
Biosynthetic Pathways
Liver/metabolism
Probiotics/administration & dosage
Akkermansia/physiology
Bifidobacterium/physiology
Lactobacillaceae/physiology
Random Allocation
Male
Mice, Inbred C57BL
Tongue/microbiology