@article {pmid42526577,
year = {2026},
author = {Yang, W and Teng, Y and Yang, Z and Song, X and He, L and Liu, Y and Tan, W and An, H and Shi, P and Hu, C and Ao, L and Guo, H},
title = {Chronic paternal exposure to low-dose OBS reprograms progeny's intestinal cholesterol metabolism and increases IBD susceptibility.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128846},
doi = {10.1016/j.envpol.2026.128846},
pmid = {42526577},
issn = {1873-6424},
abstract = {Sodium p-perfluorous nonenoxybenzenesulfonate (OBS) as a novel alternative to perfluorooctane sulfonate (PFOS) has been extensively used in numerous manufacturing processes, contributing to increasingly grim environmental contamination. Abundant evidence has highlighted the endocrine and metabolic-disrupting properties of OBS, establishing it as an unsafe surrogate for PFOS. However, the intergenerational toxicity of OBS, particularly the impact of paternal exposure on offspring, remains unexplored. Using a murine model, we demonstrated that chronic paternal exposure to low-dose OBS led to gut barrier disruption and heightened susceptibility to dextran sodium sulfate (DSS)-induced colitis in offspring. Through integrated multi-omics analyses including DNA methylome, transcriptome, metagenome, ChIP-seq and metabolome, we uncovered that OBS exposure induced hypermethylation of the Clock promoter in paternal sperm. This epigenetic modification was identified as the causal factor underlying the downregulation of the CLOCK-ABCA1 axis and consequent impairment of cholesterol efflux in offspring colon. Validation using multicolor immunohistochemistry and single-cell transcriptomics in clinical cohorts further substantiated the involvement of the CLOCK-ABCA1 pathway, not only in the disruption of intestinal homeostasis but also in inflammatory bowel disease (IBD) pathogenesis. Collectively, our study provides insight into the intergenerational toxicity of emerging PFAS, which also facilitates the identification of potential targets for the early warning and therapeutic intervention of IBD.},
}

@article {pmid42526667,
year = {2026},
author = {Cui, P and Zhang, H and Hu, T and Huang, Q and Hu, X and Wang, Q and Diwan, AD and Wang, T and Zhao, X and Lu, S and Chen, X},
title = {The Metabolite indole-3-acetic acid of Bacteroides ovatus ameliorates ovariectomy-induced bone loss by activating AhR and inhibiting oxidative stress.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.07.050},
pmid = {42526667},
issn = {1873-4596},
abstract = {Postmenopausal osteoporosis represents a systemic skeletal condition distinguished by diminished bone mass and heightened skeletal fragility. Emerging evidence has highlighted a significant relationship between bone metabolism and disturbances in gut microbiota (GM) homeostasis. However, the exact mechanisms by which GM dysbiosis contributes to postmenopausal osteoporosis remain insufficiently understood. Herein, integrating weighted gene co-expression network analysis with machine learning, a notable depletion of Bacteroides ovatus (B. ovatus) was identified in the GM of women with postmenopausal osteoporosis. Metagenomic sequencing further validated the reduced abundance of B. ovatus in ovariectomized (OVX) mice. Notably, live B. ovatus (LBO), but not heat-killed B. ovatus (KBO), effectively mitigated bone loss in OVX mice and restored intestinal mucosal barrier integrity. Both untargeted and targeted metabolomic profiling revealed substantial alterations in tryptophan metabolism in OVX mice, particularly a significant reduction in indole-3-acetic acid (IAA). Oral supplementation with IAA notably alleviated bone loss in OVX mice. Mechanistically, IAA stimulated AhR, enhancing NQO1 expression, reducing intracellular ROS buildup, and ultimately suppressing osteoclast differentiation and bone resorption. This investigation demonstrates, for the first time, the protective effects of B. ovatus and its metabolite IAA in counteracting estrogen deficiency-induced bone loss and may present a promising microbial-targeted strategy for osteoporosis prevention.},
}

@article {pmid42526894,
year = {2026},
author = {O'Halloran, DM},
title = {STRONGYLID COINFECTIONS IN SYMPATRIC CHIMPANZEES AND GORILLAS FROM THE REPUBLIC OF THE CONGO REVEALED BY FECAL METAGENOMICS.},
journal = {The Journal of parasitology},
volume = {112},
number = {4},
pages = {443-450},
doi = {10.1645/25-102},
pmid = {42526894},
issn = {1937-2345},
mesh = {Animals ; *Gorilla gorilla/parasitology ; *Feces/parasitology ; Congo/epidemiology ; *Pan troglodytes/parasitology ; *Ape Diseases/parasitology/epidemiology ; Metagenomics ; *Coinfection/veterinary/parasitology/epidemiology ; Female ; Sympatry ; *Nematode Infections/veterinary/parasitology/epidemiology ; *Strongylida/genetics/classification/isolation & purification ; Male ; *Intestinal Diseases, Parasitic/parasitology/veterinary/epidemiology ; Metagenome ; },
abstract = {Soil-transmitted strongylid nematodes are common intestinal parasites of African great apes, yet most surveys have relied on microscopy or targeted PCR assays that are limited in taxonomic breadth and comparability across hosts. I reanalyzed 46 publicly available shotgun fecal metagenomes from sympatric central chimpanzees (Pan troglodytes troglodytes; n = 18) and western lowland gorillas (Gorilla gorilla gorilla; n = 28) in the Goualougo Triangle, Nouabalé-Ndoki National Park, Republic of the Congo, to test whether host species structures genus-level strongylid community composition and relative read signal. Non-host reads were classified against a custom strongylid-focused database targeting 4 genera repeatedly reported from African apes: Ancylostoma, Necator, Oesophagostomum, and Trichostrongylus. All 4 focal genera were detected in every library under baseline filtering, and multi-genus detection remained robust under increasingly stringent read-count thresholds. However, host species differed strongly in community composition. Chimpanzee libraries had relatively even genus-level profiles, whereas gorilla libraries were consistently Necator-dominated. Gorillas also had substantially higher relative strongylid read abundance. The results show that shotgun metagenomic reanalysis can recover host-structured strongylid community signals from wildlife samples and can complement targeted parasitological surveys in conservation and One Health surveillance.},
}

Animals
*Gorilla gorilla/parasitology
*Feces/parasitology
Congo/epidemiology
*Pan troglodytes/parasitology
*Ape Diseases/parasitology/epidemiology
Metagenomics
*Coinfection/veterinary/parasitology/epidemiology
Female
Sympatry
*Nematode Infections/veterinary/parasitology/epidemiology
*Strongylida/genetics/classification/isolation & purification
Male
*Intestinal Diseases, Parasitic/parasitology/veterinary/epidemiology
Metagenome

@article {pmid42527912,
year = {2026},
author = {Tiefensee, M and Weng, N and Ohlsson, JA and Westerholm, M},
title = {Metagenomic and cultivation-based description of a syntrophic butyrate-oxidizing bacterium from a thermophilic and high-ammonia biogas process.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42527912},
issn = {1471-2180},
mesh = {Oxidation-Reduction ; Phylogeny ; *Ammonia/metabolism ; *Butyrates/metabolism ; *Metagenomics/methods ; *Biofuels/microbiology ; Metagenome ; Methane/metabolism ; Acetates/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Ammonia inhibition in anaerobic digestion can lead to butyrate accumulation and reduced methane yield. Despite the importance of syntrophic butyrate oxidation in mitigating this effect, the microorganisms and interactions involved under high-ammonia conditions remain poorly understood. Here, we combine metagenomics and cultivation studies to describe a novel ammonia-tolerant syntrophic butyrate-oxidizing bacterium and its interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens enriched from a high-ammonia, thermophilic biogas process.

RESULTS: The enrichment culture degraded butyrate at rates of 0.12-0.47 mmol/day. Amplicon sequencing and phylogenetic analyses of a retrieved metagenome-assembled genome (MAG) assigned the putative syntrophic butyrate-oxidizing bacterium (SBOB) to the genus Syntrophothermus, for which we propose the provisional species name 'Candidatus Syntrophothermus ammoniitolerans'. Metagenomic analyses revealed the genomic potential for β-oxidation and essential electron transfer pathways associated with syntrophic energy conservation. Furthermore, one additional MAG (MAG9) possessed a complete β-oxidation pathway but lacked key genes associated with reverse electron transfer, making its role as a SBOB uncertain. Acetate produced during butyrate oxidation was further oxidized by syntrophic acetate-oxidizing bacteria and ultimately converted to methane by hydrogenotrophic methanogens, illustrating a tightly coupled metabolic network that supports butyrate degradation under high-ammonia conditions. Three methanogenic MAGs, affiliated with the genera Methanoculleus and Methanothermobacter, were identified as potential hydrogen- or formate-consuming partners.

CONCLUSIONS: Together, these results identify a novel syntrophic butyrate-oxidizing candidate that enables butyrate degradation under high-ammonia conditions via tightly coupled interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens, sustaining methane production under ammonia stress.},
}

Oxidation-Reduction
Phylogeny
*Ammonia/metabolism
*Butyrates/metabolism
*Metagenomics/methods
*Biofuels/microbiology
Metagenome
Methane/metabolism
Acetates/metabolism
Anaerobiosis
*Bacteria/genetics/metabolism/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid42528583,
year = {2026},
author = {Aili, A and Deng, H and Zhang, H and Wang, W and Pan, L},
title = {Amiodarone-induced granulomatous lung injury mimicking organizing pneumonia: a case report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1848041},
pmid = {42528583},
issn = {1663-9812},
abstract = {BACKGROUND: Amiodarone-induced pulmonary toxicity (APT) has a broad clinical spectrum, and its radiologic and histopathologic appearances vary considerably. Granulomatous lung injury, however, is rarely described and may be confused with organizing pneumonia (OP) or infection.

CASE PRESENTATION: An elderly man who had been receiving 5-month amiodarone therapy developed a 3-week history of pleuritic chest pain and progressive dyspnea. Chest computed tomography (CT) demonstrated bilateral ground-glass opacities and subpleural-predominant consolidations, with scattered reversed halo signs raising the possibility of an OP-like pattern. A positive serum Cryptococcal antigen (CrAg) result obtained at an outside hospital led to empiric antifungal therapy, but the patient did not improve. After admission, bronchoalveolar lavage (BAL) revealed lymphocytosis, and metagenomic testing did not detect Cryptococcus or other pathogens; fungal stains on biopsy specimens were also negative. Percutaneous lung biopsy showed focal non-necrotizing granulomas with prominent eosinophilic inflammation. After discontinuation of amiodarone and initiation of systemic corticosteroid therapy, his symptoms improved rapidly and follow-up imaging demonstrated interval regression.

CONCLUSION: This case illustrates that an OP-like CT pattern may mask an uncommon granulomatous phenotype of amiodarone-related lung injury. A positive fungal biomarker should therefore be weighed against the microbiological work-up, tissue findings, medication history, and treatment response before infection is accepted as the final diagnosis.},
}

@article {pmid42528818,
year = {2026},
author = {Chen, M and Wang, X and Peng, G and Jiang, L and Liang, H and Cui, P},
title = {Gut microbiota induces immune-related alterations in gene expression, RNA methylation, and metabolism in glioblastoma revealed by single-cell and spatial multi-omics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1899954},
pmid = {42528818},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; RNA Methylation ; *Brain Neoplasms/metabolism/genetics/immunology/microbiology ; Mice ; Multiomics ; *Glioblastoma/metabolism/genetics/immunology/microbiology ; Humans ; *Gene Expression Regulation, Neoplastic ; Epitranscriptome ; Single-Cell Analysis ; Spatial Transcriptomics ; Epigenesis, Genetic ; Tumor Microenvironment/immunology ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling ; },
abstract = {Glioblastoma (GBM) is a highly malignant tumor with poor prognosis and limited effective treatment options. Emerging studies have suggested that gut microbiota may influence glioma progression through the gut-brain axis, though the precise mechanisms remain largely unclear. In this study, we employed a comprehensive multi-omics approach-encompassing single-cell transcriptomics, spatial transcriptomics, metagenomics, metabolomics, and m6A-seq-to investigate how antibiotic-induced gut microbiota disruption impacts glioma progression in a mouse model. Gene expression analysis revealed significant alterations in antibiotics-treated mice (ABX-treated mice), including reduced expression of Epha6 and upregulated expression of Tead1, key genes associated with glioma progression and immune modulation. Spatial transcriptomics and metabolomic profiling identified reduced methionine levels in gliomas of ABX-treated mice, linking gut-derived metabolite changes to epigenetic regulation via m6A methylation. Single-cell RNA sequencing further demonstrated an increased proportion of AC-like cells, disrupted intercellular communication, and aberrations in the EPHA and NRXN signaling pathways. These findings highlight the interplay between gut microbiota, immune signaling, and epigenetic modifications in shaping the glioma microenvironment. This study advances our understanding of the gut-brain axis in glioma biology and proposes the EPHA pathway as a promising biomarker for the immune-mediated modulation of tumor progression, thereby providing new insights into the role of the gut-brain axis in glioma regulation.},
}

Animals
*Gastrointestinal Microbiome/immunology/drug effects
RNA Methylation
*Brain Neoplasms/metabolism/genetics/immunology/microbiology
Mice
Multiomics
*Glioblastoma/metabolism/genetics/immunology/microbiology
Humans
*Gene Expression Regulation, Neoplastic
Epitranscriptome
Single-Cell Analysis
Spatial Transcriptomics
Epigenesis, Genetic
Tumor Microenvironment/immunology
Single-Cell Gene Expression Analysis
Gene Expression Profiling

@article {pmid42528820,
year = {2026},
author = {Cui, B and Li, H and Cui, R and Jiang, X and Jin, X},
title = {Metabolic dysfunction-associated steatotic liver disease with alcohol- and iron overload-related cholestatic liver injury: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805756},
pmid = {42528820},
issn = {2296-858X},
abstract = {A 38-year-old woman with a >10-year history of heavy alcohol consumption presented with acute-onset jaundice and massive hepatomegaly. Laboratory tests revealed a cholestatic-pre-dominant liver injury pattern with extreme γ-glutamyl transferase elevation (>1,000 U/L) and marked hyperferritinemia (>1,500 ng/ml). Imaging excluded extrahepatic biliary obstruction. Liver biopsy demonstrated steatohepatitis with ductular reaction and stage F2 fibrosis. Metagenomic next-generation sequencing (mNGS) was negative for infectious pathogens. After alcohol abstinence, metabolic intervention, a short empiric corticosteroid course, and supportive therapy, liver function gradually improved. This case highlights a reversible cholestatic phenotype in alcohol-associated steatotic liver injury with metabolic dysfunction and suspected secondary iron overload.},
}

@article {pmid42528906,
year = {2026},
author = {Zhang, M and Wang, S and Gao, J and Jie, J and Yu, Q and Li, D and Song, L and Fan, X},
title = {Type VI secretion system completeness shapes evolutionary trade-offs in the Acinetobacter baumannii resistome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1867466},
pmid = {42528906},
issn = {1664-302X},
abstract = {The rapid global dissemination of multidrug-resistant Acinetobacter baumannii poses a critical threat to public health, yet the role of the Type VI Secretion System (T6SS)-a contact-dependent interbacterial weapon-in shaping the antimicrobial resistome remains poorly understood. Here, we integrated clinical metagenomics and large-scale comparative genomics to investigate the association between T6SS completeness and resistome organization. T6SS status was not independently associated with overall antimicrobial resistance genes (ARGs) burden or alpha diversity after controlling for shared evolutionary history and genomic background. However, T6SS completeness was associated with distinct resistome composition across multiple lineages. T6SS-complete genomes were preferentially enriched in chromosomally associated resistance determinants, including intrinsic β-lactamases and multidrug efflux systems, alongside tighter genomic co-localization between ARGs and mobile genetic elements (MGEs), consistent with localized chromosomal integration of resistance-associated mobile elements. This foundational prerequisite was supported by experimental validation of efficient T6SS-dependent interbacterial killing in a hyper-resistant lineage. Conversely, T6SS-incomplete genomes were significantly enriched in highly potent exogenously acquired ARGs, including blaNDM-1 and blaCTX-M, frequently alongside structurally uncoupled MGEs. Together, these findings are consistent with an evolutionary trade-off model in which T6SS-complete and T6SS-incomplete A. baumannii populations exhibit distinct resistance acquisition strategies and contrasting genomic contexts of horizontal gene transfer, thereby contributing to divergent resistome organization.},
}

@article {pmid42528952,
year = {2026},
author = {Liu, X and Cheng, W and Li, C and Dessie, W and Qi, C and Ayaz, M and Xu, X},
title = {Integrated metagenomic and metabolomic insights into microbial metabolic reprogramming in the rhizosphere of the invasive plant Praxelis clematidea under low-temperature stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852122},
pmid = {42528952},
issn = {1664-302X},
abstract = {A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.},
}

@article {pmid42529042,
year = {2026},
author = {Ma, X and Guo, S and Feng, Y and Su, M and Wei, F and Liu, X},
title = {Rapid clinical validation of an RNA/DNA hybrid tagmentation-based metagenomic workflow for respiratory RNA virus detection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1849991},
pmid = {42529042},
issn = {1664-302X},
abstract = {BACKGROUND: In the post-pandemic era, co-circulation of multiple respiratory RNA viruses has increased the need for timely diagnosis and reliable recognition of mixed infections. Although reverse transcription quantitative polymerase chain reaction (RT-qPCR) remains the clinical standard for respiratory virus detection, its target-restricted design limits the detection of unexpected or coinfecting pathogens. Conventional metagenomic next-generation sequencing (mNGS) provides hypothesis-free pathogen detection, but routine clinical use is still limited by long turnaround times and complex library preparation. Therefore, a sequencing-based strategy that preserves broad, unbiased detection while offering a simplified workflow and clinically acceptable turnaround time is needed.

METHODS: We optimized and clinically validated CATCH, a rapid RNA/DNA hybrid tagmentation-based mNGS workflow, for respiratory RNA virus detection. Analytical performance was assessed using standardized reference materials, including SARS-CoV-2 and influenza A virus, with evaluations of sensitivity, reproducibility, short-term stability, and host-background interference. Clinical validation was performed in retrospective and prospective respiratory infection cohorts, and assay performance was benchmarked against RT-qPCR and multiplex PCR. The same sequencing data were further examined for semiquantitative viral assessment, coinfection detection, and exploratory respiratory microbial profiling.

RESULTS: The optimized CATCH workflow shortened library preparation to approximately 3 h, with about 35 min of hands-on time, enabling same-day sequencing-based diagnostics. Broad detection was achieved across seven clinically relevant respiratory RNA viruses. Sequencing-derived viral abundance showed a significant overall correlation with viral input concentration, supporting semiquantitative interpretation, although virus- and subtype-specific variability highlighted biological constraints on absolute quantification. Using SARS-CoV-2 and influenza A virus as representative targets, CATCH achieved clinically actionable limits of detection with high reproducibility and stability. In clinical cohorts, CATCH showed high concordance with routine molecular assays and identified mixed respiratory infections missed by targeted testing. Exploratory analyses also demonstrated the feasibility of respiratory microbial community profiling from the same sequencing dataset.

CONCLUSION: CATCH is a rapid and clinically deployable RNA virus mNGS workflow that helps bridge targeted molecular diagnostics and conventional metagenomic sequencing. By combining broad pathogen detection, coinfection identification, and semiquantitative assessment within a streamlined workflow, CATCH provides a practical framework for comprehensive respiratory RNA virus diagnosis and syndromic surveillance.},
}

@article {pmid42529077,
year = {2026},
author = {Zhao, X and McCarter, SJ and Gupta, VK and Grant, KM and St Louis, EK and Kantarci, K and Savica, R and Hill, M and Vuong, HE and Staley, C and Boeve, BF and Ross, OA and Teigen, LM and Sung, J},
title = {Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1834726},
pmid = {42529077},
issn = {2813-4338},
abstract = {BACKGROUND: Lewy body disease (LBD) is a progressive neurodegenerative a-synucleinopathy, whereas isolated REM sleep behavior disorder (iRBD) is recognized as a prodromal stage of LBD. Although growing evidence implicates the gut-brain axis in neurodegeneration, the taxonomic and functional roles of the gut microbiome across the prodromal-to-symptomatic LBD continuum remain poorly defined.

METHODS: Here, we performed shotgun metagenomic sequencing on stool samples from 25 patients with LBD (10 mild cognitive impairment due to LBD [MCI-LB] and 15 dementia with Lewy bodies [DLB]), 10 individuals with iRBD, and their household matched cohabitant controls to characterize disease-associated microbial alterations while minimizing environmental confounding.

RESULTS: Despite no significant differences in global microbial diversity, we identified convergent shifts in microbial taxa, metabolic pathways, and gene families across disease stages. Both LBD and iRBD showed increased abundance of microbial taxa potentially associated with gut barrier disruption, as well as higher abundance of functional pathways related to lipopolysaccharide biosynthesis. LBD showed lower abundance of pathways related to complex carbohydrate fermentation, and both groups showed lower abundance of pathways associated with neurotransmitter-related metabolism. In particular, pathways and gene families associated with starch degradation were reduced in LBD, and those associated with histidine-to-glutamate/ GABA metabolism were reduced in both groups.

DISCUSSION: These exploratory findings represent the first high-resolution, shotgun metagenomic characterization of gut microbiome alterations across the LBD continuum, highlighting functional patterns that may serve as candidate markers of disease progression in future longitudinal and mechanistic studies.},
}

@article {pmid42529131,
year = {2026},
author = {Huang, B and Chen, Z and Xue, W and Pu, Z and Zhou, Y and Koay, SSN and Kong, P and Zhao, Y and Tai, L and Lan, Z and Xian, Y and Chen, AJ},
title = {Synergistic Anti-Obesity Effect of Akkermansia muciniphila AKM Lab-01 and Garcinia cambogia Extract via Gut Microbiota Remodeling in Diet-Induced Obese Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {8},
pages = {e72140},
pmid = {42529131},
issn = {2048-7177},
abstract = {Obesity is a global health crisis driven by complex metabolic dysregulation. Although Akkermansia muciniphila (AKK) has emerged as a promising next-generation probiotic for metabolic health, its synergistic potential with natural anti-obesity compounds remains largely unexplored. Here, we evaluated the combined administration of pasteurized A. muciniphila (AKM Lab-01) and Garcinia cambogia extract (GCE) in a mouse model of high-fat diet-induced obesity. The combination treatment significantly ameliorated obesity-related phenotypes, including reduced body weight, decreased fat mass, improved serum metabolic parameters, and attenuated adipose tissue inflammation. Adipose tissue transcriptomic profiling revealed enhanced lipid catabolism and downregulation of pro-inflammatory pathways. Metagenomic sequencing showed marked gut microbiota remodeling, characterized by increased abundance of Lactococcus and decreased levels of Clostridium and Eisenbergiella. Integrated correlation analysis linked these microbial shifts to transcriptional reprogramming in adipose tissue. Using a 3 T3-L1 adipocyte model, we further confirmed that Lactococcus plays a potential role in regulating lipid metabolism and inflammation. Collectively, these findings strongly suggest that the AKM Lab-01 and GCE combination may exert synergistic anti-obesity effects via a gut microbiota-host metabolic axis, supporting its potential as a novel synbiotic strategy for obesity management.},
}

@article {pmid42529303,
year = {2026},
author = {Wang, W and Cen, C and Yang, J},
title = {Dominant Role of Habitat Transformation in Driving the Divergence of Health-Risk Related Microbial Functional Genes in Karst Mountain Parks: A Metagenomic Study.},
journal = {Ecology and evolution},
volume = {16},
number = {8},
pages = {e74112},
pmid = {42529303},
issn = {2045-7758},
abstract = {The transformation of natural forests into urban parks has had a profound impact on subterranean ecosystems. Nevertheless, the underlying mechanisms by which this land use change affects human health through alterations in soil microbial functional genes remain to be elucidated. Focusing on a karst mountain park in Guiyang, China, we used metagenomic sequencing to compare the abundance and composition of antibiotic resistance genes (ARGs), pathogen-host interaction genes (PHIs), and virulence factor genes (VFs) between remnant forests and artificial green spaces, and examined how plant diversity and soil chemometrics drove their variation. Habitat type emerged as the strongest driver of gene composition. PHIs and VFs were more abundant in remnant forests and positively correlated with native plant diversity, while ARGs were enriched in artificial green spaces. All three gene categories showed positive correlations with soil nitrogen content in artificial green spaces. Remnant forests harbored microbial functions linked to complex plant-microbe interactions, whereas intensive management in artificial green spaces selects for antibiotic resistance and nutrient-adaptive genes. These findings reveal distinct health risks across habitats, suggesting that differentiated park management strategies are needed to mitigate public health risks while maintaining ecological sustainability.},
}

@article {pmid42529392,
year = {2026},
author = {Cambara, JCO and Cuber, P and Khattak, F and Lebre, PH and Galgano, S and Houdijk, J and Smallman, D and Estridge, P and Allen, MJ and Short, F and Sutcliffe, M and Mkrtchyan, HV},
title = {Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868730},
pmid = {42529392},
issn = {1664-302X},
abstract = {INTRODUCTION: Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised.

METHODS: We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments - a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse - to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants.

RESULTS: Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota.

DISCUSSION: Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.},
}

@article {pmid42529424,
year = {2026},
author = {McCammon, SD and Chen See, JR and Wright, JR and Anderson, SLC and Russell, TJ and Lamendella, RM and Firneno, TJ},
title = {Spatial organization of cutaneous microbiomes reveals putative microbial contributions to host chemical defenses in the American toad.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1860796},
pmid = {42529424},
issn = {1664-302X},
abstract = {Chemical defenses are widely evolved throughout the tree of life. Animals can exploit mutualisms with toxin-producing symbionts as a mechanism of chemical defense. However, this has only begun to be explored in depth, and how these mutualisms may relate to how animals synthesize or acquire their toxins has been even less studied. True toads synthesize their own toxins and offer a novel system to study the interplay between the cutaneous skin microbiome and how it may contribute to toxin synthesis or biotransformation. In this study, we investigated whether the cutaneous microbiome of the American toad (Anaxyrus americanus) was spatially structured across body surfaces in relation to toxin storage and secretion and assessed whether microbial communities exhibit distinctive bacterial taxa involved in toxin-related biochemical pathways. To do this, we used 16S rRNA gene sequencing, diversity metrics, differential abundance comparisons, functional pathway predictions, and ecological interaction networks. Our results indicate that the dorsal and ventral cutaneous surfaces harbor distinct bacterial assemblages, with the dorsal surface being enriched for bacterial taxa associated with the predicted potential to degrade or transform structurally complex organic compounds. This study provides insights into how the toad skin microbiome may contribute to the chemical defenses of toads and could reveal novel aspects of host-microbiome interactions in amphibians.},
}

@article {pmid42529500,
year = {2026},
author = {Li, L and Wang, D and Huang, C},
title = {Enterococcus faecium pneumonia diagnosed by metagenomic next-generation sequencing in a patient with chronic obstructive pulmonary disease.},
journal = {IDCases},
volume = {45},
number = {},
pages = {e02695},
pmid = {42529500},
issn = {2214-2509},
abstract = {Enterococcus faecium is a rare pathogen in community-acquired pneumonia (CAP), and its diagnosis is challenging, particularly when prior antibiotic therapy hampers isolation by conventional culture. We report a 72-year-old man with a 6-year history of chronic obstructive pulmonary disease (COPD) who presented with fever, cough, and progressive dyspnea. Despite empirical broad-spectrum antibiotics (piperacillin-tazobactam followed by imipenem-cilastatin), his condition deteriorated into acute respiratory distress syndrome (ARDS) requiring invasive mechanical ventilation. All routine cultures of blood, sputum, and throat swabs were negative, and extensive atypical pathogen screening was unrevealing. Metagenomic next-generation sequencing (mNGS) of sputum and subsequently bronchoalveolar lavage (BAL) fluid, performed at the ISO 15189-accredited central laboratory of Qujing Central Hospital of Yunnan Province, detected high read counts of E. faecium (sputum: 22,710 reads; BAL: 7921 reads; opportunistic pathogen, classification B), with simultaneous routine screening for 31 resistance genes, 4 resistance loci, and virulence genes, all negative. Additionally, sputum mNGS detected Epstein-Barr virus (Human gammaherpesvirus 4, 6715 reads, normal microbiota, classification C), and BAL fluid mNGS detected HSV-1 (Human alphaherpesvirus 1, 407 reads, normal microbiota, classification C). Both herpesviruses had classification C and were interpreted as non-pathogenic "bystanders"; no antiviral therapy was administered. The patient gradually improved on imipenem-cilastatin plus moxifloxacin and was successfully extubated and discharged. This case suggests that E. faecium can cause severe CAP in COPD patients, and mNGS is a valuable diagnostic tool when conventional cultures are negative; herpesviruses with classification C detected by mNGS should not be overinterpreted.},
}

@article {pmid42530375,
year = {2026},
author = {Wang, Z and Gao, Q and Li, S and Fang, Z and Hu, L and Li, R and Zeng, Z and Liu, Y and Li, C and Chen, H},
title = {Epigallocatechin gallate inhibits high-fat/choline diet-induced trimethylamine production via regulation of intestinal Serratia and Lactobacillus communities.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo02528e},
pmid = {42530375},
issn = {2042-650X},
abstract = {High-fat/choline diets can induce the production of the enterogenous metabolite trimethylamine-N-oxide (TMAO). TMAO is synthesized from its precursor trimethylamine (TMA), which is generated via choline cleavage catalyzed by choline trimethylamine-lyase/choline TMA-lyase-activating enzyme (CutC/D) expressed by gut microbes; subsequently, TMA is oxidized to TMAO by flavin-containing monooxygenase 3 (FMO3) in the liver. While epigallocatechin gallate (EGCG) is well recognized for its gut microbiota-remodeling capacity, how it modulates TMA/TMAO metabolism through this pathway, along with the time-dependent effectiveness of EGCG intervention, remains to be elucidated. We conducted animal experiments to evaluate the inhibitory effect of time-dependent EGCG intervention on TMA/TMAO production induced by high-fat/choline diets in mice. We further identified gut bacterial strains associated with TMA levels using metagenomics and machine learning techniques, and verified the underlying mechanisms through in vitro anaerobic culture and molecular simulations. Results demonstrated EGCG significantly reduced TMA/TMAO levels in mice by regulating the choline-CutC/D-FMO3 axis. Specifically, Serratia exhibited a positive correlation with CutC enzyme activity, while Lactobacillus showed a negative correlation with TMA levels. Mechanistically, EGCG exerted a direct bacteriostatic effect on Serratia marcescens by disrupting its cell membrane structure and inhibiting its CutC enzyme activity. Meanwhile, EGCG significantly enriched Lactobacillus johnsonii, with the abundance of this strain peaking after long-term intervention. Although Lactobacillus johnsonii does not directly degrade TMA, it indirectly reduces TMA levels by inhibiting the growth of Serratia marcescens. Long-term continuous supplementation with EGCG yielded the optimal inhibitory effect on TMA/TMAO production. Hence, EGCG exerts its function primarily through a dual mechanism: directly inhibiting the growth and CutC enzyme activity of the TMA-producing bacterium Serratia marcescens, and indirectly antagonizing Serratia marcescens by promoting the proliferation of the beneficial bacterium Lactobacillus johnsonii. This study provides novel theoretical insights into the mechanism by which EGCG alleviates TMA/TMAO metabolic disorders induced by high-fat/choline diets via gut microbiota modulation.},
}

@article {pmid42530605,
year = {2026},
author = {Yasuda, K and Iida, N and Takeshita, Y and Masuo, Y and Honda, M and Takamura, T and Yamashita, T},
title = {Tofogliflozin alters amino acid metabolism in gut microbiota linked to hepatic transcriptomic signatures in MASLD.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42530605},
issn = {1435-5922},
abstract = {BACKGROUND: A deeper understanding of the relationship between dysbiotic gut microbiota and liver tissue-level molecular and histopathological phenotypes in metabolic dysfunction-associated steatotic liver disease (MASLD) remains needed. We aimed to characterize the associations between gut microbial metabolic functions and treatment responses in participants with MASLD.

METHODS: We performed a prespecified sub-analysis of a randomized controlled trial comparing the sodium-glucose cotransporter 2 inhibitor (SGLT2i) tofogliflozin and the sulfonylurea (SU) glimepiride in participants with MASLD and type 2 diabetes (ClinicalTrials.gov NCT02649465). Fecal whole-genome shotgun metagenomics, liver RNA sequencing, serum profiling, and histopathological assessments were integrated to investigate microbiota-host interactions.

RESULTS: Microbial metabolic pathways, rather than taxonomic composition, differed significantly between participants with MASLD and healthy controls. Among the altered microbial pathways, amino acid metabolism emerged as a prominent functional category and was selected for further investigation. Pathways related to amino acid metabolism, particularly phenylalanine metabolism, exhibited opposing patterns: phenylalanine degradation was enriched in MASLD and positively correlated with liver fibrosis scores, whereas phenylalanine biosynthesis inversely correlated with fibrosis severity. Microbial phenylalanine degradation was positively associated with 28 hepatic pathways, including the non-alcoholic fatty liver disease (NAFLD) pathway, in which mitochondria-associated genes were core-enriched. Both SGLT2i and SU treatments improved NAFLD activity scores and altered microbial metabolic pathways without significantly changing microbial species composition. Notably, SGLT2i increased phenylalanine biosynthesis pathways, which were inversely associated with liver fibrosis.

CONCLUSIONS: Gut microbial amino acid metabolism, particularly phenylalanine metabolism, is closely linked to liver fibrosis and molecular pathways in MASLD. Modulation of microbial metabolic functions may represent a promising therapeutic strategy beyond changes in microbial composition.},
}

@article {pmid42530606,
year = {2026},
author = {Cui, C and Shi, H and Naito, Y and Otani, K and Chan, FKL},
title = {Clinical applications of gut microbiome for non-invasive diagnosis of colorectal neoplasia.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42530606},
issn = {1435-5922},
abstract = {Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of cancer-related death worldwide. While screening programs have reduced mortality, current stool-based tests such as the faecal immunochemical test (FIT) and tumour marker assays, remain limited in sensitivity for adenoma detection and rely on relatively later-stage biological signals in the carcinogenic process. False positives lead to unnecessary invasive procedures, whilst missed adenomas continue to progress, highlighting the need for alternative strategies. Accumulating evidence implicates the gut microbiome in CRC pathogenesis, which involves tumour-associated dysbiosis and microbial ecosystem shifts. Multinational metagenomic studies have consistently identified reproducible microbial signatures that can serve as biomarkers of disease and may predate the biological signals used in conventional screening. PCR-based microbial markers have emerged as practical tools for clinical application, enabling sensitive and specific detection of adenomas and CRC. A recent microbial panel incorporating Fusobacterium nucleatum, Hungatella hathewayi, Christensenella hongkongensis, and a novel bacterial gene marker m3 from Lachnoclostridium demonstrated improved sensitivity for adenomas whilst maintaining comparable accuracy for CRC. International guidelines have begun to recommend combining microbiome-based assays with FIT into integrated screening programs that target multiple biologic processes across the pathogenesis. Microbiome-based stool testing represents a promising non-invasive approach that improves detection of adenomas in early-stage disease, often missed by FIT alone and could enable more refined risk stratification. Further validation across diverse populations, assessment of cost-effectiveness, and integration into established screening infrastructures will be critical for broad clinical adoption.},
}

@article {pmid42530881,
year = {2026},
author = {Lakamp, A and Aluthge, ND and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML},
title = {Impact of reducing metagenomic sequencing depth on phenotypic prediction accuracy of feed intake and average daily gain in beef cattle.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag236},
pmid = {42530881},
issn = {1525-3163},
abstract = {Metagenomic information can aid in both genomic and phenotypic predictions of economically relevant traits. Financial restraints often result in a trade-off between the number of samples sequenced and the depth of sequencing. Therefore, it is critical to understand how changes in sequencing depth impact phenotypic prediction accuracy to make optimal use of resources. This study utilized host genomic and rumen metagenomic information of 717 beef cattle to make phenotypic predictions for average daily dry matter intake (ADDMI) and average daily gain (ADG). Metagenomic samples were sequenced at an average depth of 20 million reads (20M set) and were downsampled to 50% (10M set), 25% (5M set), and 10% of the reads (2M set). Rumen microbial open reading frames (ORF) were predicted from each set of reads and used to define a random metagenomic effect in a mixed model framework. Variance components were estimated for each model using all available data, i.e., no masking of phenotypes. Cross-validation schemes were utilized to determine prediction accuracy. Models which incorporated host genomic and metagenomic information explained more variation and generally had greater prediction accuracies than models with either effect alone. Models using the 2M or 5M set resulted in smaller microbiability estimates and lower prediction accuracy for both ADDMI and ADG compared to models using the 10M or 20M sets, though these differences were often not large when measures of uncertainty were considered. For ADDMI, there were only slight differences in microbiability and prediction accuracy between different downsampled sets in most scenarios. For ADG, the 20M set had roughly equivalent microbiability estimates as the other sets but also had a notably greater prediction accuracy, dependent on cross-validation scheme. Spearman correlations of metagenomic effect solutions, termed the estimated metagenomic value (EMV), between all sets for all models were always >0.90. However, the correlations between the EMV for models with the 5M, 10M, and 20M sets were always higher than those with the EMV from the 2M set. The 10M and 20M EMV always had correlations >0.98. Thus, dependent on trait and reference population composition, metagenomic predictions from data sequenced at a depth of 2-10 million reads per sample may yield results approximately equivalent to those from data sequenced at 20 million reads per sample in terms of variance explained and phenotypic prediction accuracy.},
}

@article {pmid42531280,
year = {2026},
author = {Arjomand Fard, N and Githaka, JM and Veniamin, S and Guan, LL and Aujla, H and Kaur, A and Lerner, EP and Zaidi, D and Armet, AM and Andrews, J and Han, X and Vallance, BA and Madsen, K and Perry, T and Wine, E},
title = {Host-microbe Interactions in the Appendix of Children with Inflammatory Bowel Diseases.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00080.2026},
pmid = {42531280},
issn = {1522-1547},
support = {//Women and Children's Health Research Institute (WCHRI)/ ; 166218//Canadian Institutes of Health Research (CIHR)/ ; MT2-168050//Canadian Institutes of Health Research (CIHR)/ ; },
abstract = {The human appendix is traditionally considered a vestigial organ; however, clinical observations link it to inflammatory bowel diseases (IBD), including Crohn disease and ulcerative colitis (UC), as suggested by peri-appendicular inflammation and reported protective effect of appendectomy in UC. Despite these associations, its functional contribution remains poorly defined. Here, we performed a multi-omics analysis of appendix tissue from pediatric IBD patients and non-IBD surgical controls (n = 15) to characterize microbial composition and host molecular landscape. Metagenomic sequencing revealed Proteobacteria enrichment and reduced microbial diversity in IBD appendices. Correlations between host transcriptomes and mucus-associated microbial pathways indicated associations consistent with host-microbe interactions linked to immune activation. Fluorescence in situ hybridization confirmed bacterial localization, and functional assays of appendix-derived Klebsiella variicola isolates demonstrated invasive capacity in vitro. Our findings suggest that the appendix represents a distinct microbial niche in pediatric IBD and may contribute to host-microbe perturbations associated with disease.},
}

@article {pmid42531353,
year = {2026},
author = {Riddell V, J and Shatadru, RN and Smith, GJ and McGivern, BB and Ellenbogen, JB and Jurgensen, SK and Fofana, A and Tfaily, MM and Wrighton, KC and Sullivan, MB},
title = {Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.},
journal = {PLoS biology},
volume = {24},
number = {7},
pages = {e3003925},
doi = {10.1371/journal.pbio.3003925},
pmid = {42531353},
issn = {1545-7885},
abstract = {Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus eco-genomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.},
}

@article {pmid42531517,
year = {2026},
author = {Cheng, C and Wang, L and Li, R and Lai, W and Sun, C and Cui, J and Zhu, B and Zhang, J},
title = {Association Characteristics and Potential Mechanisms of Aging, Gut Microbiota, and Hearing Loss.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70156},
pmid = {42531517},
issn = {1749-4877},
support = {32370536//National Natural Science Foundation of China/ ; QNTS202304//CIB Youth Exploration Project/ ; //Tianchi Talents Fund of Xinjiang/ ; },
abstract = {Age-related hearing loss (ARHL) is the leading sensory disability among the global elderly, yet its pathogenesis remains unclear. The "gut-ear axis" hypothesis offers a novel perspective. Using young, middle-aged, and aging C57BL/6 mice, we systematically investigated the interplay between aging, gut microbiota, and hearing loss through auditory function tests, cochlear histology, microbiome, and metabolome profiling. Results showed that aging induced a gradient hearing decline starting at high frequencies, progressing to severe pan-frequency loss in old age. Histology confirmed the degeneration of inner hair cells and synaptic connections, alongside hair cell loss in the basal cochlea. While gut microbiota α-diversity remained stable, β-diversity shifted significantly, marked by increased Bacteroidota and decreased Bacillota. Furthermore, 22 genera, 67 species, and 207 functional pathways were identified as being commonly associated with both aging and hearing loss. Metabolomic profiling further screened out 285 metabolites significantly associated with aging, 16 of which were also correlated with hearing loss. KEGG enrichment analysis suggested that chronic inflammation mediated by arachidonic acid metabolism, energy metabolic dysfunction regulated by the PPAR signaling pathway, and actin cytoskeleton homeostasis imbalance may represent a potential axis linking systemic metabolic dysregulation to cochlear‑specific damage. Moreover, these metabolites exhibited significant correlations with gut microbiota abundance. In conclusion, aging is associated with ARHL progression alongside gut microbiota remodeling and metabolic dysregulation. These findings supported a potential relationship between gut microbial-metabolic alterations and ARHL, which suggested that the gut microbiota may represent a candidate target for future mechanistic investigation.},
}

@article {pmid42531759,
year = {2026},
author = {Pacholak, A and Musielok, Ł and Smułek, W},
title = {Effect of pyrethrins and permethrin insecticides on soil bacterial biodiversity.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120564},
doi = {10.1016/j.ecoenv.2026.120564},
pmid = {42531759},
issn = {1090-2414},
abstract = {Soil microorganisms play a key role in maintaining ecosystem stability, yet they are frequently exposed to insecticides used in agriculture and pest control. This study investigated the effects of natural pyrethrins and synthetic permethrin on soil bacterial metabolic activity, functional diversity, community structure, and biodegradation potential. Soil samples collected from a long-term protected, non-agricultural forest area were incubated with commercial formulations containing pyrethrins (Afizol AE) or permethrin (Afanisep® 25 WP) for 7 and 15 days. Microbial metabolic activity was assessed using the Alamar Blue assay and Biolog EcoPlate™ system, while bacterial community composition was analyzed through 16S rRNA gene sequencing. Additionally, the degradation of insecticide active compounds was quantified using UHPLC-QTOF-MS. Permethrin-treated soils exhibited the highest and most sustained microbial metabolic activity, whereas pyrethrin-treated soils showed an initial stimulation followed by a decline over time. Functional diversity indices revealed that permethrin initially promoted metabolic diversity, but prolonged exposure led to a reduction in substrate utilization breadth. Metagenomic analysis demonstrated pronounced shifts in bacterial community composition under both treatments, with strong selection toward Firmicutes-dominated assemblages. Biodegradation assays confirmed substantial degradation of both pyrethrins and permethrin, although incomplete removal and partial accumulation of selected compounds were observed. The obtained results highlight that both natural and synthetic pyrethroids significantly alter soil bacterial communities, emphasizing the need to consider their short-term ecological effects on soil health.},
}

@article {pmid42520923,
year = {2026},
author = {Khan, AR},
title = {Letter to the Editor regarding Neluvhola et al, Histopathological assessment of granulomatous hepatitis: a retrospective study.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102894},
doi = {10.1016/j.clinre.2026.102894},
pmid = {42520923},
issn = {2210-741X},
}

@article {pmid42521068,
year = {2026},
author = {Pavon, JAR and Neves, NADS and Martins, AP and Pinho, JB and de Souza, VJ and Nunes, MRT and Slhessarenko, RD},
title = {RNA viruses in sylvatic mosquitoes and phlebotomine sand flies from Alto Pantanal, Mato Grosso, Brazil 2019.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108258},
doi = {10.1016/j.actatropica.2026.108258},
pmid = {42521068},
issn = {1873-6254},
abstract = {The Pantanal biome harbors exceptional biodiversity but has been increasingly impacted by climate change and human activities. This region is considered a high-risk zone for zoonotic spillover, making viral studies in sylvatic mosquitoes and other invertebrates indispensable, as these vectors are involved in the transmission of pathogens of public health concern. This study aimed to describe viral genomes identified in Aedes spp., Ochlerotatus sp., Mansonia sp., Phlebotomus sp., Psorophora spp., and Anopheles spp. dipterans collected in March and June 2019, in Pirizal and Porto São Luiz, Alto Pantanal, Mato Grosso State, Brazil. Diptera specimens were pooled by genera, and nucleic acids were extracted, followed by library preparation and sequencing on the Illumina NextSeq 500/550 platform. A total of 39 putative viral sequences were recovered, including 23 potentially novel viruses. Coding-complete genomes were identified from Virgaviridae (n=1), Rhabdoviridae (n=1), and Metaviridae (n=1), as well as seven coding-complete segments from Partitiviridae (n=4) and Solemoviridae (n=3). Additionally, 29 partial genomes were recovered from Partitiviridae (n=7), Metaviridae (n=6), Chuviridae (n=2), Sedoreoviridae (n=1), Nodaviridae (n=3), Tombusviridae (n=2), Phasmaviridae (n=2), Flaviviridae (n=3), Virgaviridae (n=1), and Solemoviridae (n=2). Viral characterization in Diptera specimens has gained increasing importance with the advancement of metagenomic approaches, which contribute to global One Health initiatives by providing data that may support the prediction and prevention of future viral spillover events.},
}

@article {pmid42521693,
year = {2026},
author = {Rodríguez-Ramos, JA and Zimmerman, AE and Wu, R and Bell, SL and Alfaro, TD and Reichart, NJ and Hofmockel, KS and Nelson, WC},
title = {Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42521693},
issn = {2041-1723},
support = {FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; },
mesh = {*Soil Microbiology ; Metagenomics/methods ; *RNA, Viral/isolation & purification/genetics ; *RNA Viruses/genetics/isolation & purification ; *DNA, Viral/isolation & purification/genetics ; Soil/chemistry ; *DNA Viruses/genetics/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; Bacteria/genetics ; },
abstract = {Deciphering viral ecology in soils is challenging due to soil's high physicochemical and microbial community complexity. To enhance detection of DNA and RNA viruses, we applied different preparation methods to soils collected from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses, total soil metagenomics and metatranscriptomics, total soil metatranscriptomics with polyadenylation enrichment, and metagenomics of bacteria/archaea as well as eukaryote-enriched samples. DNA viromes outperformed total soil metagenomes in viral detection and quality. Contrastingly, RNA viromes and total soil metatranscriptomes performed similarly for viral recovery, though RNA viromes yielded higher-quality genomes. Together, our results highlight how different preparation methods can influence the recovery and quality of DNA and RNA vOTUs. Further, we demonstrate the power of different methods in identifying distinct viral communities with unique host predictions, which in turn can have significant implications for ecological investigations related to interkingdom interactions.},
}

*Soil Microbiology
Metagenomics/methods
*RNA, Viral/isolation & purification/genetics
*RNA Viruses/genetics/isolation & purification
*DNA, Viral/isolation & purification/genetics
Soil/chemistry
*DNA Viruses/genetics/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral
Bacteria/genetics

@article {pmid42521984,
year = {2026},
author = {Bogovič, P and Slunečko, J and Kodre, M and Kogoj, R and Jakob, MB and Korva, M and Ružić-Sabljić, E and Strle, F},
title = {Human Cases of Borrelia miyamotoi Disease, Slovenia, 2025.},
journal = {Emerging infectious diseases},
volume = {32},
number = {8},
pages = {1319-1322},
doi = {10.3201/eid3208.260326},
pmid = {42521984},
issn = {1080-6059},
mesh = {Humans ; *Borrelia/genetics/classification/isolation & purification ; Slovenia/epidemiology ; *Borrelia Infections/epidemiology/diagnosis/microbiology ; Female ; Male ; Animals ; Adult ; Middle Aged ; },
abstract = {We identified human Borrelia miyamotoi infections in Slovenia in 2 of 337 adults with undifferentiated fever tested positive by metagenomic sequencing and PCR. Both patients reported recent local tick bites. The illness was mild and self-limited. Our findings underscore the need to consider this pathogen in evaluating fever after tick bite.},
}

Humans
*Borrelia/genetics/classification/isolation & purification
Slovenia/epidemiology
*Borrelia Infections/epidemiology/diagnosis/microbiology
Female
Male
Animals
Adult
Middle Aged

@article {pmid42523101,
year = {2026},
author = {Zhou, X and Wei, G and Song, T and Yu, Y and Chen, J and Long, J and Tao, X and Zhang, J and Jiang, L},
title = {Metagenomic next-generation sequencing for tuberculosis diagnosis: enhanced performance and cost-effectiveness.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/spectrum.00970-26},
pmid = {42523101},
issn = {2165-0497},
abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) is a promising tool for diagnosing challenging infections like tuberculosis (TB). However, previous studies largely focused on case-specific application of mNGS in TB diagnosis. Thus, we conducted a retrospective observational study to first systematically evaluate the diagnostic performance and cost-effectiveness of mNGS for TB diagnosis. We retrieved a total of 16,776 results of the seven TB diagnostic assays, including mNGS, tuberculosis IgG antibody, TB interferon-γ release assay (TB-IGRA), TB-DNA, Xpert MTB/RIF (Xpert), culture, and acid-fast bacilli staining (AFS) from 3,757 participants with suspected TB infection at Sichuan Provincial People's Hospital from September 2021 to July 2024. Diagnostic metrics were compared against a composite reference standard. Microbial composition and a cost-utility analysis were performed. Among seven TB assays studied, the World Health Organization (WHO)-recommended assays AFS, culture, and Xpert, as well as TB-IGRA, were requested most frequently for TB diagnosis, whereas mNGS ranked last. mNGS demonstrated the highest specificity (100%), accuracy (72.3%), and area under the curve (AUC) (0.795). Its sensitivity in bronchoalveolar lavage fluid and tissue was 71.0% and 72.7%, respectively. Sequential use of mNGS after initial WHO-recommended tests (Xpert/Culture/AFS) significantly improved diagnostic performance (sensitivity, 70.4%; AUC, 0.823). Microbial analysis associated Candida albicans with TB. Cost-utility analysis showed sequential mNGS became cost-effective at higher willingness-to-pay thresholds (>200,000 RMB per correct diagnosis). mNGS offers superior specificity for TB diagnosis. A sequential strategy applying mNGS to conventional-test-negative cases provides enhanced diagnostic performance and is cost-effective at higher healthcare investment values, supporting its utility for diagnostically challenging TB.

IMPORTANCE: This study systematically assesses the diagnostic performance and cost utility of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB) in a large real-world cohort of 3,757 suspected patients, comparing it against six conventional assays (tuberculosis IgG antibody, TB interferon-γ release assay, TB-DNA, Xpert, culture, and acid-fast bacilli staining). mNGS demonstrated the highest specificity (100%), accuracy (72.3%), and area under the curve (AUC) (0.795), with sensitivities of 71.0% in bronchoalveolar lavage fluid and 72.7% in tissue. Notably, sequential use of mNGS after the World Health Organization-recommended tests significantly improved sensitivity to 70.4% and AUC to 0.823. Candida albicans showed significant differences among the three groups. The sequential mNGS strategy was cost-effective compared with no mNGS, and its cost-effectiveness increased with a rising willingness-to-pay threshold. Overall, these results highlight mNGS as a valuable supplementary tool for challenging TB cases, especially when conventional tests are inconclusive, and provide strong evidence for integrating it into diagnostic algorithms to optimize clinical decision-making and resource allocation.},
}

@article {pmid42523106,
year = {2026},
author = {Xu, S and Yang, L and Gao, J and Shi, Y and Tang, X and Cai, H and Yang, L and Han, Y and Lin, L and Meng, R and Sun, J and Guan, W-j and Tang, T and Shu, W and Cao, C and Zheng, X-y and Wang, Z and Yi, X},
title = {The associations of human genetic variations with airway microbiome, environmental exposures, and respiratory health.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0044226},
doi = {10.1128/msystems.00442-26},
pmid = {42523106},
issn = {2379-5077},
abstract = {UNLABELLED: The intricate interactions between environmental exposures, the respiratory microbiome, and host genetic variations remain inadequately understood in the context of respiratory health. This study utilized sputum metagenomic data from 1,651 individuals in our previous cohort to elucidate these associations. Mendelian randomization indicated that air pollutants (e.g., SO2, CO, and PM2.5) were associated with lung function, which is potentially mediated by microbes, such as Actinomyces, Haemophilus influenzae, and Veillonella spp. Several genetic loci associated with respiratory microbiome variation were found to be linked to genotype-dependent associations between environmental exposures and lung function. For bacteria, the MEOX1 locus (rs1973191819) was associated with lower Filifactor alocis abundance under air pollutant exposure. The FAM110D (1:26157175) and USP36 (rs1343834070) loci showed associations with higher levels of certain pathogenic taxa (e.g., Ralstonia pickettii, Neisseria) and lower levels of the commensal Oribacterium, increasing chronic obstructive pulmonary disease (COPD) risk. For fungi, DNAJC18 and CCDC57 loci exhibited associations with Candida and Penicillium abundance, respectively. These genotype-dependent associations between the microbiome and environmental exposures provide insights into airway dysbiosis and susceptibility to respiratory diseases.

IMPORTANCE: This study reveals why individuals exposed to identical air pollution exhibit varying degrees of respiratory severity, pointing to a critical missing link: our genetics. While pollution is a known disease trigger, our findings demonstrate that host genetic variation actively regulates and shapes the respiratory microbiome under environmental stress. By mapping specific genetic loci to pollutant-driven bacterial shifts, this work elucidates how host genetics filters environmental risks to govern microbial homeostasis. These results underscore the necessity of incorporating host-microbiome genetic regulation into environmental health research. Ultimately, this study shifts the paradigm toward personalized medicine, enabling the early identification of at-risk individuals and the development of targeted, microbiome-informed interventions.},
}

@article {pmid42523201,
year = {2026},
author = {Kananen, K and Tran, N and Bradley, PH},
title = {Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.15.738685},
pmid = {42523201},
issn = {2692-8205},
abstract = {UNLABELLED: In microbiome studies, associations between microbial functions and the environment are often confounded by phylogeny. While some methods explicitly account for this confounder, they require information about genome content, limiting their use in biomes where few genomes have been available. To make these methods more universally accessible, we have developed Phylogenize2, a redesigned phylogeny-aware tool for linking microbial gene families to abundance phenotypes. Phylogenize2 integrates large metagenome-assembled genome collections, including both biome-specific collections from MGnify and a broadly sampled general purpose database, GlobDB, to substantially expand species coverage, allowing its application in environments like the mouse gut and ocean. In addition, by default, Phylogenize2 uses a new robust phylogenetic testing framework that has been optimized for microbial abundance data, while also allowing the use of other comparative methods such as POMS. In an experimental mouse study, Phylogenize2 identifies that Muribaculaceae with higher abundance on a high-fat diet are enriched for proteins in the thioredoxin family, with likely roles in oxidative stress. When we apply Phylogenize2 to a polar ocean study, we find that a molybdenum-dependent PaoABC/YagTSR-like aldehyde oxidoreductase system differentiates mesopelagic from surface-dwelling Flavobacteriaceae , suggesting that aldehyde detoxification may be important for organisms that degrade marine snow. Together, these results show that Phylogenize2 expands phylogeny-aware microbiome analysis beyond the human gut and can provide insight into the genetic basis of microbiome-encoded traits in diverse environments.

IMPORTANCE: Microbiome studies often set out to identify which microbes are more or less abundant across environments, but these patterns can be difficult to interpret. Phylogenize2 is an open-source software package that allows researchers to ask whether individual microbial gene families are associated with the environment across independent branches of the microbial tree of life. By incorporating large collections of genomes from uncultivated microbes, as well as modern statistical methods designed for microbial abundance data, Phylogenize2 makes this approach practical for microbiomes beyond the human gut, including in model organisms like lab mice and free-living environments like the ocean. We also provide a pipeline that allows the use of new genome collections. In two case studies, we demonstrate that Phylogenize2 effectively prioritizes specific genes and pathways from metagenomic data, thereby leading researchers from changes in microbial abundance to more biologically interpretable explanations.},
}

@article {pmid42523339,
year = {2026},
author = {Tran, N and Kananen, K and Bradley, PH},
title = {A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.15.738679},
pmid = {42523339},
issn = {2692-8205},
abstract = {UNLABELLED: A key goal in the microbiome field is to move from taxonomic associations towards mechanistic hypotheses about microbial gene function. However, most methods for linking microbiome changes to specific genes are biased towards finding marker genes, with weak evidence for functional relevance. Phylogenetic regression can address this issue and has been previously applied to changes in microbial prevalence, but many environments (such as the gut in health vs. disease) are characterized more by changes in abundance, which presents unique statistical challenges. We show that when applied to real differential abundances from metagenomes, phylogenetic regression has an anti-conservative bias, indicating inflated false positives. We develop an alternative non-parametric method called "robust permutration," designed specifically for differential abundance data, and evaluate its performance against phylogenetic regression as well as several other phylogenetic comparative methods in realistic simulations of metagenomic data. These results show that robust permutration is the most powerful method that appropriately controls the false positive rate. We further apply robust permutration to a human case-control study of liver cirrhosis, revealing that Lachnospiraceae abundance in disease is linked to a previously uncharacterized iron- sulfur transcription factor encoded near homologs of the butyryl-CoA oxygen oxidoreductase system, a recently discovered system for oxygen detoxification. This illustrates how robust, sensitive phylogenetic methods can enable the generation of new molecular hypotheses directly from metagenomic case-control data.

IMPORTANCE: Previously, we showed that phylogenetic regression can effectively detect genes associated with microbial presence or absence while correcting for evolutionary relationships. Unexpectedly, however, we here observe that this method can lead to high false positive rates when applied to microbial abundance data. In realistic simulations, other methods we test either have similar problems with false positives, or display very low power. We outline a new statistical test that better accounts for measurement uncertainty, outliers, and model violations, achieving more balanced sensitivity and accuracy than competing methods. Applying this test to a cirrhosis study reveals an uncharacterized transcription factor enriched in disease, with an apparent role in oxidative stress based on its sequence and gene neighborhood. This suggests a functional explanation for the observed taxonomic shifts, and demonstrates how improved phylogenetic methods could help inform future microbiome-targeted treatments.},
}

@article {pmid42523359,
year = {2026},
author = {Uwamanzu-Nna, A and Olagoke, O and Shi, CX and Mengistie, HD and Asfaha, K and Read, TD and Dean, D},
title = {Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523359},
issn = {2692-8205},
abstract = {Trachoma, a chronic ocular disease caused by Chlamydia trachomatis (Ct), is the leading infectious cause of blindness worldwide. Despite WHO's SAFE (Surgery, Antibiotics, Facial cleanliness, Environmental improvement) strategy, ~100M are at risk of blindness. Using metagenomic shotgun sequencing, we characterized the ocular microbiome of 680 villagers in Amhara Ethiopia, identifying 10 Community State Types (CSTs) associated with different population characteristics. Children with the highest prevalence of inflammatory trachoma and Ct were in CST10, dominated by Haemophilus influenzae and four other Haemophilus spp. Adults with the highest prevalence of scarring trachoma were in CST3 and CST6, dominated by Corynebacterium macginleyi. CST5, dominated by Mesomycoplasma hyorhinis and Staphylococcus aureus, had the lowest prevalence of Ct and trachoma, and was the only CST without zoonotic Chlamydia spp. Both M. hyorhinis, a zoonotic porcine bacterium, and S. aureus are capable of forming biofilms, which may competitively prevent/down-regulate chlamydial infections. Other CSTs were dominated by environmental species like Vibrio. This is the first microbiome study to develop CSTs for trachoma. Pathogenic and potentially protective microbes showed distinct associations with demographic, clinical, and chlamydial characteristics, which will guide the design of microbial therapeutics as alternatives to antibiotics and strategies for WHO's global elimination of blinding trachoma.},
}

@article {pmid42523540,
year = {2026},
author = {Danner, R and Cho, J and Detwiler, Z and Williams, J and Han, JA and Yang, C and Diebold, X and Maeder, K and Van Vranken, JG and Walker, AS and Lesser, C and Chaudhari, SN},
title = {Gut microbiome derived folate metabolite suppresses colorectal cancer progression.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.14.738490},
pmid = {42523540},
issn = {2692-8205},
abstract = {The gut microbiota influences colorectal cancer (CRC) progression, primarily through the secretion of small molecule metabolites. While numerous microbial products are known to drive CRC, endogenous protective mechanisms remain largely uncharacterized. Utilizing a folate metabolomics platform, we demonstrate that the healthy gut microbiota produces folinic acid (FA), a known chemotherapeutic adjuvant also known as leucovorin. This microbially derived folinic acid is progressively depleted in mouse models of colitis-associated CRC and in human clinical metagenomic cohorts with advancing disease severity. Mechanistically, folinic acid acts as a signaling molecule that directly binds and inhibits the intracellular protease calpain-2. This interaction stabilizes epithelial E-cadherin protein expression and suppresses CRC epithelial-to-mesenchymal transition driving metastasis. Genetically manipulating gut microbial production of FA is sufficient to modulate CRC in vivo , even in the presence of chronic inflammation. This study reframes folinic acid from a chemotherapeutic enhancer to an endogenous microbial metabolite that actively suppresses CRC progression.},
}

@article {pmid42523736,
year = {2026},
author = {Togaev, U and Mathur, V and Rakhmonkulova, A and Agarwal, S and Mathur, A and Turageldiyev, S and Ruzmetov, R and Turaev, AS and Tillyabaev, Z and Matchanov, A and Sillam-Dussès, D},
title = {Comparative metagenomic analysis of gut microbiota in Anacanthotermes turkestanicus and A. ahngerianus reveals diet- and habitat-driven functional divergence.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1807673},
pmid = {42523736},
issn = {2673-8600},
abstract = {The gut microbiome of termites plays a crucial role in lignocellulose degradation and nutrient recycling. This study presents the first metagenomic characterization of the gut microbiota in two lower termite species, Anacanthotermes ahngerianus and Anacanthotermes turkestanicus, collected from distinct ecological habitats. In Uzbekistan, the first lives in building a mound in nature in the West part while the second mainly lives in contact with human constructions in the East part without building a proper mound. Both species showed similar bacterial dominance (~53%) in their guts but A. ahngerianus exhibited higher overall microbial diversity (Shannon index: 4.046 vs. 3.363; Simpson's index: 0.927 vs. 0.776). Moreover, both termite species showed differences in microbial profiles, including bacterial taxa and eukaryotic groups relevant to lower-termite gut symbiosis. Protist-associated eukaryotic reads were retained because flagellated protists are essential symbionts of lower termites, whereas unexpected non-protist eukaryotic assignments were interpreted cautiously and were not used as evidence of functional gut symbionts or host adaptation. Functional profiling revealed enrichment of pathways related to carbohydrate metabolism, amino acid transport, and energy production in both species. However, A. turkestanicus exhibited stronger bacterial dominance associated with lignocellulose degradation and nitrogen cycling, while A. ahngerianus maintained a more balanced representation of bacteria, fungi, and viruses. These findings suggest that species identity and ecological habits may be associated with differences in gut microbiome structure and predicted functional potential.},
}

@article {pmid42523741,
year = {2026},
author = {Hong, X and Cai, Z and Yu, Z and Fu, H and Cai, J and Wu, Z and Wu, X and Kuang, Z},
title = {Omadacycline for peritoneal dialysis-associated peritonitis caused by Coxiella burnetii: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1829483},
pmid = {42523741},
issn = {2296-858X},
abstract = {INTRODUCTION: Peritoneal dialysis-associated peritonitis (PDAP) is a serious complication of peritoneal dialysis (PD), contributing significantly to hospitalization rates and mortality. In recent years, infections caused by uncommon pathogens such as Coxiella burnetii have increasingly been identified, posing significant challenges to managing PDAP.

CASE PRESENTATION: We report a 62-year-old male hospitalized for recurrent PDAP unresponsive to empirical antibiotics (meropenem, later meropenem/vancomycin). Metagenomic next-generation sequencing (mNGS) of peritoneal fluid identified C. burnetii. Intravenous omadacycline was initiated as part of a multi-agent regimen (100 mg daily after 200 mg loading dose). Within 48 h, hemodynamic stability was achieved, and inflammatory markers (procalcitonin, C-reactive protein, effluent white blood cell count) normalized progressively over the subsequent week. The patient recovered fully and was discharged, and remained relapse-free during 3 months of follow-up.

CONCLUSION: This case highlights the critical importance of identifying pathogens in patients with PDAP. Despite significant confounders (concurrent broad-spectrum antibiotics, ICU support, and polymicrobial infection) that limit definitive attribution, the use of omadacycline was associated with clinical recovery and suggests a potential role as an alternative therapeutic option for Coxiella burnetii infection. Further studies are warranted to validate its efficacy.},
}

@article {pmid42523840,
year = {2026},
author = {Bankar, VR and Chapadgaonkar, SS and Bhattacharyya, K and K, P},
title = {From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance in Rauwolfia serpentina.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1796770},
pmid = {42523840},
issn = {2673-7647},
abstract = {INTRODUCTION: This study presents the first metagenomic analysis of the root and rhizosphere microbiomes of Rauvolfia serpentina, an endangered medicinal plant. Metagenomic sequencing and bioinformatics analysis were used to characterize the diverse microbial communities and their functional attributes to assess the ecological and biotechnological potential of this plant-associated microbiome.

METHODS: High-throughput Illumina sequencing and bioinformatics analysis were used to profile the microbial communities. Functional annotation was performed to identify plant growth-promoting traits using PLABASE, to predict pathways for the biosynthesis of novel bioactive compounds using antiSMASH, and to identify antimicrobial resistance genes using ResFinder.

RESULTS: The analysis revealed highly diverse microbial communities in both habitats, predominantly composed of Pseudomonadota, Bacillota, and Actinomycetota, with minor but consistent contributions from archaea and eukaryotes. Functional annotation identified extensive PGPTs, including genes associated with phosphate solubilization, nitrogen fixation, siderophore-mediated iron acquisition, and stress tolerance. The rhizosphere microbiome exhibited greater metabolic versatility and stress tolerance, characterized by a higher copy number of heavy metal efflux pumps, whereas the root microbiome was enriched in genes involved in plant hormone regulation and plant-microbe interactions. A diverse array of non-ribosomal peptide synthase, polyketide synthase, and lasso peptide pathways were predicted, underscoring the potential to produce novel bioactive compounds. These distinct functional profiles demonstrates that the protected root endomicrobiome specializes in plant signalling and nutrient assimilation, while the rhizosphere microbiome, facing higher competition, specializes in nutrient acquisition and stress resilience.

CONCLUSION: These findings provide novel insights into the ecological specialization and biotechnological potential of the R. serpentina microbiome, offering significant implications for the sustainable utilization and conservation of this endangered medicinal plant.},
}

@article {pmid42523956,
year = {2026},
author = {Zhou, M and Zhao, Y and Sun, X and Mou, W and Liu, Y and Shi, C and Li, Z and Cheng, Y and Tian, X and Fan, J and Wang, J},
title = {Chronic granulomatous disease secondary to a rare compound heterozygote mutation in an adolescent cured by hematopoietic stem cell transplantation: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1780075},
pmid = {42523956},
issn = {2296-2360},
abstract = {BACKGROUND: Chronic granulomatous disease (CGD) is a rare inherited primary immunodeficiency characterized by recurrent infections and aberrant inflammation due to defects in the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex.

CASE PRESENTATION: We report a case of recurrent pneumonia and significantly elevated IgE levels in an adolescent. Metagenomic next-generation (mNGS) sequencing contributed to the identification of Burkholderia multivorans in bronchoalveolar lavage fluid and the initiation of appropriate treatment. Whole exome sequencing (WES) revealed two point mutations in the CYBA gene. The patient was cured by hematopoietic stem cell transplantation.

CONCLUSIONS: Application of mNGS contributed to the early identification of B. multivorans and the initiation of appropriate treatment. Timely screening by WES contributed to the diagnosis of the patient.},
}

@article {pmid42524013,
year = {2026},
author = {Li, J and Lian, S and Liu, Y and Yang, X and Liu, D and Chen, J and Xiong, H},
title = {From serum inflammatory markers to fluid, tissue, and molecular assays: current advances in the laboratory diagnosis of bone and joint infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1865643},
pmid = {42524013},
issn = {2235-2988},
mesh = {Humans ; *Biomarkers/blood/analysis ; Prosthesis-Related Infections/diagnosis ; *Osteomyelitis/diagnosis ; *Molecular Diagnostic Techniques/methods ; *Arthritis, Infectious/diagnosis ; Synovial Fluid/chemistry ; *Clinical Laboratory Techniques/methods ; },
abstract = {Bone and joint infections (BJIs), including periprosthetic joint infection (PJI), fracture-related infection (FRI), and osteomyelitis, present persistent diagnostic challenges driven by biofilm formation and a high incidence of culture-negative cases. Traditional diagnostic modalities relying on peripheral serum markers and conventional cultures are often limited by insufficient specificity or prolonged turnaround times. This narrative review critically evaluates recent advances in laboratory diagnosis for bone and joint infections, with particular attention to disease-specific applicability across periprosthetic joint infection, fracture-related infection, native vertebral osteomyelitis, diabetic foot osteomyelitis, and other osteomyelitis-related conditions. Current evidence indicates that while traditional serum inflammatory markers are valuable for initial screening, their susceptibility to aseptic inflammatory confounders precludes standalone diagnostic confirmation. In contrast, localized sampling demonstrates significant superiority: novel synovial fluid biomarkers, notably calprotectin and alpha-defensin, accurately reflect the infection microenvironment and offer exceptional diagnostic specificity. At the tissue level, the integration of multiple deep-tissue sampling with preprocessing techniques like sonication has substantially enhanced the recovery of occult biofilm-encased pathogens. Furthermore, targeted and untargeted molecular assays, including multiplex PCR panels, broad-range bacterial PCR, amplicon-based sequencing, and untargeted shotgun metagenomic sequencing, have expanded the diagnostic toolkit for culture-negative, low-virulence, and polymicrobial infections. The diagnostic framework for BJIs has decisively shifted from the pursuit of a solitary "silver bullet" marker toward multimodal, culture-independent assay panels and artificial intelligence-assisted risk stratification algorithms. Future clinical breakthroughs will depend heavily on the global standardization of disease definitions, robust external validation of predictive models, and the seamless integration of advanced laboratory techniques into multidisciplinary team (MDT) workflows.},
}

Humans
*Biomarkers/blood/analysis
Prosthesis-Related Infections/diagnosis
*Osteomyelitis/diagnosis
*Molecular Diagnostic Techniques/methods
*Arthritis, Infectious/diagnosis
Synovial Fluid/chemistry
*Clinical Laboratory Techniques/methods

@article {pmid42524415,
year = {2026},
author = {Allaart, MT and Tyakht, AV and Ley, RE and Pabst, M and Stouten, GR and Angenent, LT},
title = {D- and L-lactate consumers are taxonomically, biochemically, and energetically different.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag180},
pmid = {42524415},
issn = {2730-6151},
abstract = {D- and L-lactate are routinely produced as intermediates in fermentative ecosystems. However, the microbial fate of these stereoisomers remains poorly understood. Given that D-lactate is an unavoidable byproduct of digestion and a neurotoxin, understanding its microbial turnover not only holds ecological pertinence but also the potential to uncover new links between gut microbiota metabolism and host health. Here, we used chemostat bioreactors (pH 7.0, 37°C, and a solids retention time of 4 days) to enrich for lactate-consuming communities. DL-lactate-consuming consortia were enriched, characterized, and used as inoculum for duplicate bioreactors fed exclusively with D- or L-lactate. After steady-state was reached, the fed lactate stereoisomers were switched to assess community resilience. Regardless of the fed stereoisomer, the fermentation product spectra were consistent and dominated by acetate, propionate, and CO2. However, microbial communities and biomass yields diverged sharply, with a high relative abundance of Anaerotignum in D-lactate enrichments and Acidipropionibacterium and Propionibacterium in L-lactate enrichments. Notably, the biomass yield for D-lactate feeding was less than half that for L-lactate feeding, suggesting that the two isomers are metabolized through distinct biochemical pathways despite similar product spectra. Metagenomic and metaproteomic analyses confirmed divergence in D- and L-lactate conversion at both the phylogenetic and pathway levels. Our findings reveal how the stereoisomer identity of microbes shapes their niche specialization, with implications for understanding the ecology and clinical impact of lactate metabolism.},
}

@article {pmid42524456,
year = {2026},
author = {Shao, L and Lv, G and Yuan, Y and Xu, C and Tai, H and Li, Y},
title = {Antimicrobial Management of Severe Chlamydia psittaci Pneumonia in Adults: A Narrative Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {625008},
pmid = {42524456},
issn = {1178-6973},
abstract = {Chlamydia psittaci is an obligate intracellular bacterium and an increasingly recognized cause of severe community-acquired pneumonia (CAP) in adults, with contemporary multicenter Chinese cohorts reporting severe-stratum in-hospital mortality clustering around 8-9% and higher figures in acute respiratory distress syndrome (ARDS)-enriched series. β-Lactam therapy lacks reliable activity against this pathogen, yet considerable practice variation persists in the selection, sequencing, and de-escalation of intracellularly active agents in the era of routine metagenomic and targeted next-generation sequencing (mNGS, tNGS). The aim of this review is to provide a phase- and severity-stratified, bedside antimicrobial framework for severe psittacosis in adults-clarifying when to select, continue, switch, or combine intracellularly active agents at the 48- to 72-hour ICU decision points. This narrative review, reported in accordance with the SANRA framework, synthesizes the post-2015 antimicrobial evidence for severe C. psittaci pneumonia in adults and integrates treatment phase (empirical versus targeted), severity context, organ support, and antimicrobial stewardship at the 48- to 72-hour ICU decision points. Drawing on six multicenter cohorts and the largest dedicated multicenter dataset to date (Fang 2026, n = 186; severe-stratum mortality 7/81 = 8.6%), phase-by-severity stratification reconciles apparently discordant tetracycline- and fluoroquinolone-favoring cohort signals. Doxycycline is the preferred targeted backbone in confirmed non-pregnant disease; reflex class-switching is not required when severely ill patients are already improving on an empirical fluoroquinolone at NGS confirmation. Omadacycline is a renal-sparing alternative when acute kidney injury, anticipated continuous renal replacement therapy, or unreliable doxycycline access alters the standard pathway; high-dose tigecycline is reserved for salvage; azithromycin retains its clearest targeted role in pregnancy. Apparent nonresponse at 72 hours should trigger structured reassessment for coinfection, secondary organizing pneumonia, pulmonary embolism, and inadequate antimicrobial exposure before any salvage escalation. Adjunctive corticosteroid use should follow contemporary severe-CAP guidance pending pathogen-specific data from the NCT07352865 adaptive trial. Recommendations are calibrated using GRADE-adapted certainty and strength, with explicit acknowledgment that the comparative evidence base remains overwhelmingly retrospective and geographically concentrated in Chinese tertiary hospitals.},
}

@article {pmid42524580,
year = {2026},
author = {Ji, BC and Aung, T and Smart, C and Khan, Y},
title = {A Complex Case of Behçet's Disease With Severe Genital Ulceration: Diagnostic Challenges.},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e111658},
pmid = {42524580},
issn = {2168-8184},
abstract = {Behçet's syndrome (BS) is a chronic, multisystem variable vessel vasculitis defined by recurrent oral and genital ulcers, diverse mucocutaneous lesions, and potential involvement of the eyes, joints, vasculature, central nervous system, and gastrointestinal tract. Diagnosis remains a clinical challenge given the absence of pathognomonic laboratory or histological findings. We present a case of a 36-year-old Caucasian male patient with hypothyroidism who developed a severe, rapidly progressive first episode of BS characterized by hemorrhagic vesicular and bullous skin lesions, oral ulceration, and necrotic genital ulceration requiring surgical debridement. Extensive infectious evaluation, including plasma cell-free metagenomic next-generation sequencing (cf-mNGS), was entirely negative. Serologic workup was unremarkable; HLA-B51 was negative, and pathergy was equivocal. Skin punch biopsy demonstrated pan-dermal neutrophilic inflammation with acute vasculitis and focal epidermal necrosis - a critical histopathological feature distinguishing BS from Sweet syndrome, in which true vasculitis is characteristically absent. Under the International Criteria for Behçet's Disease (ICBD), the patient scored ≥4 points (oral ulcers: 2 points; genital ulcers: 2 points; skin lesions: 1 point). He responded to high-dose corticosteroids (prednisone 50 mg daily) and colchicine, achieving full remission within nine weeks with no recurrence. This case illustrates the diagnostic complexity of BS in the absence of classic genetic markers, emphasizes histopathology as the critical discriminator from neutrophilic dermatosis mimics, and underscores the importance of systematic multidisciplinary evaluation before initiating immunosuppressive therapy.},
}

@article {pmid42524765,
year = {2026},
author = {Littlejohn, C and Chang, YC and Teles, F and Korostoff, JM and Redding, LE},
title = {Evolution of the fecal and oral microbiota after prophylactic antibiotics administered for dental surgeries.},
journal = {Journal of the American Dental Association (1939)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.adaj.2026.04.020},
pmid = {42524765},
issn = {1943-4723},
abstract = {BACKGROUND: The human oral and gut microbiomes play critical roles in maintaining overall health. Although systemic antibiotics are frequently prescribed perioperatively in dental procedures, their impact on microbiota composition and diversity remains inadequately understood. The authors' objective was to characterize the evolution of the gut and oral microbiomes after a course of antibiotics administered for dental surgeries. The authors hypothesized that the microbiome would experience disruption but eventually recover to baseline levels and that patient-related factors would influence the extent of disruption and recovery.

METHODS: Saliva and stool samples were collected from patients undergoing dental surgeries and receiving prophylactic antibiotics (n = 64) at baseline and then at 3, 10, 30, and 90 days after surgery. Microbial diversity and composition were assessed using 16S ribosomal RNA sequencing. Shotgun metagenomics sequencing was applied to a subset of samples to evaluate changes in antimicrobial resistance genes.

RESULTS: Significant (P < .01) declines in alpha diversity were observed in both oral and fecal microbiomes, most notably at days 3 and 10, with near recovery at day 90. The oral microbiome exhibited greater disruption than the gut microbiome, suggesting higher susceptibility to postoperative disturbance. Patient-level factors including sex, race, gastroesophageal reflux disease, and antibiotic type influenced baseline diversity, disruption, and recovery. Results of taxonomic analyses revealed that key health-associated genera were substantially altered postsurgery. Some antimicrobial resistance genes increased in relative abundance over time, consistent with potential long-term ecological consequences of antibiotic use.

CONCLUSIONS: The findings highlight the dynamic response of the human microbiome to antibiotic exposure and oral surgery and underscore the importance of antibiotic stewardship in practice. Further research on functional outcomes and host-microbiome interactions is warranted to optimize perioperative care in dentistry.

PRACTICAL IMPLICATIONS: Consideration of patient factors is essential to minimize unnecessary disruption of the microbiome and mitigate the risk of developing resistance.},
}

@article {pmid42524914,
year = {2026},
author = {Calixto, SL and Macedo, ACLP and Aguiar, JAK},
title = {GUT MICROBIOTA ALTERATIONS IN RODENT MODELS OF CHOLESTASIS INDUCED BY BILE DUCT LIGATION: A SYSTEMATIC REVIEW.},
journal = {Arquivos de gastroenterologia},
volume = {63},
number = {},
pages = {e25159},
doi = {10.1590/S0004-2803.24612025-159},
pmid = {42524914},
issn = {1678-4219},
mesh = {Animals ; *Cholestasis/microbiology ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Ligation ; Bile Ducts/surgery ; Mice ; *Dysbiosis/microbiology ; Rats ; },
abstract = {BACKGROUND AND OBJECTIVE: Cholestatic liver diseases are a major public health issue, marked by impaired bile flow and significant disruptions in liver and systemic physiology. Growing evidence points to the gut microbiota as a key player in cholestasis pathogenesis through gut-liver axis interactions. This systematic review aimed to synthesize and evaluate current findings on intestinal microbiota changes in rodents (rats and mice) subjected to bile duct ligation (BDL)-induced cholestasis, focusing on microbial diversity, taxonomic shifts, and potential pathophysiological implications.

METHODS: A comprehensive literature search was conducted in PubMed, Scopus, and Embase for studies published from January 2020 to February 2025, following PRISMA guidelines. Eligible studies included original research using BDL in rodents without therapeutic intervention and reporting gut microbiota profiles. Data were qualitatively analyzed, emphasizing experimental conditions and microbiome outcomes.

RESULTS: Twenty-two studies met inclusion criteria. Most used 16S rRNA sequencing; two used shotgun metagenomics. BDL consistently induced gut dysbiosis, with reductions in alpha diversity (in most studies), altered beta diversity, and shifts in dominant phyla such as Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobiota. At finer taxonomic levels, increases in Prevotella, Enterococcus, Escherichia coli, and Alistipes were common, while Lactobacillus and Ruminococcus often decreased. Elevated levels of Akkermansia muciniphila and Bifidobacterium pseudolongum may represent compensatory microbial responses.

CONCLUSION: Bile duct ligation (BDL)-induced cholestasis leads to complex changes in the microbiota that can worsen intestinal barrier integrity, increase bacterial translocation, and intensify liver inflammation. These findings reinforce the central role of the gut-liver axis and corroborate the potential of microbiota-targeted therapies in the management of cholestatic liver diseases. However, as most of the available evidence derives from experimental models, further well-designed clinical studies are needed to validate the safety, efficacy, and translational applicability of these strategies in human diseases.},
}

Animals
*Cholestasis/microbiology
*Gastrointestinal Microbiome/physiology
Disease Models, Animal
Ligation
Bile Ducts/surgery
Mice
*Dysbiosis/microbiology
Rats

@article {pmid42525193,
year = {2026},
author = {Feng, WJ and Qin, C and Zhang, MS and Luo, ZY and Chen, BW and Wu, L and Zhang, FG and Deng, JJ and Luo, XC},
title = {Seeking soil microbial degraders and enzymatic genes for efficient biomass recycling.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42525193},
issn = {1559-0291},
support = {2022-440000-4301030404-9580//The Dedicated Fund for Rural Revitalization in Guangdong Province/ ; 202206010137//Science and Technology Program of Guangzhou/ ; 2022A1515010568//Natural Science Foundation of Guangdong Province/ ; },
abstract = {Biodegradation is the most sustainable biomass recycling strategy, yet the absence of efficient microbial degraders remains a critical bottleneck. While soil microorganisms can decompose diverse biomass, their functional specificity for distinct agricultural by-products remains inadequately characterized. To address this, five agricultural by-products, including fish skin, soybean meal, shrimp shell, corn straw and chicken feather, were individually or combinatorially incubated in soil. Comparative analysis of 16 S rRNA amplicons and metagenomics from actively degrading microbial communities versus native soil identified key functional degraders. Declines in Chao1 and Shannon indices within biomass-amended soil groups indicated community simplification, driven by the dominance of novel utilizers over indigenous taxa. Genera enriched in native soil were replaced by divergent taxa across biomass types, revealing substrate-dependent community succession. LEfSe analysis identified biomass-specific utilizers at multiple taxonomic levels. Co-occurrence network analysis showed strong positive co-occurrence patterns between significantly enriched operational taxonomic units (OTUs), suggesting potential co-occurrence patterns and shared responses to biomass amendment. FAPROTAX revealed enhanced C/N/S metabolism during biomass utilization. Metagenomic screening identified markedly higher numbers of biomass-degradation genes encoding hydrolases (e.g., proteases, cellulases, chitinases), consistent with significantly elevated enzyme activities in amended soils compared to undetectable levels in controls. Among six candidate OTUs substantially enriched in chicken feather-amended soil, three species demonstrated efficient feather degradation, with some exhibiting multi-substrate capability. This study elucidates substrate-dependent biomass cycling in soil and provides candidate degraders, including Vicinamibacterales-related OTUs, unclassified Enterobacteriaceae, Sphingobacterium paludis, Sphingobacterium griseoflavum, and Lysinibacillus mangiferihumi, as well as enzymatic gene resources for engineered biomass recycling.},
}

@article {pmid42525291,
year = {2026},
author = {Gutiérrez-Ávila, JL and Gutiérrez-Rebolledo, GA and Avila-Bonilla, RG and Pardo, MES},
title = {Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {42525291},
issn = {1432-1432},
abstract = {The murine model is a standard system in translational microbiome research, yet its functional equivalence to the human microbiome remains debated. To evaluate its translational validity, we conducted a comparative whole-genome shotgun (WGS) metagenomic meta-analysis, integrating an initial retrieval of 520 datasets from 5 independent cohorts (BioProjects) across Homo sapiens (n = 202), Mus musculus (n = 75), and Drosophila melanogaster (n = 243) samples. Taxonomic and functional profiles were evaluated using strict bioinformatic quality control and batch-effect mitigation. Taxonomic profiling revealed pronounced divergence driven by host-specific ecological constraints and filtering. However, metabolic reconstruction demonstrated substantial functional equivalence, supporting the functional redundancy hypothesis for core mammalian metabolic circuits. We also noted a methodological vulnerability in our dataset: a low-depth murine sample clustered with invertebrate profiles, suggesting that technical noise or insufficient depth might artificially compress mammalian functional diversity. Comparative analysis identified sex-biased metabolic pathways conserved across mammalian hosts. Specifically, we observed a consistent enrichment of steroid metabolism in females and mineralocorticoid regulation in males. These findings indicate that functional conservation between humans and mice is modular rather than global. Consequently, the translational value of the murine model lies in domain-specific functional equivalence rather than taxonomic imitation. Moreover, the conservation of sex-specific metabolic signatures suggests that biological sex is a fundamental organising principle of microbiome function. This study highlights the necessity of mapping conserved metabolic modules and rigorously controlling inter-study variance to effectively deploy murine models in biomedical research.},
}

@article {pmid42526286,
year = {2026},
author = {Tito Tadeo, RY},
title = {Comment on: "Glucose metabolism's impact on Blastocystis presence in the human gut".},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {64},
number = {},
pages = {106736},
doi = {10.1016/j.clnu.2026.106736},
pmid = {42526286},
issn = {1532-1983},
}

@article {pmid42526571,
year = {2026},
author = {Ji, Q and Liu, S and Wang, C and Liang, G and Hou, G and Liu, X and Yu, Z and Wang, Z and Liu, R},
title = {Heavy metal (Cu(II)) Stress Alters Lysogeny-Lysis Balance and Drives Phage-mediated Transfer of Co-resistance in the Activated Sludge Process.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128858},
doi = {10.1016/j.envpol.2026.128858},
pmid = {42526571},
issn = {1873-6424},
abstract = {The co-selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) by heavy metals poses significant ecological risks. However, the contribution of bacteriophages (phages), particularly temperate phages, to this process via horizontal gene transfer (HGT) remains poorly understood. Here, we integrated metagenomics, metaviromics, and metatranscriptomics to investigate the impact of escalating Cu(II) concentrations (0.05-20.00 mg/L) on phage lifestyle dynamics and the dissemination of resistance genes in an activated sludge reactor. Our results revealed that phage-mediated HGT events of resistance genes were strongly threshold-dependent, predominantly occurring at high Cu(II) levels (10.00-20.00 mg/L). While the general temperate phage community shifted toward lysogeny to cope with stress, specific phages that mediated HGT of resistance genes exhibited higher lytic activity. Metatranscriptomic analysis further indicated upregulated transcriptional activity of HGT-associated MRGs under high Cu(II) stress, potentially conferring an adaptive advantage to hosts against metal toxicity. Notably, nearly all HGT events were associated with temperate phages, among which approximately 40% of the identified viral clusters (VCs) simultaneously harbored multiple resistance types, even in the absence of antibiotic selective pressure. Collectively, our findings highlight the important role of temperate phages in mediating resistance gene dissemination under Cu(II) stress and underscore the need to incorporate viral dynamics into resistance risk assessment in activated sludge systems.},
}

@article {pmid42166402,
year = {2026},
author = {Peta Martinez, NA and Reinoso Arnaldi, M and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in <italic>Drosophila</italic> with Kdm5 Deficiency.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-21},
pmid = {42166402},
issn = {1421-9859},
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B, or KDM5C are found in patients with intellectual disability and ASD. Here, we use a genetically tractable Drosophila model of loss-of-function of the ASD-associated chromatin regulator Kdm5 to investigate how host genetic disruption influences gut microbial composition and social behavior. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5LOF) revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: We evaluated multiple microbiota-based interventions, including probiotic supplementation with L. plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in adult Kdm5LOF flies. Gut bacterial abundance was quantified using colony-forming unit assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5LOF and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5LOF flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5LOF mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5LOF recipient flies.

CONCLUSION: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships in the context of disruption of an ASD-associated gene and for studying microbiota-based modulation of host physiology and behavior. All experiments were conducted in adult flies, and thus, these findings reflect post-developmental effects of Kdm5 disruption.},
}

@article {pmid42508343,
year = {2026},
author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK},
title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.},
journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine},
volume = {237},
number = {},
pages = {112830},
doi = {10.1016/j.apradiso.2026.112830},
pmid = {42508343},
issn = {1872-9800},
abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.},
}

@article {pmid42508663,
year = {2026},
author = {Wang, Z and Gu, Z and Yan, C and Zhou, J and Dai, B and Luo, L and Wang, X and Shi, P and Xia, S},
title = {Sulfur vacancies enhance pyrite-driven autotrophic denitrification: mechanistic insights into electron-supplying pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135508},
doi = {10.1016/j.biortech.2026.135508},
pmid = {42508663},
issn = {1873-2976},
abstract = {Pyrite-driven autotrophic denitrification (PAD) is a promising carbon-free strategy for nitrate-contaminated wastewater treatment, yet the role of sulfur vacancies (SVs) remains poorly understood. Herein, we investigated the effects of SVs on denitrification activity, interfacial reactivity, and microbial mechanisms in PAD. Electrochemical characterization and batch tests indicated that SVs introduction boosted electron release from pyrite, achieving 98.1% nitrate removal, 1.59-fold higher than pristine pyrite. By integrating X-ray photoelectron spectroscopy, density functional theory calculations, and metagenomic results, we propose a mechanistic framework in which SVs enhance the electron-supplying capacity of pyrite via two routes: (i) SVs strengthen interactions between pyrite and microbial electron shuttles (e.g., riboflavin and methyl-naphthoquinone), supporting the potential involvement of extracellular electron transfer in enhancing electron availability to denitrifiers; and (ii) SVs are expected to weaken local Fe-S bonding and promote Fe(III)-mediated pyrite oxidation, thereby favoring Fe(II) mobilization and the potential involvement of sulfur intermediates (S[0], S2O3[2-]) during PAD. These changes were accompanied by altered surface Fe/S speciation and enrichment of sulfur-oxidizing denitrifiers, particularly Thiobacillus. Additionally, SV-enriched PAD system also exhibited superior resistance to antibiotic and metal stress and achieved continuous nitrogen polishing from real secondary effluent, confirming its strong potential for engineering scalability and practical implementation.},
}

@article {pmid42509323,
year = {2026},
author = {Spazzapan, M and Raison, N and Steves, C and Sahai, A},
title = {The urinary microbiome, overactive bladder and bladder pain syndrome/interstitial cystitis - mechanisms, diagnostics and therapeutic opportunities.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
pmid = {42509323},
issn = {1759-4820},
abstract = {Overactive bladder and bladder pain syndrome/interstitial cystitis are prevalent, multifactorial disorders with poorly understood pathophysiology. The discovery of the urinary microbiome has overturned the sterile urine paradigm and created new opportunities for mechanistic and translational research. Increasing evidence suggests that bladder microbial communities are associated with urothelial signalling, immune tone and neural pathways that influence urgency, pain and treatment response. In overactive bladder, Lactobacillus-predominant profiles are associated with lower symptom burden and improved response to pharmacotherapy, whereas Gardnerella-enriched and Pseudomonadota-enriched communities positively correlate with refractory disease. In bladder pain syndrome/interstitial cystitis, microbial alterations are not based on a single pathogenic signature but converge on metabolic and immune dysregulation. Multi-omics studies integrating metagenomics, metabolomics and host immune data are beginning to define functional pathways linking microbial metabolites, epithelial barrier function and nociceptor sensitization. Results from emerging clinical trials suggest that urinary microbiome profiling might enable patient stratification and inform treatment selection, whereas interventions, such as probiotics, oestrogen therapy or dietary modulation, hold potential as adjunctive strategies. Together, these advances position the urinary microbiome as a promising contributor to lower urinary tract health and a potential target for precision urology, although the functional importance and causal role of the low-biomass urinary microbiome in disease remain crucial unresolved questions.},
}

@article {pmid42509522,
year = {2026},
author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL},
title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {42509522},
issn = {1618-0860},
support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; },
abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.},
}

@article {pmid42509999,
year = {2026},
author = {Hazan, S and Spradling-Reeves, KD and Papoutsis, A and Walker, SJ},
title = {Correction: Hazan et al. Shotgun Metagenomic Sequencing of Gut Microbiota in Triplet Sibling with ASD and Gastrointestinal Symptoms: A Descriptive Case Report. Children 2020, 7, 255.},
journal = {Children (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/children13070863},
pmid = {42509999},
issn = {2227-9067},
abstract = {The title of this publication [...].},
}

@article {pmid42510718,
year = {2026},
author = {Liu, J and Liu, S and Zhou, X and Zhong, Z and Hu, Q and Li, Q and Lin, Z and Huang, X and Zheng, B},
title = {Protective Effects of Fructus mume Extract Against Deoxynivalenol-Induced Intestinal and Liver Injury in Mice.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141172},
pmid = {42510718},
issn = {2079-7737},
support = {JZ230013//the Key Project of Fujian Provincial Education and Scientific Research Program for Young and Middle-aged Teachers/ ; KLY24109XA//Fujian Provincial Department of Finance/ ; },
abstract = {Deoxynivalenol (DON), a prevalent mycotoxin, induces intestinal and hepatic injury. Fructus mume extract (FME) possesses bioactive properties, yet its protective role against DON remains unclear. This study aimed to investigate the protective mechanisms of FME in DON-challenged mice. Male C57BL/6 mice were divided into control, DON (3 mg/kg), and DON with low-, medium-, or high-dose FME groups for 4 weeks. Analyses included histopathology, UPLC-Q-TOF-MS, network pharmacology, biochemistry, qRT-PCR, immunohistochemistry, a TUNEL assay, metagenomics, and metabolomics. FME significantly alleviated growth inhibition and tissue damage. Among the 38 components identified by UPLC-Q-TOF-MS, all 38 acted on 156 genes, including IL-1β, caspase3, and BAX, to alleviate DON-induced intestinal and hepatic injury. FME enhanced hepatic antioxidant capacity and reduced inflammation by suppressing NF-κB signaling. FME upregulated tight junction proteins, inhibited apoptosis, and restored microbial diversity by enriching beneficial bacteria. Metabolomics revealed FME reversed DON-induced metabolic disruptions in the liver. Correlation analysis indicated FME remodeled the microbiota-liver metabolite network. In conclusion, FME attenuates DON-induced intestinal injury by modulating the gut-liver axis through antioxidant, anti-inflammatory, and anti-apoptotic activities.},
}

@article {pmid42510727,
year = {2026},
author = {Meng, X and Xue, Y and Shen, M and Shen, Y},
title = {UV Aging Strengthens the Effects of Polyvinyl Chloride Microplastics on Soil Bacterial Community Structure and Predicted Functional Profiles.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141181},
pmid = {42510727},
issn = {2079-7737},
support = {42507354//National Natural Science Foundation of China/ ; 24KJB610005//Jiangsu Provincial Fundamental Science Research Program for Higher Education Institutions/ ; },
abstract = {Soil microplastics undergo aging, but how aging modifies their effects on soil bacterial communities remains unclear. Here, we conducted a 180-day incubation experiment with no PVC (CK), pristine PVC microplastics (IP), and UV-aged PVC microplastics (AP, 0.5%, w/w). UV aging markedly altered PVC surface properties: roughness increased from approximately 12.9 to 21.8 nm, water contact angle decreased from 91.44° to 82.38°, and the O/C ratio increased from 0.37 to 0.43. Bacterial richness indices were largely unchanged, whereas Shannon diversity decreased under AP, indicating reduced community evenness. Bray-Curtis analysis showed significant community separation among treatments (PERMANOVA: R[2] = 0.364, p = 0.003), with UV aging further altering the trajectory of PVC-induced community reorganization. At the genus level, AP was associated with enrichment of Methylobacillus and lower robustness in exploratory co-occurrence network analysis, suggesting a distinct bulk-soil bacterial response compared with IP. Functional prediction further suggested that AP and IP were associated with different predicted pathway profiles, with AP showing higher predicted representation of pathways related to carbon metabolism, respiratory energy metabolism, potential prokaryotic carbon fixation, environmental sensing, cellular maintenance, and antimicrobial-resistance-associated categories, whereas IP was mainly associated with transport- and communication-related predicted functions. These predicted functional patterns require further validation using metagenomic, qPCR, transcriptomic, biochemical, or chemical approaches. Overall, these findings highlight the need to consider the UV aging status of PVC microplastics when evaluating their effects on soil bacterial communities.},
}

@article {pmid42510739,
year = {2026},
author = {Liu, X and Zhao, X and Li, H and Wu, Y and Yao, Y and Wang, Z},
title = {Comparative Study on Blood Gas Indicators, Antioxidant Capacity, Intestinal Metabolome, and Microbiome in High- and Low-Performance Tumbler Pigeons.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141193},
pmid = {42510739},
issn = {2079-7737},
support = {2023B02036//The Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; },
abstract = {The purpose of this experiment is to investigate the differences in blood gas indicators, antioxidant indicators, and lactate content between high- and low-performance tumbler pigeons after exercise, and to use metabolomics and metagenomics techniques to screen for differential metabolites and bacteria related to tumbler pigeon exercise. This experiment selected 12 high-performing (HP) and 12 low-performing (LP) tumbler pigeons, half male and half female, and all pigeons were raised under the same conditions. Three experimental pigeons were grouped for exercise training, with a 20 min training session. The results showed significant differences (p < 0.05) in multiple blood gas parameters related to acid-base balance and gas exchange between the HP and LP groups after tumbler pigeon exercise. In addition, the content of glutathione peroxidase (GSH Px), superoxide dismutase (SOD), and catalase (CAT) in the liver of the HP group of tumbler pigeons was significantly lower than that of the LP group (p < 0.05). In comparison, the content of malondialdehyde (MDA) was significantly higher than that of the LP group (p < 0.05). The content of lactate (Lac) was significantly higher than that of the LP group (p < 0.05). Non-targeted metabolomics analysis revealed that differential metabolites were mainly enriched in pathways such as biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid synthesis. Intestinal metagenomics analysis revealed that the Corynebacteriaceae, Bacillus, Pseudomonad phylum and Corynebacterium were significant biomarkers with significant differences in the gut microbiota of the HP group of tumbler pigeons (p < 0.05). In summary, there are significant differences in blood physiological parameters, antioxidant capacity, lactate content, intestinal metabolites, and gut microbiota between high- and low-performance tumbler pigeons after exercise. This result provides theoretical guidance and data support for cultivating high-performance tumbler pigeons.},
}

@article {pmid42511030,
year = {2026},
author = {Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z and Li, M},
title = {Integrated Rumen Metabolomics and Metagenomics Reveal Microbe-Metabolite Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142152},
pmid = {42511030},
issn = {2076-2615},
support = {BK20241934//Natural Science Foundation of Jiangsu Province/ ; 2022YFF1001200//National Key Research and Development Program of China/ ; },
abstract = {Heat stress impairs dairy cow productivity and rumen function, but rumen metabolic features associated with natural heat tolerance remain unclear. This study generated rumen fluid metabolomic data and integrated them with previously generated metagenomic abundance data from the same heat-tolerant (HT) and heat-sensitive (HS) Holstein cows selected from a cohort of 120 cows using an entropy-weighted TOPSIS model. Untargeted LC-MS identified 116 differential metabolites, including 66 enriched in HS cows and 50 enriched in HT cows. The HS cows showed higher levels of nucleotide-related metabolites, whereas HT cows were enriched in thiamine, L-malate, and argininosuccinic acid. Pathway enrichment mainly involved nucleotide metabolism, pyrimidine metabolism, pyruvate metabolism, and thiamine metabolism. Reanalysis of metagenomic data identified 12 differential microbial taxa, including HT-enriched Prevotella and Ruminococcus flavefaciens. Spearman correlation analysis revealed phenotype-associated microbe-metabolite associations, and ROC analysis based on the discovery dataset suggested that uridine 5'-monophosphate, thiamine, L-malate, and argininosuccinic acid had exploratory potential to distinguish HT and HS cows. These findings provide exploratory evidence that rumen microbe-metabolite associations are related to natural heat tolerance in dairy cows.},
}

@article {pmid42511119,
year = {2026},
author = {Zhang, B and Ma, X and He, Z and Liu, J and Chen, P and Wang, F and Xie, J and Lv, C and Pan, F},
title = {Effects of Perilla Seed Extract Dietary Supplementation on Meat Quality, Rumen Fermentation, and Rumen Microbiome-Metabolome of Tan Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142242},
pmid = {42511119},
issn = {2076-2615},
support = {2023GAAS42//Gansu Academy of Agricultural Sciences/ ; },
abstract = {Perilla seed extract (PSE), a natural resource rich in α-linolenic acid and flavonoids, represents a promising dietary strategy to sustainably optimize rumen fermentation and improve the nutritional profile of ruminant meat. This study evaluated the effects of dietary PSE supplementation on rumen fermentation, microbiome-metabolome profiles, and subsequent meat quality in Tan lambs. Sixty 3-month-old male Tan lambs were randomly assigned to four dietary treatments (n = 15 per treatment) containing 0% (CON), 0.01% (LPSE), 0.03% (MPSE), or 0.05% (HPSE) PSE on a dry matter (DM) basis. In the rumen, the 0.03% PSE inclusion increased the propionate proportion from 20.50% to 23.80% (P-linear = 0.004) and carboxymethyl cellulase activity from 12.45 to 14.85 U/mL (P-linear = 0.007; P-quadratic = 0.045). Exploratory metagenomics showed that 0.03% PSE enriched Prevotella (18.67% to 21.06%) and Ruminococcus_E (1.20% to 2.13%), while decreasing the biohydrogenating genus Butyrivibrio compared with CON (LDA > 2, p < 0.05). These microbial shifts were accompanied by the accumulation of beneficial metabolites (e.g., small peptides and itaconic acid) and up-regulation of the pantothenate and CoA biosynthesis pathway. Consequently, the 0.03% PSE diet optimized meat quality, decreasing shear force by 12.7% (from 45.65 to 39.85 N; P-linear = 0.005, P-quadratic = 0.018) and drip loss (from 4.82% to 3.85%; P-linear = 0.022, P-quadratic = 0.015), while increasing redness (P-linear = 0.012, P-quadratic = 0.045). Furthermore, it increased meat C18:3n-3 (from 0.62% to 0.91%) and total n-3 PUFA (from 1.12% to 1.52%), while decreasing the n-6/n-3 ratio from 6.76 to 5.13 (P-linear ≤ 0.005 for all). Flavor amino acids also increased (P-linear = 0.008). These findings suggest that 0.03% PSE supplementation potentially improves lamb meat quality by favorably modulating rumen fermentation and microbe-metabolite interactions, highlighting its promise as a natural feed additive, though further validation is warranted.},
}

@article {pmid42511143,
year = {2026},
author = {Di Martino, B and Carnevale, M and Corsi, L and Sarchese, V and Pellegrini, F and Smoglica, C and Petrini, A and Martella, V and Marsilio, F and Di Profio, F},
title = {Emerging Mammarenaviruses in Wildlife: Expanding Host Range and Implications.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142263},
pmid = {42511143},
issn = {2076-2615},
abstract = {Mammarenaviruses are enveloped, ambisense, single-stranded RNA viruses capable of causing fatal hemorrhagic fevers and severe neurological disorders in humans. Although muroid rodents have historically been recognized as the primary reservoirs for major pathogens like Lassa virus, recent surveillance has revealed a significant expansion of their host range. This review aims to synthesize current global data regarding the epidemiology of mammarenaviruses in conventional reservoirs and the emergence of novel arenaviruses in non-traditional mammalian hosts. To achieve this, we comprehensively analyzed recent molecular and metagenomic surveillance data, evolutionary studies, and epidemiological reports published worldwide. Key discoveries include Wenzhou virus in Asian house shrews, Plateau Pika virus in plateau pikas, and an independent, geographically clustered of hedgehog-associated arenaviruses across Europe. Ultimately, this review underscores the global distribution of these pathogens and the critical need for continued, multi-host surveillance worldwide.},
}

@article {pmid42511188,
year = {2026},
author = {Meanti, F and Bellassi, P and Fontana, A and Dall'Asta, M and Rebecchi, A},
title = {Unveiling Microbial Dynamics in the Spontaneous Fermentation of Oat and Rice Okara Sourdoughs.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511188},
issn = {2304-8158},
support = {F/310136/01-05/X56//Ministry of Enterprises and Made in Italy/ ; },
abstract = {Sourdough fermentation is increasingly explored as a sustainable strategy for the valorisation of cereal-based by-products, although okara from oat- and rice-based beverage production remains largely underexplored. This study investigates the microbial evolution and nutritional characteristics of oat and rice okara sourdoughs obtained by spontaneous fermentation using the back-slopping technique. High-throughput sequencing revealed dynamic but matrix-dependent microbial composition. At the beginning of fermentation, oat okara was dominated by the Bacillus genus, while the Streptococcus genus was the most abundant in rice okara. After 30 days of back-slopping, the bacterial communities of both matrices were dominated by Lactobacillus, accounting for 80.1% and 73.3% of the relative abundance in oat and rice okara sourdoughs, respectively. Secondary bacterial taxa differed between matrices, with Weissella prevailing in oat okara (7.0%) and Acetobacter in rice okara (11.2%). Yeast communities showed a substrate-dependent temporal succession, being initially dominated by Pichia in both oat and rice okara sourdoughs (96.6% and 97.1%, respectively), whereas Saccharomyces became predominant at later fermentation stages, reaching 54.8% in oat okara and 83.5% in rice okara. From a nutritional perspective, okara sourdoughs exhibited promising characteristics, being rich in proteins and free amino acids, particularly glutamic acid, aspartic acid and leucine. The fatty acid profile was marked by oleic, linoleic and stearic acids, while nutritionally important minerals associated with musculoskeletal and immune function, such as calcium, zinc and selenium, were present in relevant quantities in the sourdoughs. These findings provide new insights into oat and rice okara sourdoughs and support the use of fermented okara as a sustainable ingredient with potential functional relevance.},
}

@article {pmid42511198,
year = {2026},
author = {Zhang, S and Wu, Y and Wang, F and Li, H and Zheng, N and Chen, H and Zhao, Y},
title = {Camel Milk Alleviates Chronic Fatigue Syndrome-like Symptoms in Mice by Modulating the Small Intestinal Microbiota and Inflammation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511198},
issn = {2304-8158},
support = {2025D01B138//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; },
abstract = {This study aimed to investigate the therapeutic effects of camel milk (CM) on chronic fatigue syndrome (CFS) and elucidate the mechanisms underlying the microbiota-gut-brain axis. Using a murine model of CFS induced by chronic restraint and forced swimming stress, we administered lyophilized CM (1500 mg/kg/day, equivalent to approximately 121.5 mg/kg/day in humans based on body surface area conversion using the standard allometric scaling formula) orally. CM supplementation was significantly associated with ameliorated fatigue-like behaviors, as evidenced by prolonged swimming endurance and reduced immobility time. Metagenomic analysis revealed that CM was associated with reshaping of the small intestinal microbiota, including enrichment of beneficial Lactococcus lactis and suppression of pathobionts (H. hepaticus and H. typhlonius). These microbial shifts correlated with increased luminal lactic acid, improved intestinal barrier integrity (increased villus height, reduced crypt depth), and attenuated local inflammation (reduced TNF-α and IL-6, elevated IL-10). Consequently, CM was associated with reduced bacterial translocation and systemic inflammation, and normalization of hypothalamic-pituitary-adrenal (HPA) axis hyperactivity. We conclude that CM is associated with prevention of CFS-like symptoms through modulation of the gut ecosystem and strengthening of the intestinal barrier, potentially breaking the vicious cycle of gut inflammation and HPA axis dysfunction, although causality remains to be established through fecal microbiota transplantation or similar mechanistic studies.},
}

@article {pmid42511274,
year = {2026},
author = {Huang, H and Li, X and Zhang, K and Liang, B and Bai, S and Dong, X and Yan, D},
title = {Dietary Green Alfalfa Supplementation Reduces Backfat Thickness and Improves Muscle Water-Holding Capacity in Diqing Tibetan Pigs.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {42511274},
issn = {2304-8158},
support = {XDYC-QNRC-2023-0394//Young Talent Project of the Yunnan Province Xing Dian Ying Talent Support Program/ ; 202305AF150128//Yunnan Provincial Academician Expert Workstation Project/ ; 202202AE090005, 202302AE090015//Major Science and Technology Special Projects of Yunnan Province/ ; },
abstract = {Feed scarcity constrains livestock production, particularly on the Qinghai-Tibet Plateau. The effects of green alfalfa (GA) on Diqing Tibetan pig performance remain unclear. This study aimed to evaluate GA effects on Diqing Tibetan pig performance and to explore the potential underlying mechanisms through integrated metagenomic, transcriptomic, and metabolomic analyses. Thirty-six Diqing Tibetan pigs were randomly assigned to two groups and fed either a basal diet or a diet containing 90% basal diet and 10% GA. GA did not adversely affect growth performance but reduced 6-7 rib backfat thickness and muscle water loss rate by 19.79% (FDR = 0.027) and 17.80% (FDR = 0.036), while increasing muscle moisture content by 3.51% (FDR = 0.036). GA increased cecal microbial alpha diversity, Bacteroidota-related taxa, and functional genes related to lipid and vitamin metabolism, while decreasing Bacillota and Lactobacillus johnsonii. In the longissimus dorsi, TNNI1, MYL2 and MYL3 were upregulated, whereas FOS and FOSB were downregulated; GA increased vanillyl alcohol, L-histidine, LPE (0:0/22:5), and licochalcone B, but decreased glyceryl monostearate, benzaldehyde, cortisol, tryptamine, 4-ethyloctanoic acid, 8-methylnonanoic acid, and purine. Overall, 10% GA reshaped gut microbial, muscle transcriptomic, metabolomic profiles and collectively influenced 6-7 rib backfat thickness and muscle water-holding capacity in Diqing Tibetan pigs.},
}

@article {pmid42511774,
year = {2026},
author = {Nappo, A and Abbasi, AM and Berno, G and Rueca, M and Smoquina, F and Gruber, CEM and Fabeni, L and Spezia, PG and Carletti, F and Pietrucci, D and Petricciuolo, M and Carnevali, A and Sanna, N and Talarico, C and Federici, E and Chillemi, G and Maggi, F},
title = {Comparative Analysis of Viral Communities in Hospital, University and Urban Wastewater by Shotgun Metagenomic Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511774},
issn = {1422-0067},
support = {CUP F53C24001620001//European Union Next-GenerationEU/ ; Ricerca Corrente-Linea 1 on emerging and re-emerging infections//Ministry of Health/ ; },
abstract = {Wastewater-based surveillance has emerged as a powerful approach for population-level monitoring of pathogen circulation in a timely and non-invasive manner. In this study, shotgun metagenomic sequencing was applied to wastewater samples collected from a hospital (HP), a university campus (UN), and a wastewater treatment plant (WTP). Viral sequences were taxonomically classified using Kraken2. Specifically, HP samples showed the highest viral richness, followed by WTP and UN samples (HP vs. UN, p = 0.0003; WTP vs. UN, p = 0.0018). Using Jaccard distance, significant differences were observed between WTP and UN (R[2] = 0.181, p < 0.001), WTP and HP (R[2] = 0.159, p < 0.001), and UN and HP (R[2] = 0.223, p < 0.001), and similarly, for Sørensen-Dice dissimilarity: WTP vs. UN (R[2] = 0.238, p < 0.001), WTP vs. HP (R[2] = 0.212, p < 0.001), and UN vs. HP (R[2] = 0.307, p < 0.001). Human-associated viral families were detected across all sources, predominantly Poxviridae, Orthoherpesviridae, Polyomaviridae and Circoviridae. Furthermore, the taxonomic composition of indirectly associated viruses, mainly Anelloviridae and Crassvirales, was examined. Overall, these findings support the potential of wastewater metagenomics as a reliable tool for monitoring viral diversity within environmental and public health contexts, although further research is needed to establish its operational utility for routine surveillance applications within a One Health framework.},
}

@article {pmid42511982,
year = {2026},
author = {Xu, Y and Li, C and Zhao, Y and Lei, S and Yang, W and Yao, S and Wu, K and Huang, J and Yu, Z and Chen, S},
title = {Tracking Gut Homeostasis: Key Taxa Transitions and Core Network Hyper-Connectivity as Early Signals of Dysbiosis.},
journal = {Biomedicines},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/biomedicines14071508},
pmid = {42511982},
issn = {2227-9059},
support = {2022JJ30916//Hunan Provincial Natural Science Foundation/ ; 82270564//National Natural Science Foundation of China/ ; 82470564//National Natural Science Foundation of China/ ; 2022M713521//China Postdoctoral Science Foundation/ ; },
abstract = {Background: Although the gut microbiota is generally recognized to remain relatively stable in healthy individuals, its taxonomic composition still undergoes subtle temporal fluctuations. To systematically characterize these dynamic variations, we adopted "enterotypes" as a macroscopic and practical metric to evaluate the structural dynamics of the intestinal microbial community. Methods: We longitudinally recruited a cohort of healthy adults and collected a total of 72 shotgun metagenomic fecal samples across approximately 40 days. All samples underwent metagenomic sequencing, and subjects were grouped by their predominant enterotypes and longitudinal fluctuation patterns. We evaluated the microbial markers and the longitudinal co-occurrence network topologies of different groups to clarify the potential factors causing gut microbial fluctuations. Results: Longitudinal tracking revealed that those undergoing persistent alterations in microbial communities exhibited diarrhea symptoms, accompanied by markedly greater variability in gut microbiota. The reduction in Alistipes shahii is a potential predictive marker for community instability, exhibiting a cross-validated AUC of 0.824 (95% CI: 0.760-0.888). Furthermore, the co-occurrence network and correlation analysis indicated that fluctuating communities exhibited significantly higher clustering coefficients and denser connectivity among core taxa. Rather than indicating robustness, this dense architecture reflected an increased degree of microbial interdependence within the unstable gut microbial community. Conclusions: This preliminary study discovered candidate bacteria taxa that may serve as indicators of disturbances in the gut microbiota. Furthermore, the hyper-connectivity during continuous fluctuations suggested that increased interdependent microbial relationships meant diminished gut resilience. These results offer a new perspective for detecting early signals of dysbiosis and understanding mechanisms underlying stability of gut microbiota.},
}

@article {pmid42512542,
year = {2026},
author = {Liu, L and Zhang, J and Ma, Q and Wang, J},
title = {Herpesvirus-Associated Visual Impairment: Clinical Features, Etiological Spectrum, and Treatment Outcomes in Consecutive Patients from a Tertiary Neurological Clinic.},
journal = {Brain sciences},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/brainsci16070768},
pmid = {42512542},
issn = {2076-3425},
abstract = {[Background] Herpesvirus infections can induce diverse visual impairments with permanent sequelae, yet systematic data on their clinical spectrum and outcomes remain scarce. [Methods] We conducted a single-center retrospective cohort study at the Department of Neurology, Beijing Tongren Hospital, Capital Medical University. Thirteen consecutive patients (19 affected eyes) with herpesvirus-related visual impairment admitted between January 2016 and January 2025 were enrolled. Demographic data, clinical manifestations, etiological tests (polymerase chain reaction [PCR], metagenomic next-generation sequencing [mNGS], serology), neuroimaging, treatment regimens, and visual outcomes were analyzed. [Results] The cohort had a mean age of 50.4 years (range 31-66), with male predominance (84.6%, 11/13). Varicella zoster virus (VZV) was the leading pathogen (76.9%, 10/13), followed by herpes simplex virus type 1 (HSV-1), Epstein-Barr virus (EBV), and pseudorabies virus (PRV). Eight patients (61.5%) developed optic neuritis (ON) secondary to VZV infection, and five patients (38.5%) suffered from acute retinal necrosis (ARN), which was caused by VZV (n = 2), HSV-1 (n = 2), and PRV (n = 1). Bilateral involvement occurred in 46.2% (6/13) of patients. ARN was associated with the most severe visual loss. At the disease nadir, 46.2% of patients (6/13) presented with no light perception (NLP). Notably, five of these six NLP cases were diagnosed with ARN. Etiological confirmation was achieved in only 38.5% (5/13) of cases. mNGS of cerebrospinal and vitreous fluid, alongside aqueous humor PCR, are pivotal for diagnosing HSV-1/EBV mixed infections and rare PRV infection. All patients received antiviral therapy, 11 of whom (84.6%) were treated with intravenous antiviral agents. Glucocorticoids were administered as combination therapy to all patients. However, only one of eight VZV-ON eyes showed genuine visual improvement. In VZV-ARN, the initially involved eyes stayed NLP at final follow-up, while the fellow eyes recovered vision. Still, all non-VZV ARN patients had persistent bilateral NLP during follow-up. [Conclusions] Herpesvirus-associated visual impairment is dominated by VZV, manifests as ON or ARN, and carries a high risk of severe permanent vision loss-particularly in ARN. The emergence of zoonotic PRV underscores the need for heightened clinical vigilance. Diagnostic delays and insufficient interdisciplinary collaboration contribute substantially to poor outcomes.},
}

@article {pmid42513364,
year = {2026},
author = {Zheng, L and Wang, X and Li, J and He, H and Chen, X},
title = {Metagenomic Next-Generation Sequencing Versus Conventional Microbiological Tests for Pathogen Identification and Prognostic Evaluation in Pediatric Patients with Post-Cardiac Surgery Infections: A Retrospective Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/jcm15145450},
pmid = {42513364},
issn = {2077-0383},
support = {Chinese Academy of Medical Sciences Fuwai Hospital high-level Hospital Research Fund（2025-GSP-QN-40,2025-GSP-QN-7 and 2025-GSP-GG-19）//Fu Wai Hospital/ ; },
abstract = {Object: Postoperative infection is a severe complication after pediatric cardiac surgery, which is closely associated with sepsis, multiple organ dysfunction, prolonged mechanical ventilation, extended ICU stay and increased mortality. Conventional microbiological tests (CMT) are limited by low sensitivity, long turnaround time, and poor capacity for detecting viruses and polymicrobial infections. This study aimed to compare the diagnostic efficacy of mNGS with that of CMT, and to explore the impact of polymicrobial infection on clinical outcomes in this high-risk pediatric population. Methods: A retrospective cohort study was conducted on 4889 pediatric patients admitted to the PICU after cardiac surgery from January 2025 to March 2026. A total of 510 patients were diagnosed with postoperative infections, including 879 CMT specimens and 86 mNGS specimens enrolled for analysis. Pathogen detection rates, pathogen spectrum and antimicrobial resistance profiles were compared between the two detection methods. Clinical prognostic indicators including mechanical ventilation duration, PICU length of stay and the requirement for continuous renal replacement therapy (CRRT) were further compared between patients with polymicrobial infection and monomicrobial infection. Results: Respiratory tract infection accounted for 87.8% of all postoperative infections, and Gram-negative bacteria were the predominant pathogens, accounting for 65.9%. The overall pathogen detection rate of mNGS was significantly higher than that of CMT (79.1% vs. 56.5%, p < 0.001). Notably, mNGS exhibited significantly better performance in detecting viruses (37.2% vs. 5.8%, p < 0.001), anaerobic pathogens and polymicrobial infections (38.2% vs. 5.4%, p < 0.001). Patients with polymicrobial infections had significantly longer mechanical ventilation time, longer PICU stay, and higher CRRT utilization rate (all p < 0.05), indicating a poorer clinical prognosis. Gram-negative bacteria showed high resistance to penicillins and early-generation cephalosporins, but remained susceptible to carbapenems and β-lactamase inhibitor combination agents. Gram-positive bacteria showed a high resistance rate to penicillin, while maintaining 100% susceptibility to vancomycin and linezolid. Conclusions: mNGS serves as a more sensitive and comprehensive tool for pathogen detection in children with post-cardiac surgery infections, especially for viral and polymicrobial infections. Polymicrobial infection is an independent risk factor for adverse clinical outcomes. Routine application of mNGS in critically ill children may help guide targeted antimicrobial therapy and improve prognosis.},
}

@article {pmid42513896,
year = {2026},
author = {Ma, P and Ma, F and Hu, Q and Zhang, W and Gu, H and Wei, D and An, Z},
title = {Study on Gut Microbiota Adaptation of Plateau Zokor (Eospalax baileyi) to High-Altitude Environments.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071390},
pmid = {42513896},
issn = {2076-2607},
abstract = {To further investigate altitude-associated variations in gut microbiota and serum metabolites of plateau zokors (Eospalax baileyi) and elucidate their adaptive mechanisms to high-altitude environments, we performed fecal metagenomic sequencing and serum metabolomic profiling (Q200 platform) on individuals from high (3700 m, n = 6) and low (2700 m, n = 6) elevations, followed by integrated analysis of microbial and metabolomic datasets. Results indicated that in high-altitude plateau zokors, the relative abundance of Firmicutes decreased, while that of Bacteroidota increased. The dominant genera within this group were identified as Bacteroides and unclassified members of the Lachnospiraceae family. Moreover, the abundances of Bacteroides and unclassified members of the Muribaculaceae family increased with elevation. At the species level, seven fully annotated differentially abundant taxa were identified: Candidatus Amulumruptor caecigallinarius, Schaedlerella arabinosiphila, Muribaculum gordoncarteri, Heminiphilus faecis, Prevotellamassilia timonensis, Staphylococcus aureus, and Bacteroides graminisolvens. KEGG enrichment analysis indicated significant upregulation (p < 0.05) of energy supply pathways, such as oxidative phosphorylation, and antioxidant-related pathways, including β-alanine and lysine metabolism, in the high-altitude group. Conversely, cysteine and methionine metabolism pathways were markedly downregulated (p < 0.05). Serum levels of ursodeoxycholic acid and tauroursodeoxycholic acid (TUDCA) were significantly elevated (p < 0.05), while deoxycholic acid (DCA) levels decreased (p < 0.05). In conclusion, the composition and function of gut microbiota, along with serum metabolite profiles, differ significantly (p < 0.05) between plateau zokors from different altitudes. Through synergistic interactions between gut microbiota and host metabolites, plateau zokors develop adaptive mechanisms that integrate energy metabolism, oxidative stress response, intestinal barrier integrity, and mucosal immunity. This ultimately facilitates their acclimatization to high-altitude extreme environments characterized by hypoxia and low temperatures.},
}

@article {pmid42513908,
year = {2026},
author = {Carvalho, APA and Almada, MS and Leal, CD and Fernandes, J and Costa, MC and Fonseca, VS and Giovanetti, M and Alcantara, LCJ and Araújo, JC},
title = {International Airport Wastewater as a Sentinel Site for Genomic Surveillance of Human Viruses and Bacteriophages.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071402},
pmid = {42513908},
issn = {2076-2607},
support = {424004/2021-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 01779-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 306899/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 0000000-X//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
abstract = {Airports are strategic targets for wastewater-based epidemiology because they concentrate highly mobile populations and may provide early signals of pathogen circulation. However, metagenomic investigations of airport wastewater remain limited, particularly in South America. Here, we present one of the first hybrid-capture target-enriched metagenomic investigations of airport wastewater in Brazil, integrating the detection of human-associated viruses and bacteriophage-derived host signatures to evaluate airports as sentinel surveillance sites. Seven untreated wastewater samples collected from a major Brazilian airport between December 2021 and March 2023 were concentrated, subjected to nucleic acid extraction, and analyzed using hybrid-capture target-enriched next-generation sequencing. Taxonomic analysis identified 615 viral and bacteriophage-associated taxa, including 440 viruses and 175 bacteriophages. Among the viral fraction, 21 human-associated viral taxa representing eight viral families were selected for detailed analysis. Norovirus GII was detected in all samples, while Mamastrovirus 1 and JC polyomavirus were detected in six of seven samples. SARS-CoV-2 and dengue virus type 1 were simultaneously detected in the March, 2023 sample. The bacteriophage fraction comprised 47 host-associated phage groups, with Streptococcus-associated phages predominating across samples. These findings demonstrate that airport wastewater can capture diverse human viral and bacteriophage-derived signatures associated with population mobility, supporting its application in environmental genomic surveillance and early-warning systems for emerging and circulating pathogens.},
}

@article {pmid42513909,
year = {2026},
author = {Luo, D and Ponsero, AJ and Wright, K and Baker, DJ and Telatin, A and Townsley, C and Giotis, ES},
title = {Microbiome Stability in Wild and Rehabilitated Insectivorous Bats Revealed by Shotgun Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071403},
pmid = {42513909},
issn = {2076-2607},
support = {MR/Z506242/1/MRC_/Medical Research Council/United Kingdom ; RGS\R2\242527//Royal Society/ ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG2260/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.},
}

@article {pmid42513924,
year = {2026},
author = {Li, F and Suo, L and Bian, K and Sun, K and Yang, C and Tang, J},
title = {First Report of Bergeyella zoohelcum Associated with Hemorrhagic Pneumonia in Forest Musk Deer (Moschus berezovskii): Evidence from Bacterial Culture, 16S rRNA Sequencing, and Metagenomic Analysis.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071418},
pmid = {42513924},
issn = {2076-2607},
support = {2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; 2024k-08//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; },
abstract = {Hemorrhagic pneumonia is a severe and often fatal disease in captive forest musk deer (Moschus berezovskii), but the pathogen remains incompletely understood. Based on incomplete statistics, the estimated incidence in captive populations ranges from 20% to 80%, with the disease occurring mainly in autumn, winter, and early spring. The disease has an acute onset and rapid progression. Due to the species' strong stress response, affected animals rarely show behavioral changes, making early detection difficult. In this study, we investigated a mortality case presenting with oral bleeding and hematemesis on a forest musk deer farm. Postmortem examination revealed diffuse hemorrhagic pneumonia, and lung tissue samples were collected for histopathology, bacterial isolation, full-length 16S rRNA gene sequencing, and DNA/RNA virome sequencing. Histological examination showed extensive alveolar hemorrhage, fibrinous exudate, and macrophage infiltration. Bacterial culture and 16S rRNA gene sequencing identified Bergeyella zoohelcum as the predominant bacterium, accounting for 100% of the bacterial community in the lung tissue. Virome analysis revealed predominantly DNA bacteriophages (e.g., Cirlivirales, Cremevirales, Microviridae) and no known pathogenic RNA viruses; only seven low-abundance, unclassified RNA viral contigs of low completeness were detected. These results indicate that B. zoohelcum is the likely causative agent of hemorrhagic pneumonia in this case, with no evidence of viral involvement. This study provides the first direct association of B. zoohelcum with hemorrhagic pneumonia in forest musk deer, highlighting its pathogenic potential and the importance of monitoring this bacterium in captive populations.},
}

@article {pmid42513986,
year = {2026},
author = {Gan, L and Fang, S and Wu, H and Yao, T and Chen, W and Li, Y and Han, Y and Zhou, L},
title = {Metagenomic Insights into the Seasonal Distribution and Dissemination Risks of Biocide and Metal Resistance Genes in a Subtropical Coastal Ecosystem.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071480},
pmid = {42513986},
issn = {2076-2607},
support = {No. GXKEYLA-2023-01-1//Ministry of Agriculture and Rural Affairs/ ; },
abstract = {The widespread use of antimicrobial biocides and metals has led to the continuous accumulation of biocide and metal resistance genes (BMRGs) in the environment. The issue is of growing concern, as it reduces the efficacy of these agents and poses a potential threat to coastal ecological security. However, the extent of coastal BMRG pollution, its transmission mechanisms, and the influence of seasonal variations on its assembly remain poorly understood. In this study, metagenomic sequencing was employed to investigate BMRGs, microbiomes, and mobile genetic elements (MGEs) within the subtropical nearshore ecosystem of the Beibu Gulf during the autumn and winter seasons. A total of 33 BMRG types and 457 subtypes were detected, with higher subtype diversity in winter than in autumn (440 vs. 326 subtypes). Notably, genes resistant to multi-biocides exhibited the highest diversity, whereas those resistant to both biocides and metals were the most abundant. Co-occurrence network analysis showed that 22 of the 23 detected BMRGs in the winter network were associated with MGEs, especially transposase-related elements such as tnpA. Path modeling indicated that BMRG abundance was more strongly associated with bacterial community composition in autumn, whereas MGE-related variables showed stronger associations in winter. These findings suggest a pronounced seasonal shift in the underlying mechanisms shaping BMRG dynamics, with bacterial communities playing a dominant role in autumn and MGEs playing a more critical role in winter. This seasonal shift highlights the need for season-specific monitoring of BMRGs, coastal pollution control, and resistance-risk management in subtropical coastal ecosystems.},
}

@article {pmid42513994,
year = {2026},
author = {Duan, C and Wang, D and Tan, L and Wang, Q and Tan, Z and Cheng, Y},
title = {Habitat-Dependent Ecological Differentiation of Soil and Water Microbiomes in High-Altitude Alpine Meadow Ecosystems on the Qinghai-Tibetan Plateau.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071489},
pmid = {42513994},
issn = {2076-2607},
support = {2023-NK-147//Science and Technology Department of Qinghai Province/ ; },
abstract = {High-altitude ecosystems are characterized by extreme environmental conditions that strongly influence microbial community structure and function. However, whether soil and water microbiomes exhibit similar ecological responses to environmental variation in alpine meadow ecosystems on the Qinghai-Tibetan Plateau remains poorly understood. Here, we combined 16S rRNA gene amplicon sequencing and metagenomic sequencing to compare soil and water microbiomes across two regions (LZ and NQ) with distinct physicochemical profiles. Environmental heterogeneity was more pronounced in water habitats, where all measured parameters (pH, total nitrogen, total organic carbon, and chemical oxygen demand) varied significantly between sites (p < 0.001). Correspondingly, water microbiomes exhibited greater regional differentiation than soil microbiomes, evidenced by stronger beta-diversity separation (PERMANOVA, R[2] = 0.667 vs. 0.376) and a lower proportion of shared ASVs (65.3% vs. 97.2%). Ecological assembly analysis revealed a sharp contrast: water communities were primarily governed by deterministic processes (accounting for >80% of assembly, with heterogeneous selection as the dominant driver), whereas soil microbiomes were dominated by stochastic processes (>50%). Furthermore, water microbiomes underwent more intense network restructuring, with interaction complexity increasing significantly from 70 nodes and 268 edges in the LZ region to 130 nodes and 577 edges in the NQ region, whereas soil networks remained relatively stable (146 nodes/368 edges to 128 nodes/391 edges). Functional profiling further indicated broader regional redistribution in water compared to the relatively conserved functional framework of soil communities. Resistome analysis identified distinct ARG structures between habitats while revealing 25 overlapping categories, suggesting potential ecological connectivity. Collectively, our findings demonstrate that water microbiomes are more sensitive to regional environmental variation than soil microbiomes, with aquatic communities responding through deterministic restructuring and heightened interaction complexity. These results provide quantitative evidence that high-altitude soil and water microbiomes adopt distinct ecological strategies, offering new insights into the mechanisms governing microbial adaptation and antibiotic resistance distribution.},
}

@article {pmid42514009,
year = {2026},
author = {Zheng, H and Zhang, Y and Wang, Z and Li, D},
title = {Bacterial Diversity, Structure, and Function in Rhizosphere and Bulk Soils of Grapevines: Comparing Gravelly, Calcareous, and Aeolian Sandy Textures.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071504},
pmid = {42514009},
issn = {2076-2607},
support = {U20A2042//Key Project of the National Natural Science Foundation of China Regional Innovation and Devel-opment Joint Fund/ ; 2025QN03197//National Natural Science Foundation of Inner Mongolia Autonomous Region/ ; CARS-29-zp-03//Water Physiology and Water-saving Cultivation in the National Grape Industry Technology System/ ; },
abstract = {Soil texture is a key determinant shaping bacterial communities in vineyard ecosystems, yet how different soil textures modulate bacterial characteristics in rhizosphere versus bulk soils during grapevine growth remains poorly understood. This study collected rhizosphere and bulk soil samples from five commercial Vitis vinifera cv. Cabernet Sauvignon vineyards in the eastern piedmont of Helan Mountain, Ningxia, China, spanning three distinct textures (gravelly, calcareous, and aeolian sandy soils). Shotgun metagenomic sequencing, soil physicochemical analysis, and four soil enzyme activity (alkaline phosphatase, urease, catalase, and invertase) measurements were conducted, using PERMANOVA and RDA to identify dominant driving factors. The results showed that bacteria accounted for 97.6% of all annotated sequences, representing the dominant group in soil microbial communities. Significant differences in bacterial abundance and alpha diversity (Chao1, ACE, Shannon, and Simpson) were observed in bulk soils across textures, whereas rhizosphere soils showed significant abundance differences but similar diversity levels. However, the 50 cm bulk soil sampling distance may have attenuated the true rhizosphere effect, and these findings should be interpreted with this methodological constraint in mind. Notably, bacterial community structure differed significantly between soils of the same pedogenic type but different textures, confirming that soil texture, rather than pedogenic classification, is the primary driver. Thirteen dominant bacterial phyla (>1% relative abundance) were identified, with Proteobacteria (47.7%), Actinobacteriota (22.9%), and Acidobacteriota (6.5%) as the main taxa. Mantel tests revealed significant correlations between nitrogen, phosphorus, organic matter contents and enzyme activities in rhizosphere soils (r ≥ 0.4, p < 0.01). RDA indicated that total phosphorus (TP), organic matter (OM), alkali-hydrolyzable nitrogen (AN), Mg, pH, available K (AK), and enzyme activities were key drivers of bacterial community structure (p < 0.05). Annotated metabolic functions based on KEGG orthology indicated lower overall metabolic pathway abundances in gravelly soils compared to calcareous and aeolian sandy soils. In conclusion, soil texture, rather than broad pedogenic classification, primarily shapes vineyard bacterial communities, providing a theoretical basis for precision viticulture and sustainable soil management.},
}

@article {pmid42514018,
year = {2026},
author = {Yin, Y and Zhao, B and Li, R and Wang, R and Peng, J and Xia, B and Tian, J},
title = {Identification of Leptotrichia hofstadii as a Post-Treatment Recurrence Biomarker in Severe Early Childhood Caries.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071513},
pmid = {42514018},
issn = {2076-2607},
support = {82301078//National Natural Science Foundation of China/ ; L232110//Beijing Natural Science Foundation/ ; },
abstract = {Recurrence remains a significant challenge following the treatment of Severe Early Childhood Caries (S-ECC). This study aimed to identify candidate recurrence-related biomarkers for S-ECC and elucidate their potential pathogenic mechanisms. Through metagenomic sequencing of supragingival plaque from 32 children at one month post-treatment, we identified Leptotrichia hofstadii as one of the potential biomarkers for S-ECC recurrence (AUC = 0.8438 for the sequencing set and AUC = 0.75 for the validation set). In vitro dual-species biofilm assays using crystal violet staining and Confocal Laser Scanning Microscopy (CLSM) demonstrated that L. hofstadii promotes early-stage S. mutans colonization and extracellular polysaccharide (EPS) formation through contact-dependent synergistic interactions. Scanning electron microscopy revealed that L. hofstadii may function as a spatial scaffold within dual-species biofilm. Furthermore, this synergy significantly accelerates environmental acidification, leading to earlier attainment of the critical demineralization threshold (pH 5.5). At the transcriptional level, carbohydrate metabolism-related pathways were upregulated in dual-species biofilm, including starch and sucrose metabolism, PTS and ABC transporters. Additionally, the fruA gene, which degrades fructan in EPS was downregulated in the dual-species biofilm compared with S. mutans monoculture. These findings suggest that L. hofstadii facilitates a cariogenic microenvironment by enhancing the metabolic activity of S. mutans biofilms. Collectively, this study identifies L. hofstadii as a potential biomarker for S-ECC recurrence prediction and provides preliminary insights into possible interspecies mechanisms, offering valuable clues for future research into targeted preventive strategies.},
}

@article {pmid42514045,
year = {2026},
author = {Wang, M and He, Q and Qiu, Y and Huang, L and Zhang, Y and Ye, D and He, Z and Wen, C},
title = {High Humidity Exacerbates Rheumatoid Arthritis in Mice via Prevotella stercorea-Mediated Chondroitin Sulfate Degradation.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071540},
pmid = {42514045},
issn = {2076-2607},
support = {82405212//National Natural Science Foundation of China/ ; 82274382//National Natural Science Foundation of China/ ; 82474147//National Natural Science Foundation of China/ ; },
abstract = {Background: Rheumatoid arthritis (RA) is influenced by environmental exposures. High humidity has been clinically associated with worsened joint symptoms, but the microbial and metabolic mechanisms remain unclear. We investigated whether a gut microbiota-metabolism axis contributes to humidity-associated aggravation of collagen-induced arthritis (CIA). Methods: CIA mice were maintained under normal or high relative humidity. We integrated 16S rRNA and metagenomic sequencing, liquid chromatography-tandem mass spectrometry metabolomics, and intestinal barrier assessments. Fecal microbiota transplantation (FMT) was performed to evaluate microbiota dependency. Based on multi-omics findings, we quantified chondroitin sulfate (CS) and conducted functional experiments involving Prevotella stercorea (P. stercorea) supplementation, CS administration, and in vitro degradation assays. Results: High humidity aggravated arthritis severity and systemic inflammation, including increased interleukin-6, interleukin-17A, and granulocyte colony-stimulating factor, and was accompanied by impaired intestinal barrier integrity. FMT supported a microbiota-dependent contribution. Metagenomic analysis identified enrichment of P. stercorea and glycosaminoglycan degradation pathways under high humidity. CS abundance was reduced in articular cartilage, P. stercorea degraded CS in vitro and was associated with cartilage CS loss in vivo, and CS supplementation attenuated arthritis under high humidity and reduced the arthritis-promoting effects associated with P. stercorea. Conclusions: High humidity is associated with microbiota-dependent functional remodeling, enhanced CS degradation, and aggravated arthritis in CIA mice. These findings suggest that humidity-associated alterations in microbial CS metabolism may link environmental exposure to cartilage disruption and joint inflammation.},
}

@article {pmid42514066,
year = {2026},
author = {Nawaz, MA and Nawaz, MZ and Haider, SZ and Alghamdi, HA and Yan, W},
title = {Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071561},
pmid = {42514066},
issn = {2076-2607},
support = {RGP2/665/46//King Khalid University/ ; },
abstract = {Small non-coding RNAs (sRNAs) are ubiquitous post-transcriptional regulators that enable rapid bacterial adaptation to fluctuating environments. Previous reviews have largely focused on sRNA mechanisms in model organisms. This review integrates computational prediction, meta-omics-based discovery, and synthetic biology applications of small regulatory RNAs in marine and environmental prokaryotes, providing a multi-layered perspective from identification to functional and engineering applications. The current landscape of sRNA identification tools is critically evaluated, with emphasis on strategies to overcome challenges such as false-positive predictions. Recent advances in mapping the RNA interactome and emerging evidence of previously underappreciated roles of sRNAs in environmental adaptation are discussed. Additionally, metagenomic and metatranscriptomic studies revealing the diversity of environmental sRNAs in uncultured microbial communities are summarized, highlighting their ecological significance. Finally, a curated overview of synthetic sRNA applications in metabolic engineering, including target genes and enhanced product yields, is provided as a resource for strain engineering. Collectively, this review provides a holistic view of prokaryotic sRNA biology, distinguishing it from more narrowly focused studies. Overall, sRNAs are highlighted as key regulatory elements linking microbial environmental adaptation with emerging biotechnological applications through advances in meta-omics guided discovery and synthetic RNA engineering.},
}

@article {pmid42514075,
year = {2026},
author = {Ferreira, NE and Mendes-Correa, MC and Costa, ACD},
title = {Editorial for the Special Issue "Advances in Viral Metagenomics".},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071570},
pmid = {42514075},
issn = {2076-2607},
abstract = {Viral metagenomics has fundamentally transformed how we investigate the virosphere [...].},
}

@article {pmid42514080,
year = {2026},
author = {Chang, Y and Liu, X and Song, L and Xu, F and Zhang, Z and Yu, M and Wu, G and Zhang, D and Xu, C},
title = {Cold Exposure Shifts Gut Microbial Butyrate Synthesis Toward the Lysine-Dependent and But-Mediated Terminal Pathways to Enhance Cold Tolerance in Min Pigs.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071575},
pmid = {42514080},
issn = {2076-2607},
support = {32302709//National Natural Science Foundation of China/ ; ZL2024C012//Heilongjiang Provincial Natural Science Foundation/ ; LH2023C013//Heilongjiang Provincial Natural Science Foundation/ ; },
abstract = {This study combined seasonal observation in Min pigs and acute cold challenge experiments in Min pigs and Large White pigs to analyze changes in gut butyrate synthesis under cold exposure and its association with thermogenesis. Compared with summer, Min pigs in winter showed significantly higher Bacteroidota abundance (p = 0.006), lysine-pathway genes (p < 0.05), and relative gene abundance of the but terminal pathway (p < 0.05). Fecal (47.96 vs. 40.24 µmol/L, p = 0.020) and serum (4.64 vs. 2.17 µmol/L, p = 0.046) butyrate were also elevated and correlated with 10 thermogenesis-related genes (p < 0.05). Acute cold challenge increased serum butyrate (p = 0.017) and SLC16A1 expression (adjusted p = 0.027) only in Min pigs. Min pigs exhibited higher lysine pathway abundance and greater but terminal contribution than Large White pigs. Metagenomic binning recovered 40 lysine-pathway MAGs (27 unique to Min pigs) and 15 dual-pathway MAGs (11 unique to Min pigs), with Bacteroidota MAGs harboring complete lysine and dual terminal pathways. Collectively, cold exposure correlates with enrichment of lysine-dependent and but terminal butyrate synthesis pathways, highlighting butyrate-producing bacteria as candidate taxa for further investigation of cold-induced gut metabolic remodeling in pigs.},
}

@article {pmid42514086,
year = {2026},
author = {Zheng, Y and Ma, N and Zhao, B and Li, Y and Tian, Y and Liu, J and Quan, Y},
title = {Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071583},
pmid = {42514086},
issn = {2076-2607},
support = {YDZJ202601ZYTS183//Jilin Province Science and Technology Department/ ; },
abstract = {Wastewater systems are critical reservoirs where antibiotic resistance genes, antibiotic-resistant bacteria, and pathogens converge and disseminate into receiving waters, posing risks to ecosystems and public health. Metagenomics enables culture-independent surveillance of resistome and pathogens in wastewater. After the COVID-19 pandemic, the rapid expansion of wastewater-based epidemiological surveillance, together with growing emphasis on the One Health framework, has further promoted the integration of wastewater metagenomic monitoring with public-health surveillance strategies. However, no bibliometric study has systematically mapped the global research landscape at the intersection of metagenomics, wastewater systems, antimicrobial resistance, and pathogen surveillance. This study retrieved 1161 publications from the Web of Science Core Collection and used CiteSpace to conduct bibliometric analyses. From 2010 to 2025, annual publications increased from 1 to 219, with 72.7% of the total output concentrated between 2021 and 2025. China led in publication output but showed low betweenness centrality, whereas Australia and Sweden served as key intermediaries. Keyword analysis revealed a gradual thematic evolution from the basic detection of antibiotic resistance genes in activated sludge, through studies of dissemination mechanisms, to recent work on One Health and wastewater surveillance. Literature co-citation analysis showed that integration between environmental monitoring and public health literature remains limited, suggesting that the translation of metagenomic surveillance data into health risk assessment frameworks is still at an early stage. By mapping the field's knowledge structure and gaps, this review highlights priorities for advancing wastewater-based Antimicrobial Resistance surveillance, including standardizing analytical methods, developing artificial intelligence-assisted resistome analysis, promoting equitable participation from underrepresented regions, and operationalizing One Health surveillance, thereby supporting the translation of wastewater monitoring into actionable public-health solutions.},
}

@article {pmid42514091,
year = {2026},
author = {Valiakhmetov, EE and Frolov, M and Sukhanov, AY and Miftakhov, AK and Validov, SZ},
title = {Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071587},
pmid = {42514091},
issn = {2076-2607},
support = {FMEG-2027-0007//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity-no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome-and sensitivity, with limits of detection of 0.01-0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850-15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring.},
}

@article {pmid42514099,
year = {2026},
author = {Flores-Fernández, CN and Hiron, TK and Dobrijevic, D and Zavaleta, AI and Jeffries, JWE and O'Callaghan, CA and Lye, GJ and Ward, JM and Cárdenas-Fernández, M},
title = {Taxonomic and Functional Comparative Metagenomics of Peruvian Salterns: Insights into Microbial Communities and Aminotransferase Potential.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071595},
pmid = {42514099},
issn = {2076-2607},
support = {BB/M027864/1//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/R021627/1//BBSRC ERA CoBioTech/ ; EP/S024883/1//Engineering and Physical Sciences Research Council/ ; 007-2014-FONDECYT//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; EP/S01778X/1//Future Biomanufacturing Research Hub/ ; },
abstract = {Metagenomic analysis of extreme environments is essential in biotechnological research. This work aimed to determine and compare the microbial diversity of two Peruvian saline environments and characterise their functional profiles. Soil metagenomic DNA (mDNA) was analysed from Maras and Pilluana salterns, both with a thalassohaline origin but with different geographical and environmental conditions. Maras samples exhibited more diversity and a remarkably higher abundance of archaea (phylum Euryarchaeota). The most dominant bacterial phyla across all the samples were Pseudomonadota and Actinomycetota. Multiple pathways specific to archaea were more abundant in Maras, as were pathway-related synthesis and degradation of compatible osmolytes such as glycine betaine and ectoine. The most abundant pathways in Pilluana were associated with fatty acid biosynthesis and oxidation. A total of 49 and 47 metagenomic-assembled genomes (MAGs) were retrieved from Maras and Pilluana samples, respectively. Bacterial MAGs were mainly classified within the phyla Psudomonadota, Actinomycetota, Planctomycetota, and Gemmatimonadota. Additionally, a total of 20 putative aminotransferases class III (ATs, PF00202) from Maras3 were cloned and expressed in E. coli Rosetta, and their substrate scoping was assayed against several aldehyde and ketone substrates; AT pQR3082 and pQR3090 showed unique broad substrate acceptance for aromatic and aliphatic substrates. Our study provides new insights into the microorganisms and metabolic pathways of these unique extreme environments, highlighting the promising biotechnological potential of metagenomic ATs.},
}

@article {pmid42514486,
year = {2026},
author = {Chen, X and Wang, J and Tang, L and Zeng, Z and Gao, D and Yi, Y and Qin, L and Xiao, Y and Yang, H and Yang, B},
title = {From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/plants15142118},
pmid = {42514486},
issn = {2223-7747},
support = {Grant No. YLS-2025-ZY02030//Yuelushan Laboratory Breeding Program/ ; No. 22A0151//the Scientific Research Fund of Hunan Provincial Education Department/ ; No. CX20251060//the Hunan Province Graduate Student Scientific Research Innovation Project/ ; No. 31800076//the National Natural Science Foundation of China/ ; No. 2019JJ50245//Natural Science Foundation of Hunan province, China/ ; 2024RC2052//Joint Talent Introduction Program of Yuelushan Laboratory/ ; },
abstract = {Plant endophytes can regulate host plant growth, improve stress resistance, and facilitate the biosynthesis of secondary metabolites, with great research value and application potential. However, traditional approaches for the isolation, cultivation and identification of plant endophytes are constrained by low culturability, limited species diversity, and loss of their original ecological functions inside host tissues. In recent years, integrated multi-omics strategies combining metagenomics, metatranscriptomics, and metaproteomics have exhibited the greatest potential to mitigate culturability limitations by enabling genome-guided targeted strain isolation and in situ functional activity profiling, among which the cultivation and targeted isolation of endophytes benefit most from omics integration. These approaches drive a paradigm shift from conventional blind screening to precise targeted isolation, and from generic medium culture to omics-guided rational cultivation, greatly improving the accuracy of strain identification and functional characterization. Nevertheless, current omics-based strategies still face inherent limitations including high experimental costs, complex operational procedures, and challenging data interpretation. The most critical future direction lies in establishing standardized experimental protocols and shared resource databases, combined with microfluidic platforms and artificial intelligence-assisted bioinformatics analysis, to address the core bottlenecks restricting endophyte isolation, cultivation and identification. This review is the first to systematically summarize research progress on traditional approaches, omics technologies and emerging strategies for plant endophyte isolation, cultivation and identification, highlights prevailing challenges and developmental trends in this field, and provides methodological references for the efficient exploitation and sustainable utilization of plant endophyte resources.},
}

@article {pmid42514595,
year = {2026},
author = {Wang, LJ and Ji, F and Qi, SY and Li, QF and Zhao, M and Xu, CJ and Li, YT and Zhang, AL},
title = {Pine-Extracted Volatile Oils Suppress Root Rot in Psammosilene tunicoides Through Direct Antifungal Activity and Rhizosphere Microbiome Modulation.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/plants15142228},
pmid = {42514595},
issn = {2223-7747},
support = {No.20254916CE340047//Yunnan Key Laboratory of Chinese Medicine Processing/ ; },
abstract = {Frequent outbreaks of root rot in Psammosilene tunicoides W. C. Wu & C. Y. Wu severely compromise the quality of its medicinal materials and hinder its large-scale cultivation. Interestingly, wild P. tunicoides growing under pine trees rarely experience this disease. To explore the potential basis of root rot suppression, we evaluated the direct antifungal activity of pine-derived volatile oils and the associated changes in the rhizosphere microbiome. GC-MS showed that pine turpentine was dominated by α-pinene (45.50%) and longifolene (28.20%). In vitro assays confirmed its highly efficient inhibition (81.65-94.71%) against major root rot pathogens in P. tunicoides. Beyond direct antifungal effects, metagenomic analysis indicated that volatile oil (SYR) treatment was associated with shifts in the rhizosphere microbiome, including increased relative abundances of potentially beneficial taxa, such as Paenibacillus, Trichoderma, and Geosiphon. Pine volatiles might be associated with shifts in the rhizosphere microbial community of P. tunicoides, potentially involving plant-mediated changes in root exudation and the enrichment of certain beneficial microbes. However, it remains to be further elucidated regarding the specific mechanisms underlying these community changes. Functional prediction of the microbial community suggested a predominance of metabolic pathways, secondary metabolite biosynthesis, and flagellar assembly in the SYR group. Conclusively, pine volatiles may contribute to root rot suppression through two potential processes: direct pathogen inhibition and beneficial microbiome enrichment. This study provides a theoretical basis for establishing sustainable agroforestry co-planting systems for P. tunicoides.},
}

@article {pmid42514670,
year = {2026},
author = {Ericsson, AC},
title = {A Comprehensive Review of the Equine Gut Microbiome in Health and Disease.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070659},
pmid = {42514670},
issn = {2306-7381},
abstract = {Molecular microbiology has revolutionized our understanding of the complex host-associated microbiomes required for normative development and physiology. Horses and other members of the family Equidae are particularly reliant on the early maturation and lifelong maintenance of an unusually rich hindgut microbiome for optimal digestion and overall health and performance. Research on the equine gut microbiome has accelerated in the past several years, necessitating a renewed appraisal of the field. The present work is a comprehensive and critical review of the literature regarding the bacterial gastrointestinal microbiome of horses. First, the developmental trajectory of the foal gut microbiome is discussed, followed by descriptions of the taxonomic membership of the core equine gut microbiome, its primary functions and effects on host physiology, and intrinsic and extrinsic factors that shape the equine microbiome during health, with a focus on diet and supplements. Next, evidence supporting adverse effects on the equine gut microbiome of gastrointestinal conditions including colic and colitis, extraintestinal conditions including obesity and laminitis, and pharmacological interventions including antibiotics and non-steroidal anti-inflammatory drugs is summarized. Lastly, clinical and experimental research investigating the effects of treatments targeting the gut microbiome of horses, including probiotics, prebiotics, and fecal microbiome transfer, is critically examined. Conclusions summarize the connection between natural (i.e., wild) equine behavior and the health of the equine gut microbiome and the impacts of human management.},
}

@article {pmid42514689,
year = {2026},
author = {Abi, K and Xia, Z and Gou, L and Zhang, W and Ji'e, K and Li, S and Gao, T and Banma, W and Yang, F},
title = {Integrated 16S rRNA and Metagenomic Analysis of Pulmonary Microbiota in Sheep with Pneumonia.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070679},
pmid = {42514689},
issn = {2306-7381},
support = {SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Mutton Goat & Sheep/ ; 2024CXTD08//Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University/ ; },
abstract = {Sheep are a major livestock species in China, yet pneumonia-related mortality poses a significant obstacle to intensive farming. In this study, 115 sheep lung samples were collected and classified into different pneumonia severity groups based on lung lesion scoring. Subsequently, this study employed 16S rRNA sequencing to systematically investigate the structure and diversity of the pulmonary microbiota in sheep, including alpha diversity, beta diversity, and LEfSe analyses. Metagenomic techniques were also applied to analyze the abundance of metabolic pathways, exploring the associations between functional gene differences and pneumonia severity, as well as putative antibiotic resistance genes, virulence factors, and the species contributions of functional genes in severe pneumonia cases. Microbial richness and diversity were significantly higher in the severe pneumonia group than in the healthy/mild lesion group (p < 0.05). While the dominant microbial structures were similar across the groups, notable differences were observed in the abundance of respiratory disease-associated genera, with Pasteurella, Mannheimia, Mycoplasma, Bibersteinia, and Moraxella identified as significantly enriched in severe cases. Moreover, several genera originating from the gut and oral cavity were also associated with pneumonia, suggesting a potential gut-lung axis. Carbohydrate metabolism was the most prevalent pathway in all groups, whereas amino acid metabolism was significantly enriched in the severe pneumonia group. Putative antibiotic resistance genes were differentially enriched; the severe pneumonia group showed significant enrichment of genes conferring resistance to aminoglycosides, tetracyclines, and polymyxins. Virulence factor analysis identified nutritional/metabolic factors and adhesion as the predominant virulence mechanisms. Species contribution analysis further revealed that Mannheimia, Mycoplasma, Pasteurella, and Moraxella were the predominant species associated with functional gene enrichment. In conclusion, the current study reveals associations between changes in the pulmonary microbiota structure and function and the severity of pneumonia in sheep, aiming to provide a foundation for future hypothesis-driven research on the role of the pulmonary microbiota in pneumonia progression.},
}

@article {pmid42514698,
year = {2026},
author = {Sun, Y and Xu, S and Luo, Z and Fan, T and Zhou, X},
title = {Analysis of Bacterial Diversity in Fresh Milk from Commercial Dairy Farms in Xinjiang Based on Metagenomic Sequencing.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070688},
pmid = {42514698},
issn = {2306-7381},
support = {2023NY03-1//Xinjiang Production and Construction Corps/ ; 2024AB035//Xinjiang Production and Construction Corps/ ; },
abstract = {To investigate the biological characteristics of microbes in fresh milk, this study gathered fresh milk from seven large-scale dairy farms in the southern and northern regions of Xinjiang, analyzing the composition and abundance of bacterial communities in these samples through metagenomic sequencing technology. Firmicutes, Proteobacteria, and Actinobacteria were consistently identified as the dominant phyla across all samples, with stable relative abundance patterns across regions. At the genus level, the genera with the highest relative abundances were Sporosarcina, Streptococcus, and Escherichia, with relative abundances of 2.51-2.58%, 2.23-2.27%, and 1.93-1.97%, respectively. While exploring species richness, it was observed that the XN group had the most OTUs, the DR group had the fewest, and there were significant differences in community structure between the ND group and the other six groups. Further Alpha diversity analysis revealed no significant variation in Chao1 indices across the seven sample groups, highlighting a significant difference in Shannon index for ND samples, and no significant differences in Shannon indices between the CJ, JY, KT, DR, and TR samples. Shifting focus to functional potential, the top three relative abundances in the microbial metagenome KEGG functional library are biological systems, human diseases, and environmental information processing; additionally, within the CAZy (Carbohydrate-Active enZymes) database, the three most abundant categories are glycosyltransferases (GT), glycoside hydrolases (GH), and carbohydrate-binding modules (CBM). By delineating these patterns, this study demonstrates the microbial spectrum characteristics of fresh milk from southern and northern Xinjiang, China, offering a theoretical foundation for enhancing the quality of fresh milk in the area.},
}

@article {pmid42514990,
year = {2026},
author = {Kumar, M and Suleimenova, S and Nuralibekov, S and Kasymbekov, Y and Sabyrzhan, T and Isbekov, K and Assylbekova, S and Fefelov, V and Pangereyev, B and Karamendin, K and Kydyrmanov, A},
title = {Metagenomic Characterization and Molecular Screening of Pathogens in Freshwater Amphipods (Gammarus lacustris) from Kazakhstan: Implications for Aquaculture Biosecurity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070663},
pmid = {42514990},
issn = {2076-0817},
support = {BR23591095//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
abstract = {Freshwater amphipods of the genus Gammarus are important trophic components of aquatic ecosystems and are increasingly considered a potential bioresource for aquaculture. However, their role in the maintenance and transmission of infectious agents remains poorly understood. This study evaluated the presence of major crustacean and fish pathogens in Gammarus lacustris populations from Kazakhstan and characterized associated viral communities using metagenomic sequencing. Six pooled samples collected from freshwater ecosystems across Kazakhstan were screened using PCR and RT-PCR assays targeting World Organisation for Animal Health (WOAH)-listed pathogens, including White Spot Syndrome Virus, Taura Syndrome Virus, Infectious Myonecrosis Virus, Aphanomyces astaci, and Aphanomyces invadans. In parallel, high-throughput sequencing (Illumina NovaSeq) was performed to assess virome composition and structure. No WOAH-listed pathogens were detected, suggesting a low detectable occurrence of major notifiable agents under the conditions of the present study. Metagenomic analysis revealed a virome dominated by RNA viruses, particularly picorna-like viruses (Picornaviridae), Dicistroviridae, and Marnaviridae. Phylogenetic and genome organization analyses identified potentially novel or highly divergent viral lineages within Picornavirales. Collectively, these findings suggest a favorable epizootiological profile of G. lacustris populations while highlighting freshwater amphipods as hosts of diverse and partially uncharacterized viral communities relevant to aquatic disease surveillance and aquaculture biosecurity.},
}

@article {pmid42515020,
year = {2026},
author = {Dalle Carbonare, L and Vareschi, A and Dervishi, K and Deiana, M and Locatelli, E and Minoia, A and Piritore, FC and Ruggiero, A and Barbu, IC and Zipeto, D and Piubelli, C and Valenti, MT},
title = {High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070693},
pmid = {42515020},
issn = {2076-0817},
support = {FUR LDC//University of Verona/ ; FUR MTV//University of Verona/ ; Fondi Ricerca Corrente" - L3P6//Ministry of Health/ ; },
abstract = {In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10[5] cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98-100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies.},
}

@article {pmid42515023,
year = {2026},
author = {Montoya, JG and Cho, SM and Smith, S and Gomez, CA and Contopoulos-Ioannidis, DG},
title = {The Hidden Risk of Toxoplasmosis in the Expanding Immunomodulated Host Population: A Call for Guidelines and Registries in Patients on Biologics, Small Molecules, and Cellular Therapies.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070696},
pmid = {42515023},
issn = {2076-0817},
abstract = {Targeted immunotherapies with biologics, small molecules, and CAR T-cell therapies have revolutionized treatment across autoimmune, chronic inflammatory, oncologic, and transplant-related conditions. However, they have also expanded the population of patients susceptible to opportunistic infections. Toxoplasma gondii (T. gondii), a globally prevalent parasite, has emerged as an underrecognized pathogen in this immunomodulated host population. Toxoplasmosis, in such patients, can occur either through reactivation of a chronic/latent/past infection or from an acute/primary infection and may be severe and even fatal. We present here the recommendations for such patients from the Remington Lab, the National Reference Center for Toxoplasmosis in the US. Screening for Toxoplasma infections is needed at baseline prior to starting targeted immunotherapy to identify seropositive patients who would benefit from prophylaxis or pre-emptive strategies and seronegative patients who would benefit from measures to prevent primary/acute infections. Prompt diagnosis of Toxoplasma disease (toxoplasmosis) with molecular tools (T. gondii PCR and/or agnostic metagenomics next-generation sequencing), and prompt initiation of anti-Toxoplasma therapy, can be lifesaving and prevent permanent neurocognitive sequelae and vision loss. The immunomodulatory effects of these therapies persist for several months after discontinuation, thereby extending the window of vulnerability. T. gondii-seropositive women are at increased risk of vertical transmission, even if targeted immunotherapy was discontinued several months before conception. We make a call for education, guidelines, prospective registries, targeted research, and addition of toxoplasmosis risk in the Warnings section of drug leaflets (and particularly so for T. gondii-seropositive women who intend to conceive after having been on targeted immunotherapies).},
}

@article {pmid42515101,
year = {2026},
author = {Weng, M and Zhou, G and Wu, Q and Chen, Q and Li, J and Wang, Z and Li, W},
title = {Mycobacterium tuberculosis and Mycobacterium avium Complex Cutaneous Co-Infection: Diagnostic and Therapeutic Challenges.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070774},
pmid = {42515101},
issn = {2076-0817},
abstract = {Cutaneous co-infection with Mycobacterium tuberculosis (MTB) and Mycobacterium avium complex (MAC) is extremely rare and easily missed due to overlapping histopathological features. We report a previously healthy, HIV-negative middle-aged woman who presented with a progressive destructive mass in the left inguinal-perineal region. Imaging revealed sinus tract formation, osteolytic bone lesions, and chronic inflammation in the right middle lobe of the lung. Initial metagenomic next-generation sequencing (mNGS) detected 3756 reads of the Mycobacterium tuberculosis complex (MTBC) and 111 reads of Mycobacterium intracellulare (M. intracellulare); the latter was interpreted as possible colonization or contamination because of its low abundance. Empirical anti-tuberculosis therapy produced only transient partial improvement, followed by paradoxical worsening, local recurrence, and new bone destruction. After a high suspicion of mixed infection, a MAC-directed combination regimen (including azithromycin and a short course of amikacin) was added, leading to complete clinical cure; subsequent repeat cultures confirmed the presence of MAC. This is the first report of cutaneous MTB-MAC co-infection in the inguinal-perineal region of an adult without overt immune abnormalities, accompanied by disseminated bone lesions. This case highlights that in regions where nontuberculous mycobacteria (NTM) are co-endemic, atypical destructive skin lesions with paradoxical worsening despite initial response to anti-tuberculosis therapy should raise suspicion of MAC co-infection. The combination of mNGS and conventional culture facilitates identification of mixed infections and guides precision therapy, but mNGS results must be interpreted cautiously in the clinical context.},
}

@article {pmid42515556,
year = {2026},
author = {Martino, F and Panmei, K and Duchen, D and Thomas, DL and Kandathil, AJ and Clipman, SJ},
title = {Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070704},
pmid = {42515556},
issn = {1999-4915},
support = {1DP2DA056130-01/NH/NIH HHS/United States ; R01DA058567/NH/NIH HHS/United States ; },
abstract = {Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log10 copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log10 input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds.},
}

@article {pmid42515578,
year = {2026},
author = {Meyer, C and Jackson, VLN and de Haan, F and Bolhuis, H and Allen, MJ and Monier, A and Brussaard, CPD},
title = {Infection Dynamics and Coexistence of Two Novel Arctic Phytoplankton Viruses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070726},
pmid = {42515578},
issn = {1999-4915},
support = {na//University of Amsterdam/ ; na//Royal Netherlands Institute for Sea Research/ ; },
abstract = {Marine algal viruses exhibit a high level of diversity, and closely related viruses targeting the same algal host species can stably coexist. Here we report an example of a single virus-host system concealing hidden complexity. We discovered two double stranded (ds) DNA viruses infecting the Arctic picophytoplankter Micromonas polaris coexisting in culture for over a decade. Genomic sequencing of the lysate originally characterized as MpoV-44T revealed that it comprises two distinct prasinoviruses with ~203-204 kb genomes (MpoV-44T.A and MpoV-44T.B), of which conserved regions only accounted for 36% (the nucleotide level). The viruses were subsequently separated and compared at both genomic and phenotypic levels. In dual infection studies using a single host strain under nutrient-replete conditions, MpoV-44T.A outcompeted MpoV-44T.B. Yet MpoV-44T.B-like viruses were more abundant than MpoV-44T.A-like ones in natural Arctic metagenomes. This apparent paradox may be explained by differences in host strain specificity and/or possible resilience to nutrient stress by MpoV-44T.B, which we hypothesize based on genomic data. This work unveils hidden virus diversity, illustrating that the dynamics of viral coexistence are not always easily predictable, and underscores the importance of studying the underlying mechanisms at play.},
}

@article {pmid42515580,
year = {2026},
author = {Yin, L and Huang, P and Xu, Y and Peng, O and Zhu, K and Xie, E and Yang, S and Liu, J and Li, X and Yan, Z and Qin, J and Lin, W},
title = {Avian Orthoreovirus in China: Molecular Evolution, Transmission Ecology, Immune Modulation, and Integrated Control in the Genomic Era.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070728},
pmid = {42515580},
issn = {1999-4915},
support = {2023YFD1301800//the National Key R&D Program of China/ ; 2024090301, YF2025NYRC03 and 2024020101//the Science and Technology Plan Program of Yunfu city/ ; 2024CXTD15//the Fourth Round of Guangdong Provincial Modern Agricultural Industry Technology System Innovation Team Construction Project/ ; 2023B1212070018//the Science and Technology Plan Program of Guangdong Province/ ; },
abstract = {Avian orthoreovirus (ARV) has re-emerged as one of the most important viral pathogens affecting modern poultry production worldwide. In China, the epidemiological landscape of ARV has undergone a substantial transformation over the past decade, characterized by increasing genotypic diversity, frequent genome reassortment, an expanding host range, and recurrent vaccine-breakthrough outbreaks. Growing evidence indicates that contemporary ARV populations evolve within a dynamic multispecies transmission network shaped by intensive poultry production, host adaptation, and vaccine-associated selective pressures. Recent molecular studies have revealed extensive genetic heterogeneity among circulating strains and highlighted the limitations of conventional σC-based classification systems for accurately describing viral evolution, pathogenicity, and antigenic diversity. Whole-genome analyses further demonstrate that reassortment among chicken-origin, duck-origin, and goose-origin orthoreoviruses plays a pivotal role in generating novel viral variants with altered biological properties. In parallel, accumulating evidence suggests that ARV exerts broad immunomodulatory effects through the disruption of innate antiviral signaling, impairment of lymphoid organ function, interference with vaccine responsiveness, and the enhancement of susceptibility to secondary infections. These findings indicate that ARV should be regarded not only as an arthrotropic pathogen but also as an important immunopathological agent influencing flock health and productivity. This review summarizes current knowledge of ARV in China, with an emphasis on molecular epidemiology, genomic evolution, reassortment mechanisms, transmission ecology, immune interference, vaccine escape, and integrated prevention strategies. Particular attention is given to the increasing importance of whole-genome surveillance, phylodynamic analysis, and multispecies epidemiological monitoring for understanding contemporary ARV evolution. Future perspectives involving structural vaccinology, precision immunization, metagenomics-assisted surveillance, and predictive evolutionary modeling are also discussed. Collectively, sustainable ARV control will likely require genome-informed and adaptive prevention frameworks integrating virology, immunology, epidemiology, and precision poultry management.},
}

@article {pmid42515587,
year = {2026},
author = {Yuan, L and Zhang, N and Yuan, M and Xu, J and Liu, Z and Li, Z},
title = {Novel Species Diversity in China's Northeastern Border Region.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070735},
pmid = {42515587},
issn = {1999-4915},
support = {No. 2025ZD01900100//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; },
abstract = {The northeastern region of China is characterized by complex ecosystems, including forests and wetlands, and borders North Korea, Russia, and Mongolia. It serves not only as a natural reservoir for various microorganisms but also as a critical geographical and ecological hub for cross-border exchanges in Northeast Asia. Based on metagenomics and meta-transcriptomics investigations, this study systematically reviews the current research status of novel pathogens in the northeastern border region of China. It systematically organizes the newly discovered species, their classifications, and geographical distributions, with a focus on analyzing novel viruses that have potential pathogenicity to humans. The novel viruses identified in the northeastern border region belong to 11 viral families, including 9 from the Nairoviridae, 4 from the Rhabdoviridae, 3 each from the Astroviridae, Picornaviridae, and Parvoviridae, and 1-2 from other viral families, indicating a broad diversity of newly discovered viruses. These novel viruses are found in a wide range of hosts, including humans, ticks, minks, Marmota sibirica, and Myodes rufocanus, underscoring the significant public health risks these viruses pose. Geographically, the novel viruses discovered in the northeastern border region show a clustering pattern, with new species primarily concentrated in areas bordering Russia and North Korea. This highlights the unique role of the region as a hotspot for cross-border pathogen transmission and risk. The findings provide a systematic scientific reference for understanding the spectrum of unknown novel pathogens and their geographical distribution in the northeastern border region, assessing the risk of emerging infectious diseases, and optimizing active surveillance systems.},
}

@article {pmid42515641,
year = {2026},
author = {Liu, W and Wang, Y and Ma, J and Liang, X and Yang, L},
title = {Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070789},
pmid = {42515641},
issn = {1999-4915},
support = {42407182//National Natural Science Foundation of China/ ; },
abstract = {Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.},
}

@article {pmid42515794,
year = {2026},
author = {Frăsinariu, OE and Ștreangă, V and Rugină, AL and Mîndru, DE and Vintilă, TC and Bădulescu, OV and Bararu-Bojan, I and Lupu, VV and Lupu, A and Mihai, A and Loghin, II and Popescu, DE and Teșoi, DF},
title = {Gut Microbiota and Metabolic Dysfunction-Associated Steatotic Liver Disease: From Dysbiosis to Metagenomic Insights and Therapeutic Perspectives.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {7},
pages = {},
doi = {10.3390/ph19071113},
pmid = {42515794},
issn = {1424-8247},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as the most common chronic liver disorder in the pediatric population, closely paralleling the global rise in childhood obesity. Increasing evidence highlights the gut-liver axis as a key contributor to MASLD pathogenesis, with gut microbiota dysbiosis influencing hepatic steatosis through multiple interconnected mechanisms, including increased intestinal permeability, endotoxemia, altered bile acid metabolism, and modulation of host energy homeostasis. In children, the characterization of microbiota signatures associated with MASLD remains challenging due to heterogeneity across studies, age-related microbial dynamics, and methodological variability. This review synthesizes current evidence regarding the role of the gut microbiota in pediatric MASLD, focusing on pathogenetic pathways, reported microbial patterns, and microbiota-targeted therapeutic strategies, while incorporating relevant mechanistic evidence from adult studies where pediatric data remain limited. Although several taxa have been repeatedly associated with pediatric MASLD, findings are not yet sufficiently consistent for clinical application. Interventions such as probiotics, prebiotics, and dietary modulation show promising but still preliminary results, with limited high-quality pediatric trials available. A deeper mechanistic understanding and standardized study designs are needed to clarify causality and to support microbiota-based precision approaches in pediatric MASLD management.},
}

@article {pmid42515825,
year = {2026},
author = {Kean, K and Mayne, RM and Reid, K and Secret, S and Singleton, BK and Rockett, R and Rajendra, P and Harvala, H and Breuer, J and Azim Ansari, M and Lythgoe, K and Simmonds, P and Golubchik, T},
title = {A Snapshot of the UK Blood Donor Plasma Virome: A Retrospective Cross-Sectional Cohort Study.},
journal = {Journal of medical virology},
volume = {98},
number = {8},
pages = {e71081},
doi = {10.1002/jmv.71081},
pmid = {42515825},
issn = {1096-9071},
support = {NIHR203338//National Institute for Health and Care Research/ ; },
abstract = {Estimates of population prevalence and genetic diversity of bloodborne viruses in healthy humans are essential to support population-scale monitoring for transfusion transmission risk. In the UK and globally, blood donations are routinely screened for a limited number of high-consequence pathogens, but the full composition of the plasma virome remains to be characterized. Using a novel quantitative targeted metagenomics sequencing approach, we analyzed previously unscreened plasma donations collected by NHS Blood and Transplant in England for all major pathogenic and known commensal human bloodborne viruses, and quantified their viral burden. Here we show that in a representative sample of 5064 UK blood donors in pools of 24 collected over a 1-month period, the virome was dominated by a small number of largely persistent species, representing < 10% (10/106) of previously identified human bloodborne viruses. The principal genera of human anelloviruses (TTV, TTMV and TTMDV) were detected in 89% of pools, albeit at low read count, inconsistent with measured anellovirus viral loads. In contrast, human pegivirus type 1 (HPgV-1), had an estimated population prevalence of 3.7% (95% CI 3.0%-4.4%), with high read count and complete genome recovery in around one half of positive pools, consistent with high titer in plasma. Less common detections included one species of gemykibovirus in five separate plasma pools, one hepatitis C virus (genotype 1a), and polyomaviruses and herpesviruses with prevalences between 0.04% (parvovirus 4, BK polyomavirus) to 0.41% (human herpesvirus 6). Phylogenetic analyses revealed mixed TTV, TTMV, and TTMDV populations and almost exclusively genotype 2 HPgV-1, consistent with known genotype distributions in Europe. Our results provide a baseline for describing the healthy plasma virome in UK blood donors.},
}

@article {pmid42515960,
year = {2026},
author = {Kopp, AR and Uhlemann, AC},
title = {Gut dysbiosis and multidrug-resistant colonization in solid organ transplantation.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001303},
pmid = {42515960},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize recent advances in the understanding of the interplay between gut dysbiosis and MDRO colonization and infection in SOT patients.

RECENT FINDINGS: Recent studies have added complementary metagenomics, internal transcribed spacer sequencing, metabolomics, and pathway analysis to descriptive microbiome profiling. Enhanced ecologic frameworks have identified microbial, functional, and clinical signatures associated with MDRO colonization and infection. Microbiome-targeting interventions are emerging as strategies to reduce morbidity associated with MDRO infection.

SUMMARY: MDRO infection is a significant cause of post-transplant mortality. Persistent gut dysbiosis peri-transplant reduces colonization resistance and predisposes patients to adverse clinical outcomes. Understanding the dynamics of this process will aid in the care of these high-risk patients.},
}

@article {pmid42516269,
year = {2026},
author = {López-Martínez, KP and Hereira-Pacheco, S and Hernández-Oaxaca, D and López-Ruiz, F and Vázquez-Rosas-Landa, M},
title = {rbims: an R package for integrative functional profiling and pathway-level discrimination in metagenome-assembled genomes.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1831383},
pmid = {42516269},
issn = {2673-7647},
abstract = {Metagenomics enables the recovery of metagenome-assembled genomes (MAGs), providing access to the metabolic potential of uncultured microbial communities that drive ecosystem function and biogeochemical cycles. However, as MAGs datasets increase in size and complexity, comparing functional repertoires and identifying ecologically meaningful traits across experimental gradients becomes increasingly difficult. Here, we present rbims, a modular R package for integrative functional profiling of MAGs and metagenomic datasets. rbims supports annotations from KEGG, dbCAN, InterProScan, MEROPS, and PICRUSt2, and enables the calculation of gene presence/absence, raw abundance, and pathway coverage, as well as metadata-informed comparative analyses and publication-ready visualizations. Beyond descriptive profiling, rbims implements an exploratory discriminant framework that combines compositional differential analysis (ALDEx2) with random forest-based feature ranking to prioritize candidate metabolic traits associated with environmental factors. Importantly, it extends gene-level analysis to pathway-level directional bias testing, allowing users to evaluate whether the majority of genes within a metabolic route are consistently enriched toward a given condition. We applied rbims to 42 MAGs recovered from a hydrocarbon enrichment experiment in the North Atlantic Ocean. The workflow identified widespread hexadecane and phenanthrene degradation potential, detected enriched oxidoreductase-related protein families, and revealed a strong pathway-level directional bias toward deep-water MAGs for phenanthrene, naphthalene, and hexadecane degradation pathways. By integrating annotation parsing, quantitative trait analysis, statistical discrimination, and visualization in a reproducible framework, rbims provides a user-friendly platform for functional interpretation in genome-resolved metagenomics.},
}