@article {pmid41639055,
year = {2026},
author = {Lai, D and Mosier, D and Palmer, M and Mayali, X and Johnston, J and Saldivar, W and Covington, JK and Jiao, JY and Murali, R and Seymour, CO and Liu, L and Hua, ZS and Li, WJ and Weber, PK and Pett-Ridge, J and Colman, DR and Boyd, ES and Nunoura, T and Dodsworth, JA and Hedlund, BP},
title = {Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68859-6},
pmid = {41639055},
issn = {2041-1723},
support = {1557042//National Science Foundation (NSF)/ ; 2038420//National Science Foundation (NSF)/ ; 80NNSC17KO548//National Aeronautics and Space Administration (NASA)/ ; 80NSSC25M0046//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10[6] cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.},
}

@article {pmid41638592,
year = {2026},
author = {Xiao, Y and Cheng, Z and Cai, J and Guo, Z and Chen, J and Su, Y and Cao, F and Chen, D},
title = {Metagenomic and metatranscriptomic analysis of sulfur-driven autotrophic denitrification coupled with carbon assimilation: roles of sulfur-to-nitrogen ratio and hydraulic retention time.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134153},
doi = {10.1016/j.biortech.2026.134153},
pmid = {41638592},
issn = {1873-2976},
abstract = {The sulfur autotrophic denitrification (SAD) process is a promising technology for nitrogen-containing wastewater treatment, with research predominantly focused on nitrate and sulfide transformations, while the potential for inorganic carbon assimilation remains underexplored. In this study, a long-term stable SAD system was maintained in an airlift bioreactor by adding an inorganic carbon source to evaluate the effects of sulfur-to-nitrogen (S/N) ratio and hydraulic retention time (HRT) on operational performance. Under optimal operating conditions (S/N = 3:2; HRT = 8h), the system sustained high performance, achieving 99.56 ± 1.47% nitrate removal, 60.28 ± 4.19% elemental sulfur yield, and 46.48 ± 4.07% inorganic carbon assimilation efficiency. Biomass sulfur acted as a sink for extracellular free organic carbon (EFOC), thereby alleviating its accumulation-induced negative feedback on carbon assimilation. Microbial community analysis revealed a substantial enrichment of the autotrophic sulfur-oxidizing bacterium Sulfurovum, showing a marked 9.46-fold increase in relative abundance compared with the original sludge. At S/N = 3:2, metagenomic and metatranscriptomic analyses detected a 6.39-fold increase in the transcription of CBB cycle genes (rbcL/rbcS), driving a clear shift in metabolic flux toward carbon assimilation. Shortening the HRT (4 h) preferentially activated the denitrification pathway, which was evidenced by an 84.65% rise in nosZ expression (from 2,623.29 to 4,844.01 TPM), thereby bolstering N2O reduction. Our findings offered critical insights for designing engineering solutions that enable concurrent efficient denitrification, sulfur recovery, and reduced carbon emissions.},
}

@article {pmid41638346,
year = {2026},
author = {Behrens, LMP and Fernandes, GDS and Gonçalves, GF and Nunes, FVM and Weimer, RD and Moreira, JCF and Dorn, M},
title = {Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.019},
pmid = {41638346},
issn = {1873-7544},
abstract = {Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.},
}

@article {pmid41638332,
year = {2026},
author = {Wu, B and Zhang, N and Yang, G and Yu, N and Xie, Z and Xia, J and Luo, W and Liu, X and Wang, D and Zhang, Y and Tang, L},
title = {Unraveling the microbial and functional mechanisms driving rapid algal-bacterial granular sludge formation in mariculture wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123941},
doi = {10.1016/j.envres.2026.123941},
pmid = {41638332},
issn = {1096-0953},
abstract = {Algal-bacterial granular sludge (ABGS) has unique advantages and broad application prospects in the treatment of mariculture wastewater. However, the rapid granulation process and performance evolution of ABGS under high salt stress have not been clearly defined. Compared with AGS, the influence of algal intervention on the structural integrity and metabolic activity of particles under the same salinity gradient is also unknown. Therefore, in this study, a parallel ABGS and AGS system was established. The results showed that intertwined algal filaments provided a structural skeleton for particle formation and led to complete granulation of ABGS within 20 days. Compared with conventional AGS, ABGS formed under high-salinity conditions exhibited a larger average particle size (1.07 mm), higher biomass (7.59 g/L) and higher extracellular polymeric substance (EPS) secretion (258.56 mg/g VSS). Additionally, chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal efficiencies exceeded 99% and 66%, respectively. Metagenomic analysis revealed that Thauera, Fragilaria and Nitzschia were dominant taxa associated with granule formation and stabilization. ABGS also showed an elevated abundance of functional genes associated with nitrogen metabolism (nxrA, nasA, and nasD) and polysaccharide metabolism (glmM, glmU, and pmm-pgm), which were in accordance with the enhanced nitrogen removal and granulation capability. Increased abundance of tricarboxylic acid cycle genes further indicated the superior granulation performance of ABGS. Overall, this study clarifies the morphological evolution and microbial functional mechanisms underlying rapid ABGS formation in mariculture wastewater, offering valuable insights for engineering optimisation and application of this technology in saline wastewater treatment.},
}

@article {pmid41638014,
year = {2026},
author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L},
title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {292},
number = {},
pages = {107742},
doi = {10.1016/j.aquatox.2026.107742},
pmid = {41638014},
issn = {1879-1514},
abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.},
}

@article {pmid41637515,
year = {2026},
author = {Liu, X and Cheng, X and Zhang, Y and Zhao, R and Wang, W and Li, Y and Chen, ZQ and Qiu, X and Tuovinen, OH and Bull, ID and Evershed, RP and Wang, H},
title = {High-efficiency methane consumption by atmospheric methanotrophs in subsurface karst caves: The irrefutable methane sink.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eady5942},
pmid = {41637515},
issn = {2375-2548},
mesh = {*Methane/metabolism ; *Caves/microbiology ; Oxidation-Reduction ; *Atmosphere/chemistry ; Soil Microbiology ; Phylogeny ; },
abstract = {Subsurface karst systems represent substantial but underexplored methane sinks, yet the identities and activities of cave-dwelling methanotrophs remain poorly characterized. We detected increased methane oxidation rates from 2.9 ± 0.1 to 90.7 ± 4.5 ng·g[-1]·hour[-1] while supplied with 2 to 500 parts per million (ppm) CH4 to cave sediments. Atmospheric methanotroph Upland Soil Clusters γ (USCγ), responsible for this oxidation, was further assigned to three genera within the family Candidatus (Ca.) Methyloligotrophaceae, including two previously unrecognized genera. Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging and the produced [13]C-PLFAs (phospholipid fatty acids) and [13]CO2 in [13]CH4-fed microcosm confirmed methane as both carbon and energy sources. These methanotrophs exhibited low half-saturation constant (Km; 138.8 ± 15.8 ppm), high carbon assimilation efficiency (>50%), and metabolic versatility, as revealed by metagenomics and metatranscriptomics analyses. By extrapolating global distribution of Ca. Methyloligotrophaceae and comparing methane oxidation rates between caves and soil ecosystems, we conservatively estimate that subsurface karst in southwest China sequester ~0.56 Tg CH4 annually. These findings highlight the ecological importance of karst ecosystems as a previously overlooked methane sink.},
}

*Methane/metabolism
*Caves/microbiology
Oxidation-Reduction
*Atmosphere/chemistry
Soil Microbiology
Phylogeny

@article {pmid41637508,
year = {2026},
author = {Kaur, G and Crawford, SE and Javornik Cregeen, S and Surathu, A and Ayyar, BV and Apostol, CV and Phuc, HN and Ettayebi, K and Boussattach, A and Zeng, XL and Blutt, SE and Doddapaneni, H and Muzny, DM and Coarfa, C and Anish, R and Prasad, BVV and Atmar, RL and Ramani, S and Estes, MK},
title = {Overcoming host restrictions to enable continuous passaging of GII.3 human norovirus in human intestinal enteroids.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb0455},
pmid = {41637508},
issn = {2375-2548},
mesh = {Humans ; *Norovirus/physiology/genetics ; Virus Replication/drug effects ; *Caliciviridae Infections/virology ; *Intestines/virology ; *Host-Pathogen Interactions ; *Organoids/virology ; Chemokines/metabolism/genetics ; Gastroenteritis/virology ; },
abstract = {The establishment of human intestinal enteroids (HIEs) as a model for human norovirus (HuNoV) replication has been transformative for studying this leading cause of gastroenteritis. However, indefinite passaging of HuNoVs in HIEs remained a challenge, necessitating the use of patient stool samples as viral inocula. Using RNA-seq, we identified CXCL10, CXCL11, and CCL5 as up-regulated chemokines, suggesting their potential as host restriction factors. TAK-779, a CXCR3/CCR5/CCR2 antagonist, enhanced GII.3 HuNoV replication and viral spread in a dose- and time-dependent manner, enabling successful passaging of GII.3 HuNoV in two different HIE lines and generation of viral stocks. Sequencing passaged virus revealed one consensus change in the major capsid protein and several dynamic adaptations, suggesting emergence of variants. TAK-779 also enhanced replication of GI.1 and GII.17 strains, but not GII.4, suggesting strain-specific host interactions. This breakthrough in passaging provides insight into HuNoV-host interactions, establishes a scalable in vitro system for virus propagation, and opens avenues for structural, biochemical, and therapeutic studies.},
}

Humans
*Norovirus/physiology/genetics
Virus Replication/drug effects
*Caliciviridae Infections/virology
*Intestines/virology
*Host-Pathogen Interactions
*Organoids/virology
Chemokines/metabolism/genetics
Gastroenteritis/virology

@article {pmid41637142,
year = {2026},
author = {Dos Santos, SJ and Gloor, GB},
title = {Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70307},
pmid = {41637142},
issn = {2691-1299},
mesh = {Uncertainty ; *Gene Expression Profiling/methods ; *Software ; *Transcriptome ; Humans ; Principal Component Analysis ; *Metagenomics/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods ; },
abstract = {Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter-sample differences in sequencing depth instead being driven by technical variation rather than biological factors. Recent work has demonstrated that normalizations used in all analysis tools make incorrect assumptions about the biological scale of the system in question, leading to unacceptably high false-discovery rates in the output. To mitigate this, analysts can acknowledge and account for the uncertainty of the overall system scale during normalization by building scale models of the data-a feature that has been integrated into the ALDEx2 R package. Here, we provide reproducible examples that demonstrate how to incorporate scale models into differential expression analyses of RNA-seq data using bulk transcriptome and metatranscriptomic datasets, as well as the consequences of not doing so. We also show how to use the output of ALDEx2 to create high-level exploratory visualizations of their data through principal component analysis. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using a simple scale model for differential expression analysis to avoid dual-cutoff P value/significance thresholds Basic Protocol 2: Implementing a full informed scale model to correct scale-related data asymmetry in differential expression analyses Basic Protocol 3: Visualizing ALDEx2 outputs using a compositional approach: Principal component analysis.},
}

Uncertainty
*Gene Expression Profiling/methods
*Software
*Transcriptome
Humans
Principal Component Analysis
*Metagenomics/methods
Sequence Analysis, RNA/methods
RNA-Seq/methods

@article {pmid41636536,
year = {2026},
author = {Della-Negra, O and Servien, R and Milferstedt, K and Hamelin, J and Klopp, C and Hoede, C},
title = {Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0131025},
doi = {10.1128/mra.01310-25},
pmid = {41636536},
issn = {2576-098X},
abstract = {Twenty-five high-quality metagenome-assembled genomes (MAGs) were recovered from photogranules to treat synthetic wastewater. They were dominated by Leptolyngbya boryana. Cyanobacterial MAGs encoded photosynthesis and nitrogen fixation pathways, supporting internal oxygen and nitrogen cycling. Most heterotrophic MAGs contributed to nitrogen removal, highlighting the metabolic complementarity within photogranules studied for wastewater treatment.},
}

@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226425},
doi = {10.1128/spectrum.02264-25},
pmid = {41636495},
issn = {2165-0497},
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

@article {pmid41636304,
year = {2026},
author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J},
title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13541},
pmid = {41636304},
issn = {1520-5851},
abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.},
}

@article {pmid41635749,
year = {2025},
author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É},
title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100333},
pmid = {41635749},
issn = {2667-114X},
abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.},
}

@article {pmid41635321,
year = {2026},
author = {Ozturk, SZ and Aydin, B and Cifcibasi, E},
title = {Antibiotic Resistance Genes in the Subgingival Microbiome in Periodontitis: A Scoping Review of Prevalence, Mobility, and Future Directions.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e100685},
pmid = {41635321},
issn = {2168-8184},
abstract = {The objective of the study is to evaluate the prevalence, diversity, and mobility of antibiotic-resistant species and resistance genes within the subgingival microbiome of patients with periodontitis. A systematic scoping review was conducted in accordance with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. Five electronic databases were searched for studies published between January 2020 and December 2025 that used molecular techniques (shotgun metagenomics, PCR/qPCR, 16S + PCR) to detect antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the subgingival plaque of patients with clinically diagnosed periodontitis. Only peer-reviewed articles presenting original data were included; reviews, animal studies, and investigations lacking clear methodological details were excluded. Data extraction included study design, sample size, identified ARGs, associated MGEs, and clinical context. Nine eligible studies involving over 900 subgingival samples were identified. A core resistome was consistently identified across all cohorts, predominantly comprising tetracycline genes (tetM, tetQ, tet32) and macrolide-lincosamide determinants (ermB, ermF, msrD), as well as β-lactamase genes such as cfxA. Sites affected by periodontitis showed higher abundance of these ARGs than healthy controls. Mobile elements, especially Tn916-family conjugative transposons, were often associated with macrolide resistance genes, suggesting potential for horizontal transfer. Methodological differences prevented meta-analysis, and no study compared results based on the 2017 stage/grade classification of periodontitis. The subgingival resistome in periodontitis features a consistent set of tetracycline, macrolide, and β-lactam resistance genes that are increased in disease and frequently associated with mobile transposons. Currently, the evidence remains primarily descriptive; future research should include standardized antibiotic washout periods, longitudinal follow-up, stage/grade stratification, and integrated multi-omics approaches to evaluate functional activity and guide personalized antimicrobial therapies.},
}

@article {pmid41635301,
year = {2025},
author = {Jin, X and Ren, L and Ren, X and Wang, J},
title = {Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.},
journal = {Biosafety and health},
volume = {7},
number = {1},
pages = {5-16},
pmid = {41635301},
issn = {2590-0536},
abstract = {It is crucial to understand how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sheds in human respiratory tract, but this question remains elusive due to technical limitations. In this study, we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named RedeCoronaVS to systematically dissect SARS-CoV-2 shedding modes with single-cell data as reference. Our study demonstrated that SARS-CoV-2 particles were the dominant mode of viral shedding in the very early infection phase (≤24 h after hospitalization). Within the first week after hospitalization, SARS-CoV-2 replicas within host cells dominated viral shedding alongside viral particles. One week later, viral fragments became the dominant mode in patients with mild or moderate symptoms, while viral replicas still dominated in some patients with severe symptoms. In addition to epithelial cells, SARS-CoV-2 replicas in neutrophils, macrophages, and plasma cells also played significant roles and were associated with sampling time and disease severity.},
}

@article {pmid41634852,
year = {2026},
author = {Yan, A and Li, X and Cheng, J and Cheng, Y and Gebeyew, K and Tan, Z and Kang, J and He, Z},
title = {The developmental trajectory and maturation of the Hulunbuir sheep (Ovis aries) microbiome.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {10},
pmid = {41634852},
issn = {2524-4671},
support = {32350410422//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; 32350410422//the National Natural Science Foundation of China/ ; 32302783//Natural Science Foundation of China/ ; },
abstract = {The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.},
}

@article {pmid41634818,
year = {2026},
author = {Schuster, L and Greening, C and Malerba, ME and Trevathan-Tackett, S and Athukorala, N and Ricci, F},
title = {Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams.},
journal = {Microbiome},
volume = {14},
number = {},
pages = {},
pmid = {41634818},
issn = {2049-2618},
support = {APP1178715//National Health and Medical Research Council/ ; FT240100502//Australian Research Council/ ; DE220100752//Australian Research Council/ ; DE210101029//Australian Research Council/ ; ECPF24-4273843556//Faculty of Medicine, Nursing and Health Sciences, Monash University/ ; },
abstract = {BACKGROUND: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.

RESULTS: We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.

CONCLUSIONS: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.},
}

@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02350-8},
pmid = {41634815},
issn = {2049-2618},
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}

@article {pmid41634410,
year = {2026},
author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY},
title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10753-025-02436-9},
pmid = {41634410},
issn = {1573-2576},
support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; },
}

@article {pmid41491012,
year = {2026},
author = {Li, L and Khan, M and Haak, L and Verma, SC and Pagilla, K},
title = {High prevalence of tomato brown rugose fruit virus in domestic wastewater as a potential viral indicator for treatment systems.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4698},
pmid = {41491012},
issn = {2045-2322},
abstract = {UNLABELLED: Waterborne pathogenic viruses present a critical public health challenge, particularly in potable water reuse systems where stringent safety standards must be met. Achieving the necessary Log Reduction Values (LRVs) for viruses in water treatment remains difficult due to their low prevalence and high detection limits. This study investigated tomato brown rugose fruit virus (ToBRFV) as a novel viral indicator to assess advanced treatment efficacy of advanced treatment systems in achieving target Log10 Reduction Values (LRVs) for pathogenic viruses. Over 13 months, wastewater samples from the Reno-Sparks Metropolitan Region (Nevada, USA) were analyzed using metagenomics and RT-qPCR to compare ToBRFV, pepper mild mottle virus (PMMoV), and MS2 bacteriophage. Results demonstrated that ToBRFV was consistently detected at high concentrations across all samples, exhibiting minimal seasonal variability. In contrast, PMMoV showed moderate fluctuations, while MS2 was detected at lower levels. The robustness and stability of ToBRFV suggest it could serve as a reliable indicator for verifying LRVs in potable reuse systems, complementing existing methods. Additionally, its plant-based origin reduces human health risks during handling. These findings support ToBRFV’s potential to enhance treatment monitoring and public health safeguards. Further research should validate its applicability across diverse geographic and climatic conditions, as well as its correlation with enteric virus removal, to optimize water reuse frameworks.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34782-x.},
}

@article {pmid41634308,
year = {2026},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38302-3},
pmid = {41634308},
issn = {2045-2322},
support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.},
}

@article {pmid41633490,
year = {2026},
author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS},
title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-aged children.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.01.017},
pmid = {41633490},
issn = {1097-6825},
abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

OBJECTIVE: To characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-aged children with asthma.

METHODS: We performed metagenomic sequencing and RT-qPCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely three times over one year. Surveys on parent-reported cold and asthma symptoms were administered routinely every two months. We evaluated multi-kingdom changes to the nasal microbiome during infection. A sPLS-DA model identified microbial signatures associated with prospective viral infection risk.

RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus most prevalent. Cold and asthma symptoms within the prior 14 days had a sensitivity of 79% and 59%, respectively, for RT-qPCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted OR 0.41 [95% CI, 0.25 - 0.67]; P < 0.001), whereas phageome profiles increased risk (adjusted OR 3.74 [1.85 - 7.55]; P < 0.001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.

CONCLUSION: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.},
}

@article {pmid41633147,
year = {2026},
author = {Klaes, S and Gerundt, K and Deobald, D and Henneberger, L and Escher, B and Adrian, L and Cooper, M},
title = {Sequential exposure to anoxic/oxic conditions leads to biotransformation and reduced sitagliptin toxicity in urban hyporheic zones.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141299},
doi = {10.1016/j.jhazmat.2026.141299},
pmid = {41633147},
issn = {1873-3336},
abstract = {Pharmaceuticals are increasingly recognized as contaminants of concern in aquatic environments. Sitagliptin, an antidiabetic drug that carries a C-CF3 group, which is a precursor of the persistent trifluoroacetic acid, is excreted largely unmetabolized and inefficiently removed in wastewater treatment plants, leading to its widespread detection in surface waters. The hyporheic zone, a region between surface water and groundwater, serves as a natural bioreactor with high microbial activity and diverse redox conditions, offering the potential for sitagliptin attenuation. This study explored the biotransformation of sitagliptin in hyporheic sediments under varying redox conditions through batch experiments and field observations. We showed that batch experiments can complement field observations to capture both mechanistic insights and their environmental relevance. Batch experiments revealed amide hydrolysis and N-acetylation of sitagliptin under anoxic conditions, with subsequent deamination and oxidation of transformation products under oxic conditions. Metagenome-resolved metaproteomics suggested Pseudomonas asiatica as a key player in the oxic transformation. Field analysis of pore water samples identified up to 6.47 µg L[-1] sitagliptin and ten transformation products with concentrations of up to 4.82 µg L[-1] . Amide hydrolysis products were the most abundant transformation products and preferentially formed under anoxic conditions. All investigated transformation products exhibited lower cytotoxicity and oxidative stress responses than sitagliptin in in vitro bioassays, highlighting the toxicity reducing potential of the hyporheic zone. By identifying conditions that promote sitagliptin transformation and characterizing its transformation products toxicologically, our work provides parameters for enhanced sitagliptin removal in aquatic environments and improved risk assessment of fluorinated trace organic contaminants.},
}

@article {pmid41633137,
year = {2026},
author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R},
title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.},
journal = {Forensic science international. Genetics},
volume = {83},
number = {},
pages = {103435},
doi = {10.1016/j.fsigen.2026.103435},
pmid = {41633137},
issn = {1878-0326},
abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.},
}

@article {pmid41633112,
year = {2026},
author = {Tang, X and Bao, Y and Li, J and Liu, B and Huang, Y and Hou, L and Lee, PKH and Han, P},
title = {Microplastics promote N2O emissions by enhancing nitrification via ammonia-oxidizing bacteria in estuarine and coastal sediments.},
journal = {Water research},
volume = {293},
number = {},
pages = {125458},
doi = {10.1016/j.watres.2026.125458},
pmid = {41633112},
issn = {1879-2448},
abstract = {Estuarine and coastal ecosystems are critical interfaces between land and ocean, serving as sinks for anthropogenic pollutants such as ammonium and microplastics. However, the impact of microplastic pollution on nitrification processes in these environments remains largely unexplored. This study investigates the coastal region of the Yangtze River to examine how different microplastic types (polyethylene terephthalate, polypropylene, and polyethylene) affect nitrous oxide (N2O) emissions and the dynamics of nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) Nitrospira, and nitrite-oxidizing Nitrospira. Results from incubation experiments show that all microplastic types significantly increase N2O emissions across sediment samples. The reconstructed representative metagenome-assembled genomes revealed that AOA belong to group I.1a, while AOB are classified within the Nitrosomonas genus. Microplastics were found to have a stronger stimulatory effect on AOB, which are linked to higher N2O production, than on AOA, which are associated with low N2O production, thereby enhancing N2O emissions during nitrification. Furthermore, AOB genomes encode a range of putative plastic-degrading enzymes, which may partially explain their enrichment in microplastic-contaminated environments, although other factors such as differential tolerance to ammonium or oxidative stress cannot be ruled out.},
}

@article {pmid41633028,
year = {2026},
author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y},
title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.},
journal = {Research in veterinary science},
volume = {203},
number = {},
pages = {106092},
doi = {10.1016/j.rvsc.2026.106092},
pmid = {41633028},
issn = {1532-2661},
abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.},
}

@article {pmid41632347,
year = {2026},
author = {Yang, H and Hensley, MK and Nguyen, VD and Al-Yousif, NS and Britton, N and Haidar, G and Yang, L and Shah, F and Bain, W and Wang, X and Qin, S and Ahmed, AA and Blauwkamp, T and Bercovici, S and Kaufman, BA and Redding, KM and Fitch, A and Methé, B and Benos, PV and McVerry, BJ and Morris, A and Kitsios, GD},
title = {Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.},
journal = {Intensive care medicine experimental},
volume = {14},
number = {1},
pages = {10},
pmid = {41632347},
issn = {2197-425X},
support = {R01HL176668/HL/NHLBI NIH HHS/United States ; P01 HL 114453/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Biological heterogeneity in host inflammatory responses to severe pneumonia predicts clinical outcomes and may influence the effectiveness of immunomodulatory therapy. The upstream drivers of this heterogeneity remain poorly defined. We hypothesized that microbial translocation from the lungs to the bloodstream, detectable via multi-compartment metagenomic analysis, contributes to divergent host responses in pneumonia.

METHODS: In this nested case-control study of mechanically ventilated patients with severe pneumonia, we collected paired plasma and endotracheal aspirate samples at baseline. Plasma samples underwent microbial cell-free DNA (mcfDNA) sequencing, and endotracheal aspirates were analyzed by Nanopore metagenomic sequencing. Host-response biomarkers were measured in both plasma and endotracheal aspirate samples. Microbial translocation of pulmonary origin was defined by the genus-level concordance of detectable taxa between matched endotracheal aspirate and plasma samples.

RESULTS: Among 98 patients (76 pneumonia, 22 controls), plasma mcfDNA was markedly higher in microbiologically confirmed pneumonia compared with culture-negative pneumonia (median 4015 vs. 210 molecules/μL, p = 0.0006). Pulmonary microbial translocation was identified in 31 (41%) pneumonia patients and correlated significantly with plasma soluble ST2 levels, independent of clinical severity. Patients classified into the prognostically adverse hyperinflammatory subphenotype exhibited greater translocating microbial DNA levels compared to hypoinflammatory patients (p = 0.04), further linking translocation to host-response heterogeneity.

CONCLUSIONS: Microbial lung-to-blood translocation is a measurable biological process associated with systemic inflammatory heterogeneity in severe pneumonia. This pathway may represent a novel mechanistic target for precision therapeutic strategies aimed at mitigating immune dysregulation.},
}

@article {pmid41632094,
year = {2026},
author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N},
title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag007},
pmid = {41632094},
issn = {1574-6941},
abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.},
}

@article {pmid41631112,
year = {2026},
author = {Ji, X and Wang, M and Jin, P and Kong, L and Xu, Y and Chen, W and Liu, B and Wang, Q},
title = {Intracranial hepatitis B virus (HBV) infection following intracerebral hemorrhage in a patient with seronegative occult HBV infection.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02502},
pmid = {41631112},
issn = {2214-2509},
abstract = {Hepatitis B virus (HBV) infection is primarily associated with liver diseases but can also manifest with various extrahepatic complications. While numerous extrahepatic manifestations have been reported in acute or chronic hepatitis B patients, intracranial HBV infection remains clinically rare. A 43-year-old male had a pre-existing diagnosis of serologically negative occult HBV infection (OBI), which was initially diagnosed by detecting HBV DNA in serum while HBsAg, anti-HBs, anti-HBe, and anti-HBc were all negative. Following intracerebral hemorrhage, the patient's consciousness gradually restored through a course of rehabilitation therapy. Subsequently, the patient developed persistent fever and his level of consciousness progressively deteriorated. Serological testing confirmed the presence of HBsAg and HBeAg, the HBV loads in the serum was high, subsequent metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid (CSF) revealed positivity for HBV. After 8 weeks of treatment with entecavir, the HBV loads in the serum and CSF decreased significantly, the patient's consciousness improved, and the patient's temperature returned to normal. This study first reported a seronegative OBI patient developing intracranial HBV infection following intracerebral hemorrhage and clarified the diagnostic value of mNGS in rare intracranial infections.},
}

@article {pmid41630880,
year = {2026},
author = {Liu, MK and Liu, CY and Tang, YM and Liu, Y and Su, Y and Tian, XH and Feng, J and Ni, XL},
title = {Innovative use of unhulled rice in Baijiu brewing: impact on flavor and microbial composition.},
journal = {Food chemistry: X},
volume = {34},
number = {},
pages = {103569},
pmid = {41630880},
issn = {2590-1575},
abstract = {The quality of light-flavor Baijiu (LFB), a traditional Chinese liquor, is strongly influenced by fermentation raw materials. Traditional Baijiu brewing uses rice husk as an excipient, requiring energy-intensive steaming to remove off-flavors-a process that increases production time and costs. This study introduces an innovative co-fermentation technique using unhulled rice (Jingkangyou/Pinxiangyou varieties) with sorghum, improving LFB quality while reducing expenses. Metagenomic and flavoromic analyses compared three groups: a rice husk control and two experimental groups with varying proportions of unhulled rice. Results showed significant flavor differences, with D-lactic acid, leucinic acid, and putrescine levels correlating significantly positively to unhulled rice content. Experimental groups exhibited altered microbial diversity, flavor profiles, and physicochemical properties compared to the control. Key metabolic pathways, including galactose, phenylalanine, and lysine metabolism, were significantly modified, indicating unhulled rice reshaped biochemical reactions. These findings advance understanding of LFB fermentation dynamics and offer strategies for raw material optimization.},
}

@article {pmid41630783,
year = {2026},
author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS},
title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100544},
pmid = {41630783},
issn = {2666-5174},
abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.},
}

@article {pmid41630746,
year = {2025},
author = {Yang, B and Zhang, Y and Su, S and He, J and Hu, J and Wang, K},
title = {Metagenomic next-generation sequencing identifies tick-carried pathogens on Tarim Red Deer in Southern Xinjiang.},
journal = {Open veterinary journal},
volume = {15},
number = {11},
pages = {6109-6117},
pmid = {41630746},
issn = {2218-6050},
mesh = {Animals ; *Deer/parasitology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; China/epidemiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Ticks/virology/microbiology ; },
abstract = {BACKGROUND: Ticks are important vectors for a wide range of pathogens, including viruses, bacteria, and protozoa, that impact both humans and animals. Recent advances in metagenomic sequencing have established it as a powerful tool for uncovering the microbial diversity within ticks, enabling the discovery of previously unrecognized pathogens.

AIM: This study aimed to enrich the pathogen database for Tarim red deer in southern Xinjiang and provide experimental data to aid in the diagnosis, prevention, control, and treatment of viral diseases in Tarim red deer.

METHODS: Metagenomic sequencing was employed to analyze the viral species carried by ticks parasitizing the red tarim deer. Additionally, enzyme-linked immunosorbent assay based antibody testing was conducted on 195 red deer samples from four farms M01, M02, M03, and M04 to detect antibodies against the Orf virus.

RESULTS: Next-generation sequencing was used to obtain partial sequences of viruses and bacteria, with further analysis focusing on viruses with higher abundance, such as mule deer pox virus and Orf virus. Serological testing for Orf virus antibodies in 195 red deer samples identified 7 positive cases, resulting in a positivity rate of 3.59% (7/195). Positivity rates were 5.26% (4/76) and 6.12% (3/49) for farms M02 and M04, respectively, whereas no seropositive individuals were identified at farms M01 and M03.

CONCLUSION: This study expands the current knowledge of tick-borne pathogens in southern Xinjiang by identifying diverse viral species associated with tick-infested Tarim red deer. The findings confirm the presence of Orf virus in red deer populations, particularly on farms M02 and M04. These results underscore the importance of ongoing surveillance efforts and offer valuable insights into the diversity and geographical distribution of tick-associated viruses within the arid and semi-arid ecosystems of southern Xinjiang.},
}

Animals
*Deer/parasitology
High-Throughput Nucleotide Sequencing/veterinary
Metagenomics
China/epidemiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Ticks/virology/microbiology

@article {pmid41630294,
year = {2026},
author = {Li, R and Liu, X and Song, G and Zhang, CQ and Shen, LJ and Li, WX and Bai, ZP},
title = {Misdiagnosis of pulmonary paragonimiasis as tuberculosis: A case report.},
journal = {Medicine},
volume = {105},
number = {5},
pages = {e47555},
pmid = {41630294},
issn = {1536-5964},
mesh = {Humans ; *Paragonimiasis/diagnosis/drug therapy ; Female ; Adolescent ; *Tuberculosis, Pulmonary/diagnosis/drug therapy ; *Diagnostic Errors ; Praziquantel/therapeutic use ; Antitubercular Agents/therapeutic use ; Anthelmintics/therapeutic use ; *Lung Diseases, Parasitic/diagnosis/drug therapy ; Animals ; },
abstract = {RATIONALE: Pulmonary paragonimiasis and pulmonary tuberculosis exhibit overlapping clinical and imaging manifestations, resulting in frequent misdiagnosis in endemic areas. This case underscores the value of metagenomic next-generation sequencing (mNGS) in correcting such misdiagnoses and emphasizes the importance of managing drug-drug interactions between antituberculosis agents and praziquantel.

PATIENT CONCERNS: An 18-year-old female from Yunnan, a paragonimiasis-endemic region, presented with recurrent cough, expectoration, and hemoptysis for 4 years. She was initially diagnosed with pulmonary tuberculosis based on a positive tuberculin pure protein derivative test and chest computed tomography findings but failed to respond to antituberculosis therapy.

DIAGNOSES: Pulmonary paragonimiasis (initially misdiagnosed as pulmonary tuberculosis).

INTERVENTIONS: In-hospital tuberculosis-related tests (GeneXpert MTB/RIF, sputum/bronchoalveolar lavage fluid culture, bronchoscopic biopsy) were negative. Bronchoalveolar lavage fluid mNGS identified 87 Paragonimus sequences, and Paragonimus antibody enzyme-linked immunosorbent assay was positive. A history of raw crab ingestion was confirmed. Antituberculosis treatment was discontinued for 4 weeks (due to drug interaction), followed by oral praziquantel (1.2 g, 3 times daily for 3 consecutive days).

OUTCOMES: Hemoptysis resolved within 15 days of treatment initiation, and peripheral blood parameters returned to normal ranges. Chest computed tomography at 2 months posttreatment showed marked reduction in lesion size, and complete resolution of pulmonary cavities was observed at the 6-month follow-up, with no recurrence of symptoms.

LESSONS: For chronic respiratory symptoms unresponsive to antituberculosis treatment in endemic regions, proactive inquiry of raw freshwater crustacean consumption history and combined use of serology/mNGS can improve diagnostic accuracy. A 4-week washout period after rifampicin discontinuation is critical before praziquantel administration.},
}

Humans
*Paragonimiasis/diagnosis/drug therapy
Female
Adolescent
*Tuberculosis, Pulmonary/diagnosis/drug therapy
*Diagnostic Errors
Praziquantel/therapeutic use
Antitubercular Agents/therapeutic use
Anthelmintics/therapeutic use
*Lung Diseases, Parasitic/diagnosis/drug therapy
Animals

@article {pmid41630175,
year = {2026},
author = {Lim, SJ and Breitbart, M},
title = {Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {2},
pages = {e70065},
pmid = {41630175},
issn = {1550-7408},
support = {//University of South Florida/ ; OCE- 2527605//National Science Foundation/ ; },
mesh = {Animals ; *Sea Urchins/parasitology/microbiology ; Phylogeny ; *Oligohymenophorea/genetics/isolation & purification/classification ; Base Composition ; Genome, Mitochondrial ; Sequence Analysis, DNA ; },
abstract = {A scuticociliate most closely related to Philaster apodigitiformis caused mass mortalities of diadematoid sea urchins and was cultured as Philaster sp. isolate FWC2. We sequenced the metagenomic content of this isolate, which was predicted to represent ≤ 56% of the complete genome. Based on k-mer counts, the haploid genome size was predicted to be 122-136 Mbp. We assembled and annotated a 4,088 bp nuclear ribosomal operon, a 41,396 bp mitochondrial genome with 19.22% G + C content, 24 protein-coding genes, 6 tRNA genes, and 2 rRNA genes, and a protein sequence homologous to β-PKA in Philaster apodigitiformis potentially involved in host infection.},
}

Animals
*Sea Urchins/parasitology/microbiology
Phylogeny
*Oligohymenophorea/genetics/isolation & purification/classification
Base Composition
Genome, Mitochondrial
Sequence Analysis, DNA

@article {pmid41630101,
year = {2026},
author = {Zheng, A and Wang, F and Li, Y and Li, W and Wu, W and Gan, J and Jin, Y},
title = {Concurrent pulmonary candidiasis and tuberculosis in type 2 diabetes mellitus: immune pathogenesis and multidisciplinary management challenges: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-05853-y},
pmid = {41630101},
issn = {1752-1947},
abstract = {BACKGROUND: Type 2 diabetes mellitus predisposes to opportunistic pulmonary infections. We report sequential invasive pulmonary candidiasis followed by tuberculoma in a patient with newly diagnosed type 2 diabetes mellitus and summarize diagnostic pitfalls and management lessons.

CASE PRESENTATION: A 67-year-old Han Chinese man with no previously known diabetes presented with cough and severe hyperglycemia (random glucose 36.3 mmol/L; HbA1c 12.7%). Initial chest computed tomography showed right‑upper‑lobe consolidation. Bronchoalveolar lavage metagenomic next‑generation sequencing detected abundant Candida albicans and sputum Gram stain showed Gram‑negative bacteria predominance; sputum culture yielded no definite pathogen, blood cultures were negative, and human immunodeficiency virus test was negative. After intravenous then oral fluconazole plus intensive insulin therapy, the consolidation regressed. Suspected secondary organizing pneumonia was treated with tapering methylprednisolone. One month later, a new 1.5 cm × 1.3 cm solid nodule appeared in the prior lesion bed. computed tomography‑guided biopsy revealed necrosis, and tissue metagenomic next-generation sequencing confirmed Mycobacterium tuberculosis; standard anti‑tuberculosis therapy was initiated.

CONCLUSION: In patients with diabetes and pulmonary lesions, concomitant or sequential fungal and tuberculous infections should be actively sought with stepwise microbiology (including bronchoalveolar lavage and tissue‑based methods) and early molecular testing (metagenomic next-generation sequencing/Xpert). Steroid exposure for organizing pneumonia may worsen or unmask tuberculosis and must be weighed against infectious risk. Multidisciplinary care (endocrinology-pulmonology-infectious diseases) and rigorous glucose control are essential.},
}

@article {pmid41630069,
year = {2026},
author = {Jia, X and Zhang, Y and Tian, B and Zhang, G and Mao, S and Qian, W and Sun, D and Liu, J},
title = {Integrative analysis of rumen microbiota and host multi-organ interactions underlying feed conversion efficiency in Hu sheep.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {19},
pmid = {41630069},
issn = {1674-9782},
support = {2021YFF1000703//National Key Research and Development Program of China/ ; KJJQ2025020//Fundamental Research Funds for the Central Universities/ ; HS202302//Research Fund of Tarim University/ ; },
abstract = {BACKGROUND: Rumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host-microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs.

RESULTS: We applied a multi-omics strategy-combining rumen metagenomics and host multi-organ transcriptomics-in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid-degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism.

CONCLUSIONS: The rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.},
}

@article {pmid41629888,
year = {2026},
author = {Luo, M and Xiao, X and Wu, Y},
title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-06531-0},
pmid = {41629888},
issn = {1471-2431},
support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; },
}

@article {pmid41629580,
year = {2026},
author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N},
title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37506-x},
pmid = {41629580},
issn = {2045-2322},
support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; },
abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.},
}

@article {pmid41629563,
year = {2026},
author = {Suksa, W and Li, WJ and Luo, ZH and Jiao, JY and Ponce, V and Nuñez-Montero, K and Arce-Johnson, P and Sharma, NR and Thamchaipenet, A and Narsing Rao, MP},
title = {Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37544-5},
pmid = {41629563},
issn = {2045-2322},
support = {PHD/0136/2561//The Royal Golden Jubilee Ph.D. Program (RGJ Ph.D.), Thailand Research Fund, National Research Council of Thailand (NRCT)/ ; },
abstract = {Metagenomic analysis of the hot spring led to the recovery of a high-quality metagenome-assembled genome (MAG), MPNR_HS_01, affiliated with the phylum Actinomycetota. Taxonomy analysis assigned the MAG to "Candidatus Solincola", clustering closely with "Candidatus Solincola tengchongensis". MPNR_HS_01 was 2.82 Mb in size, assembled into 27 contigs, with a G+C content of 63.4%, 49 tRNAs, 4 rRNAs, 98.7% completeness, and no detectable contamination. Functional annotation revealed the presence of complete glycolysis and nonoxidative pentose phosphate pathways, while the tricarboxylic acid cycle was incomplete. Notably, MPNR_HS_01 encoded Wood-Ljungdahl pathway, suggesting carbon assimilation. Energy conservation was supported by hydrogenases, heterodisulfide reductase, Rnf complex, and V-type ATPase. Stress adaptation traits included genes for heat shock proteins, proline biosynthesis, and ion transporters involved in osmotic homeostasis. Although lacking flagellar machinery, MPNR_HS_01 possessed type IV pili and genes associated with twitching motility. Secondary metabolite analysis identified a betalactone biosynthetic gene cluster. Genome-relatedness analyses showed that MPNR_HS_01 was distinct from "Candidatus Solincola" species, with both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values falling below the established species threshold (95-96% ANI and 70% for dDDH), supporting its designation as a novel species, for which we propose the name "Candidatus Solincola uaceae" sp. nov.},
}

@article {pmid41629364,
year = {2026},
author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC},
title = {Linking the microbiome to the complement system in geographic atrophy.},
journal = {NPJ genomic medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41525-026-00550-7},
pmid = {41629364},
issn = {2056-7944},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.},
}

@article {pmid41629097,
year = {2026},
author = {Lyu, WT and Jia, QQ and Tong, X and Fan, H},
title = {[STAT1 gain-of-function mutation leading to disseminated Talaromyces marneffei infection combined with hemophagocytic syndrome: a case report].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {2},
pages = {184-187},
doi = {10.3760/cma.j.cn112147-20250730-00456},
pmid = {41629097},
issn = {1001-0939},
mesh = {Humans ; Male ; Talaromyces ; Adult ; *Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology ; *STAT1 Transcription Factor/genetics ; *Gain of Function Mutation ; *Mycoses/genetics/complications/microbiology ; Antifungal Agents/therapeutic use ; Mutation ; },
abstract = {This study reports a 28-year-old HIV-negative male with a STAT1 gain-of-function mutation who presented with a systemically disseminated Talaromyces marneffei (TM) infection, which was complicated by hemophagocytic lymphohistiocytosis (HLH). The patient presented with recurrent fever, weight loss, oral mucosal ulcers, as well as lymphopenia and markedly elevated inflammatory markers during the acute phase of the illness. Imaging revealed scattered ground-glass opacities and nodular shadows in both lungs, as well as localized bronchiectasis, and splenomegaly. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and bone marrow aspirate specimens revealed TM-specific sequences. Whole-exome sequencing was performed to elucidate the underlying mechanism of recurrent fungal infections. This revealed a de novo heterozygous dominant mutation in the STAT1 gene (c.1151G>A, p.Gly384Asp), localized to the DNA-binding domain at amino acid position 384. This confirmed a STAT1 gain-of-function (STAT1-GOF) variant, which is consistent with the clinical phenotype of impaired antifungal immunity. Over the clinical course, the patient developed HLH. Following a two-week course of intravenous amphotericin B liposome (5 mg/kg per day), followed by oral voriconazole maintenance therapy (200 mg, twice daily), the patient exhibited significant improvements in clinical symptoms and laboratory parameters. Notably, the marked resolution of HLH was closely linked to the successful eradication of the fungal infection. This case highlights three critical clinical implications: (1) Patients with a predisposition to primary immunodeficiency disorders (e.g., STAT1-GOF mutations) should be evaluated for disseminated TM infections, even if they are HIV-negative; (2) mNGS is instrumental in etiological diagnosis and facilitates early intervention for fungal infections; (3) early identification of genetic defects establishes a theoretical basis for precision medicine and guides targeted therapeutic strategies.},
}

Humans
Male
Talaromyces
Adult
*Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology
*STAT1 Transcription Factor/genetics
*Gain of Function Mutation
*Mycoses/genetics/complications/microbiology
Antifungal Agents/therapeutic use
Mutation

@article {pmid41628881,
year = {2026},
author = {Sun, G and Guo, S and Yao, Y and Lin, Z and Gao, H and Stauber, RH and Li, BC and Ding, GB},
title = {Facile immobilization of an unstable recombinant α-L-rhamnosidase on magnetite nanoparticles for efficient naringin biotransformation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150652},
doi = {10.1016/j.ijbiomac.2026.150652},
pmid = {41628881},
issn = {1879-0003},
abstract = {α-L-Rhamnosidase is a significant biocatalyst that specifically cleaves terminal α-L-rhamnose group from natural flavonoid diglycosides, enabling the biocatalytic production of high-value flavonoid glucosides like prunin from naringin. Compared to its precursor naringin, prunin exhibits superior solubility and bioavailability, making this enzymatic conversion commercially valuable for the food and pharmaceutical industry. However, the industrial application of free α-L-rhamnosidases faces significant challenges, including enzyme instability, difficulty in recovery, and unsatisfactory reusability. To address these issues, this study developed an innovative magnetically recoverable biocatalyst (Fe3O4-Rha) through covalent immobilization of recombinant α-L-rhamnosidase from human fecal metagenome onto Fe3O4 nanoparticles using EDC/NHS chemistry, and the immobilization parameters were systematically optimized. The successful preparation of Fe3O4-Rha was verified by TEM, FTIR, TGA, and SQUID analysis. Fe3O4-Rha retained the catalytic property of free Rha in terms of optimal pH and temperature but exhibited superior tolerance on organic solvent especially ethanol and isopropanol. Moreover, Fe3O4-Rha could effectively biotransform naringin to prunin and maintained 61.34% of initial activity after 5 cycles. In a scaled-up reaction system, Fe3O4-Rha also efficiently converted naringin into prunin and the complete conversion was achieved within 10 h. This work successfully developed a magnetically recoverable immobilized α-L-rhamnosidase system for the efficient and reusable biotransformation of naringin, offering a promising approach for the enzymatic modification of bioactive small molecules using biological macromolecular catalysts.},
}

@article {pmid41628768,
year = {2026},
author = {Frizzera, A and Vázquez, N and Sacristán, H and Tapella, F and Lovrich, G and Khalaf, A and Bojko, J and Cremonte, F},
title = {Patagonian king crabs (Lithodes santolla and Paralomis granulosa) and their diseases: Pathogen survey and taxonomic clarification of Areospora rohanae (Microsporidia).},
journal = {Journal of invertebrate pathology},
volume = {216},
number = {},
pages = {108560},
doi = {10.1016/j.jip.2026.108560},
pmid = {41628768},
issn = {1096-0805},
abstract = {Lithodid crabs constitute a valuable natural resource with commercial interest; however, their health status in South America is scarcely studied. The presence of pathogens may have a negative impact on affected populations, endangering the fishery. This study surveys the symbionts present in populations of the king crab, Lithodes santolla, and the stone/false king crab, Paralomis granulosa, using histology, transmission electronic microscopy, and molecular analyses to characterise various symbionts. The histological and molecular data revealed a wide range of infections in L. santolla, including prokaryotic microorganisms, Areospora rohanae (Microsporidia), apicomplexan gregarines, ciliated protozoans, ectoparasitic crustaceans, and various epibiotic associations. In the case of P. granulosa, apicomplexan gregarines, ciliated protozoans, and various ectoparasites were observed. Molecular analyses confirmed the presence of the microsporidian A. rohanae, occurring at high prevalences (30%) in L. santolla, and some bacterial associations. We use metagenomic tools to extract a partial genome of this parasite to aid in its identification and taxonomic position, which leads us to erect the taxonomic orders Astathelohaniida and Areosporida and further clarify the previously assigned: "Glugeida+". The results of this study represent the first broad survey for symbionts in both king crab species and take us another step forward to a more accurate microsporidian taxonomy.},
}

@article {pmid41628665,
year = {2026},
author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM},
title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: a proof-of-concept placebo-controlled randomized trial.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.01.630},
pmid = {41628665},
issn = {1522-9653},
abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.},
}

@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}

*Chagas Disease/microbiology/parasitology
Animals
Mice
Trypanosoma cruzi
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid41627733,
year = {2026},
author = {Hałakuc, P and Maciszewski, K and Karnkowska, A},
title = {Euglenid Extrachromosomal DNA: Assembly and Annotation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {109-120},
pmid = {41627733},
issn = {1940-6029},
mesh = {*Computational Biology/methods ; *Molecular Sequence Annotation/methods ; DNA, Ribosomal/genetics ; Genome, Mitochondrial ; *Euglenozoa/genetics ; Genome, Plastid ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Euglenids (Euglenozoa) contain several forms of extrachromosomal DNA (ecDNA) in their cells, including the ribosomal DNA operon (rDNA), the mitochondrial genome (mtDNA), and, in photosynthetic species, the plastid genome (ptDNA). These ecDNA elements can be easily and accurately assembled and annotated even from limited sequencing data, such as single-cell genomic or metagenomic datasets. They are an important source of information for phylogenomic analyses, metabarcoding and evolutionary studies. In this chapter, we present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of extrachromosomal DNA from whole-genome datasets. The pipeline was developed with euglenids in mind and takes into account their unique genomic features, but can also be adapted for other Euglenozoa (and protists). This approach enables the recovery of organellar and rDNA sequences with high confidence and supports both targeted studies and large-scale environmental analyses.},
}

*Computational Biology/methods
*Molecular Sequence Annotation/methods
DNA, Ribosomal/genetics
Genome, Mitochondrial
*Euglenozoa/genetics
Genome, Plastid
DNA, Mitochondrial/genetics
Phylogeny
Genomics/methods
Sequence Analysis, DNA/methods

@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}

Humans
Infant
Vietnam
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification/virology
*Bacteriophages/genetics/isolation & purification/classification
Child, Preschool
Male
Female
Metagenome
Diarrhea/microbiology
Southeast Asian People

@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Forests
DNA, Bacterial/genetics
Endangered Species
Conservation of Natural Resources
Time Factors
Sequence Analysis, DNA

@article {pmid41627236,
year = {2026},
author = {Yu, M and Wang, Y and Huangfu, K and Wu, S and Huang, H and Ma, Z and Wang, Y and Qiu, Y and Liu, S},
title = {Oxygen Vacancy-Engineered High-Entropy Oxide Nanozymes for Spatiotemporal Cascading Antifouling in Marine Environments.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e13363},
doi = {10.1002/smll.202513363},
pmid = {41627236},
issn = {1613-6829},
support = {52272271//National Natural Science Foundation of China/ ; },
abstract = {The catalytic versatility and compositional tunability of oxidative attack-based nanozymes offer a promising strategy for marine antifouling, yet their performance is often constrained by insufficient active-site accessibility, transient catalytic intermediates and restricted diffusion. Inspired by haloperoxidases (HPOs) in marine organisms, this study reports oxygen vacancy (Vo)-enriched high-entropy oxides (Vo-HEO) as multifunctional nanozymes to address these challenges. The entropy-stabilized multicomponent lattice, synergistically coupled with abundant Vo sites, reconfigures electronic structures and diversifies catalytic pathways, enabling efficient HPO-mimetic generation of hypobromous acid (HOBr), which is a selective and long-lived biocide (half-life > 36 days) capable of disrupting bacterial quorum sensing (QS) signals and oxidizing key biomolecules. By further integrating persistent HOBr with highly reactive hydroxyl radicals, Vo-HEO establishes a spatiotemporally cascading protective regime at the substrate interface, combining long-range QS suppression in the bulk phase with rapid oxidative eradication at the nano-biological interface, ultimately reducing bacterial adhesion by 90%. Microbiological characterization and metagenomic sequencing analyses further verify that Vo-HEO systematically collapses the coordination of microbial communication and energy metabolism across temporal and spatial scales. Collectively, this work demonstrates intelligent regulation of marine microecology and establishes a paradigm for adaptive antifouling design.},
}

@article {pmid41628276,
year = {2026},
author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E},
title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013576},
doi = {10.1371/journal.pntd.0013576},
pmid = {41628276},
issn = {1935-2735},
abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.},
}

@article {pmid41626594,
year = {2026},
author = {Sapino, R and Fernández-González, Á and Castresana, J},
title = {Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.},
journal = {Evolutionary applications},
volume = {19},
number = {2},
pages = {e70199},
pmid = {41626594},
issn = {1752-4571},
abstract = {Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.},
}

@article {pmid41626263,
year = {2026},
author = {Liu, Y and Fu, H},
title = {Pulmonary Tropheryma whipplei Infection Presenting With Multiple Thick-Walled Cavities on Chest CT: A Case Report and Literature Review.},
journal = {Respirology case reports},
volume = {14},
number = {2},
pages = {e70487},
pmid = {41626263},
issn = {2051-3380},
abstract = {Whipple's disease (WD) is a rare chronic multisystem infectious disease caused by the actinomycete Tropheryma whipplei. Pulmonary involvement is uncommon, and its clinical manifestations lack specificity, with diverse imaging findings, making it prone to misdiagnosis. We report a rare case of a 50-year-old woman who presented with a 2-week history of cough. Chest CT showed multiple thick-walled cavities in both lungs, a highly unusual presentation for WD pneumonia. Routine microbiological tests, including acid-fast staining and culture of bronchoalveolar lavage fluid (BALF), were negative, which made the diagnosis challenging. Metagenomic next-generation sequencing (mNGS) of BALF detected T. whipplei, confirming the diagnosis of WD pneumonia. After oral doxycycline treatment, follow-up chest CT showed complete resolution of the pulmonary cavities. This case demonstrates that multiple thick-walled cavities may be a characteristic imaging manifestation of WD pneumonia, highlights the diagnostic value of mNGS for this rare infection, and supports oral doxycycline monotherapy as an effective treatment option for isolated pulmonary TW infection.},
}

@article {pmid41626090,
year = {2026},
author = {Chen, L and Tang, M and Wang, Q and Jiang, H},
title = {Why a Mycobacterium Avium Infected Patient Showed a Positive Xpert MTB/RIF Result?.},
journal = {Clinical case reports},
volume = {14},
number = {2},
pages = {e71965},
pmid = {41626090},
issn = {2050-0904},
abstract = {This article discusses whether a MAC infected patient with a positive Xpert MTB/RIF test has a co-infection with Mycobacterium tuberculosis (MTB). The patient presented with chronic, indolent pulmonary patchy shadows on imaging but lacked typical symptoms. The MTB antigen-specific interferon-gamma enzyme-linked immunospot assay (T-SPOT.TB) was negative. Bronchoalveolar lavage fluid (BALF) testing yielded conflicting results: Xpert MTB/RIF assay detected trace levels of MTB DNA, whereas reverse dot blot hybridization confirmed the presence of Mycobacterium avium complex (MAC); in contrast, metagenomic next-generation sequencing (mNGS) returned a negative result for all pathogens. Mycobacterial culture ultimately returned positive; however, the MPB64 assay-employed for species identification-yielded a negative result, indicating a probable nontuberculous mycobacterial (NTM) infection. Despite contradictory lab results, the patient's symptoms and culture findings favored MAC infection. However, MTB infection could not be definitively ruled out in this patient, so a treatment regimen combining anti-tuberculosis and anti-MAC medications (isoniazid, rifampicin, ethambutol, and azithromycin) was initiated, leading to significant radiographic improvement. The discordance between the positive Xpert MTB/RIF result and other diagnostic evidence highlights important diagnostic challenges, underscoring the need for integrated clinical interpretation and providing actionable insights for clinicians.},
}

@article {pmid41625985,
year = {2026},
author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {15},
pmid = {41625985},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.},
}

@article {pmid41625959,
year = {2026},
author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR},
title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100344},
pmid = {41625959},
issn = {2666-5662},
abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.},
}

@article {pmid41625836,
year = {2025},
author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y},
title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e100451},
pmid = {41625836},
issn = {2168-8184},
abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.

METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).

RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.

CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.},
}

@article {pmid41625740,
year = {2025},
author = {Su, J and Liu, K and Wu, X and Lin, B and Ying, F and Zhu, Y and Li, M and Guo, P},
title = {Case Report: Confocal microscopy in the early diagnosis of microsporidial keratitis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1745070},
pmid = {41625740},
issn = {2296-858X},
abstract = {This report describes a rare case of microsporidial stromal keratitis (MSK) complicated by corneal perforation in a 69-year-old male farmer with a 5-month history of ocular redness, pain, photophobia, and epiphora. In vivo confocal microscopy (IVCM) revealed pathognomonic findings-hyperreflective double-walled spore casings and vesicular clusters, providing the earliest diagnostic clues for microsporidia infection. Subsequent metagenomic next-generation sequencing (mNGS) and histopathology confirmed Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted anti-microsporidial therapy, achieving globe preservation and visual improvement. This case underscores IVCM's pivotal role in diagnosing MSK, particularly in atypical presentations. Because MSK remains a rare corneal disorder, its insidious progression necessitates high clinical vigilance. In summary, IVCM's ability to detect microsporidial structures in real-time significantly enhances early diagnosis, complementing molecular methods like mNGS. We conclude that IVCM, as a non-invasive and rapid diagnostic tool, provides a convenient and efficient means for the early differentiation of challenging corneal infections.},
}

@article {pmid41625489,
year = {2026},
author = {Zhou, L and Liu, J and Li, S and Xiong, Y and Qin, F and Luo, Z and Huang, D and Chen, H and Wang, X},
title = {Association between anxiety symptoms on risky e-biking riding behavior among adolescents: based on gut-brain axis.},
journal = {Comprehensive psychoneuroendocrinology},
volume = {25},
number = {},
pages = {100337},
pmid = {41625489},
issn = {2666-4976},
abstract = {OBJECTIVE: This study aimed to investigate the association between anxiety symptoms and risky e-bike riding behavior (RERB) among adolescents and to explore whether gut microbiota mediates this relationship.

METHODS: Adolescents using e-bikes were recruited through a combined online and offline recruitment approach. Data collection involved supervised electronic questionnaire completion in face-to-face settings, with biological samples collected independently by participants. Anxiety symptoms were assessed using the Generalized Anxiety Disorder-7 scale. RERB were evaluated via a structured questionnaire, yielding separate scores for aggressive behaviors (ABS), violation behaviors (VBS), and negligent behaviors (NES), along with total behavior scores (TBS). Fecal samples were obtained for metagenomic sequencing to characterize gut microbiota composition. Multiple linear regression was employed to elucidate the associations between anxiety symptoms and RERB. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the potential mediating role of gut microbiota in these associations.

RESULTS: A total of 71 adolescents were included in this cross-sectional study. Anxiety symptoms were significantly associated with RERB, including TBS and VBS (both P < 0.05). Among the 15 microbial genera identified from fecal samples, 17 species showed significant association with both anxiety symptoms and RERB. PLS-PM modeling revealed a significant mediating effect of specific gut microbiota in the anxiety→behavior pathway, particularly for TBS and VBS. In contrast, for ABS, a reverse pathway-microbiota→anxiety→behavior-was found significant.

CONCLUSIONS: Anxiety symptoms were significantly associated with RERB among adolescents. Specific gut microbiota may mediate these associations, suggesting a potential microbiota-brain-behavior pathway.},
}

@article {pmid41624871,
year = {2025},
author = {Zhu, H and Hu, L and Feng, Z and Zhang, Z and Zhu, H and Li, H},
title = {Case Report: Murine typhus complicated by symmetrical peripheral gangrene: first report and diagnostic insights from metagenomic next-generation sequencing.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1746919},
pmid = {41624871},
issn = {1664-3224},
mesh = {Humans ; Female ; High-Throughput Nucleotide Sequencing ; Aged ; *Gangrene/diagnosis/etiology ; Metagenomics/methods ; *Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Rickettsia typhi/genetics ; Doxycycline/therapeutic use ; },
abstract = {BACKGROUND: Murine typhus, a flea-borne infection caused by Rickettsia typhi, often presents with nonspecific symptoms that delay diagnosis. While usually self-limiting, it can rarely progress to multiple organ dysfunction syndrome (MODS). We report the first case of murine typhus complicated by symmetrical peripheral gangrene (SPG), in which metagenomic next-generation sequencing (mNGS) enabled rapid diagnosis and guided timely doxycycline therapy.

CASE PRESENTATION: A 69-year-old female from South China was hospitalized with persistent abdominal pain and low-grade fever. She was a farmer and had suspected animal exposure. Laboratory investigations revealed hypoxia, abnormal coagulation profile, hepatorenal impairment, and thrombocytopenia. Despite empirical antibiotic therapy, her condition deteriorated progressively, manifested as hemodynamic instability, respiratory failure, and the emergence of purpuric-petechial cutaneous eruptions. Immediate interventions were initiated, including administration of vasoactive agents and mechanical ventilation. Based on mNGS, R. typhi was confirmed, she received targeted antibiotic treatment with intravenous doxycycline (100 mg twice daily). On the hospital day 16, gangrene of all four extremities became evident. The patient underwent amputation of all four extremities and survived, with systemic symptoms gradually resolving during 6-months follow-up.

CONCLUSION: This first reported case of murine typhus complicated by symmetrical peripheral gangrene (SPG) establishes its potential to cause life-threatening multiorgan failure. Metagenomic next-generation sequencing (mNGS) resolved the diagnostic challenge by rapidly identifying Rickettsia typhi, guiding life-saving doxycycline therapy and underscoring its value in severe zoonotic infections.},
}

Humans
Female
High-Throughput Nucleotide Sequencing
Aged
*Gangrene/diagnosis/etiology
Metagenomics/methods
*Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology
Anti-Bacterial Agents/therapeutic use
*Rickettsia typhi/genetics
Doxycycline/therapeutic use

@article {pmid41624426,
year = {2026},
author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N},
title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e178484},
pmid = {41624426},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.},
}

@article {pmid41623646,
year = {2025},
author = {Thagulisi, F and Baatjies, L and Sharma, A and Ngom, JT and Nyambo, K and Jooste, T and Tapfuma, KI and Mavumengwana, V},
title = {Antimycobacterial activity of intertidal sediment-derived bacteria from False Bay, South Africa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745248},
pmid = {41623646},
issn = {1664-302X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health burden due to the pathogen's ability to develop resistance to current treatment options. Consequently, drug discovery studies are essential for identifying new antimycobacterial agents with novel mechanisms of action. This study investigated the antimycobacterial activity of crude extracts derived from mixed culturable bacteria isolated from intertidal marine sediments. The bacterial diversity of the bioactive mixed cultures was characterized using 16S rRNA gene-based metagenomic analysis. Their pathogen-targeted effects were evaluated against Mycobacterium smegmatis mc[2]155 and M. tuberculosis H37Rv, and THP-1-derived macrophages infected with M. smegmatis mc[2]155. Of the 48 mixed bacterial crude extracts derived from 17 intertidal marine sediments, five-PPB1, GCR1, BB1, PPB2, and CR1-demonstrated strong antimycobacterial activity against M. smegmatis mc[2]155 and M. tuberculosis H37Rv with minimum inhibitory concentrations ranging from 31.25 to 62.50 μg/mL and 7.8125 to 15.625 μg/mL, respectively. At 62.50 μg/mL, CR1 significantly reduced the intracellular M. smegmatis mc[2]155 burden in THP-1-derived macrophages, resulting in 28.08 ± 4.25% mean decrease in bacterial survival (p < 0.0001) and 94.4% ± 1.14 mean growth inhibition. From the CR1 mixed cultures, nine axenic bacterial isolates were cultivated, and their resulting crude extracts were evaluated for bioactivity. The identified isolates included Marinobacter maritimus, Psychrobacter celer, Pseudomonas benzenivor, Bacillus altitudinis, Bacillus aerius, Bacillus stratosphericus, and Paenibacillus glucanolyticus. Metabolite profiling of axenic crude extracts identified several compounds, including tenacibactin B, maremycin D1, and tubercidine. These findings suggest that South African intertidal marine sediments host diverse microbial communities capable of producing novel antimycobacterial agents.},
}

@article {pmid41623642,
year = {2025},
author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL},
title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1738456},
pmid = {41623642},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.},
}

@article {pmid41623638,
year = {2025},
author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Wan, Z and Zhang, T and Zhang, C},
title = {The human plasma anellome exhibits age- and sex-dependent patterns with links to cardiometabolic health in older adults.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716110},
pmid = {41623638},
issn = {1664-302X},
abstract = {The human plasma virome is dominated by anelloviruses which are increasingly associated with several clinical conditions including among others HIV-1, COVID-19, autoimmune diseases, and cardiovascular and metabolic diseases. Due to their high genetic divergence, most studies investigated human anellome at broad family or genus level. These approaches obscure the contributions of specific anellovirus species to clinical conditions. We conducted plasma metagenomics in 218 individuals from young (0-16 years) and old (63-100 years) cohorts to resolve the anellome at the species level and examine its patterns across age, sex, and associations with cytokines and cardiometabolic outcomes. Older adults exhibited near-universal anellovirus detection and significantly higher abundance compared with youth. Species-specific analysis revealed that Alphatorquevirus_homin1 and Alphatorquevirus_homin13 were markedly enriched in diseased older adults. Predictive modeling based on machine learning algorithms distinguished disease status in the young cohort with high accuracy (AUC = 0.86), but performance was limited in the elderly (AUC = 0.58), suggesting a lack of diagnostic value in advanced age. Specific species abundances and diversity were associated with stroke and coronary heart disease, while cytokine correlations revealed module-specific immune signatures: Gammatorquevirus-dominated modules associated positively with pro-inflammatory cytokines and growth factors (e.g., IL-1β, IL-15, VEGF), whereas Beta- and some Alphatorquevirus-dominated modules showed predominantly negative correlations with several inflammatory and regulatory mediators (e.g., IL-6, TNF-α, IL-10). These findings demonstrate that the anellome is influenced by age and immune status and shows associations with cardiometabolic health, although these relationships do not guarentee diagnostic or causal significance. Additonally, we found no significant differences of Human endogenous retrovirus K Env expression between disease and healthy controls. This work underscores the importance of resolving human anollome to species level in future longitudinal studies to strengthen their clinical significance and biomarker potential.},
}

@article {pmid41623634,
year = {2025},
author = {Zeng, J and Gong, L and Qin, S and Fang, P and Shu, F and Zhang, W and Zhou, Y and Li, X and He, Q and Sun, P and Deng, H},
title = {Multi-omics reveals glutinous rice varieties shape Baijiu flavor via microbial and metabolic modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721127},
pmid = {41623634},
issn = {1664-302X},
abstract = {INTRODUCTION: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.

METHODS: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.

RESULTS: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.

DISCUSSION: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.},
}

@article {pmid41484707,
year = {2026},
author = {Zhou, Z and Zheng, X and Yang, W and Cui, Y and Gao, Y and Xia, J and Wang, Y and Gao, Y and Lu, M and Zhang, D and Wang, H and Chen, L},
title = {A rare case of peritoneal dialysis-associated peritonitis caused by Coxiella burnetii diagnosed by mNGS.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {233},
pmid = {41484707},
issn = {1471-2334},
abstract = {We report a rare case of peritoneal dialysis (PD)-associated peritonitis caused by Coxiella burnetii, an intracellular pathogen typically associated with Q fever. A 28-year-old female with lupus nephritis and end-stage kidney disease on PD presented with cloudy effluent and abdominal pain after consuming undercooked lamb. Despite initial empirical broad-spectrum antibiotic therapy (cefazolin/ceftazidime protocol), clinical symptoms persisted. Conventional bacterial, fungal, and mycobacterial cultures were negative. Metagenomic next-generation sequencing (mNGS) of the peritoneal effluent identified C. burnetii DNA. The treatment was transitioned to doxycycline and hydroxychloroquine resulted in clinical improvement and normalization of inflammatory markers. This case underscores the diagnostic value of mNGS in culture-negative peritonitis and emphasizes C. burnetii as an emerging pathogen in immunocompromised PD patients, particularly with zoonotic exposure histories.},
}

@article {pmid41623622,
year = {2025},
author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z},
title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722632},
pmid = {41623622},
issn = {1664-302X},
abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.

METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.

RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.

DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.},
}

@article {pmid41623619,
year = {2025},
author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W},
title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714276},
pmid = {41623619},
issn = {1664-302X},
abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.

OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.

METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.

RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.

CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.},
}

@article {pmid41623458,
year = {2026},
author = {Li, QM and He, LS and Wang, Y},
title = {Small proteins from prokaryotes in the marine water column at full ocean depth.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114585},
pmid = {41623458},
issn = {2589-0042},
abstract = {Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors.},
}

@article {pmid41623309,
year = {2026},
author = {Luo, Y and Ding, H and Pan, J and Xu, G},
title = {Use of metagenomic next-generation sequencing to diagnose Tropheryma whipplei infection-related pneumonia: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {3},
pages = {75},
pmid = {41623309},
issn = {1792-1015},
abstract = {Whipple's disease is caused by Tropheryma whipplei (T. whipplei), an uncommon pathogen that is often related to gastrointestinal symptoms. Extraintestinal involvement, particularly pulmonary manifestations, is rare and poses notable diagnostic challenges. An objective technique for identifying undiscovered infections is the application of metagenomic next-generation sequencing (mNGS). The present case report described a 55-year-old female presenting with community-acquired pneumonia (CAP), who received empirical treatment with moxifloxacin, ultimately diagnosed through mNGS performed on bronchoalveolar lavage fluid. The results indicated that the patient was infected with T. whipplei and that the patient exhibited notable clinical improvement within 2 weeks following intravenous moxifloxacin during hospitalization and continuation of oral moxifloxacin following discharge. The present case report highlighted the utility of mNGS in diagnosing atypical infections and identified T. whipplei as a potential etiological agent of CAP in immunocompetent hosts.},
}

@article {pmid41622335,
year = {2026},
author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T},
title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {41622335},
issn = {1618-0860},
abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.},
}

@article {pmid41622302,
year = {2026},
author = {Li, S and Zhang, J and Han, L and Yu, Y and Mousa, AA and Zhu, W and Leng, J and Xie, F and Mao, S},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the role of the gayal rumen and hindgut microbiome in high-efficiency lignocellulose degradation.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {18},
pmid = {41622302},
issn = {1674-9782},
support = {U2202203//Joint Funds of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gayal (Bos frontalis), a semi-domesticated bovine species, demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo, suggesting the presence of a specialized gastrointestinal microbiome. However, the functional mechanisms underlying this host-microbiome interaction remain poorly understood. Here, we conducted integrated metagenomic and metatranscriptomic analyses of rumen, cecum, and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.

RESULTS: The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle, evidenced by significantly higher (P < 0.05) fiber digestibility, cellulase and xylanase activities, and increased volatile fatty acids production despite identical feed intake. Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle, with notable enrichment of taxa specialized in lignocellulose degradation. Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes, particularly AA6, AA2, and AA3, primarily encoded by Prevotella, Cryptobacteroides, Limimorpha, and Ventricola. These enzymes are known to modify lignin structure to increase polysaccharide accessibility. These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade, especially effective in dismantling lignin barriers.

CONCLUSIONS: This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.},
}

@article {pmid41622108,
year = {2026},
author = {Deng, Z and Sanchis-López, C and Hernández-Plaza, A and Davín, AA and Huerta-Cepas, J},
title = {TreeProfiler: Large-scale metadata profiling along gene and species trees.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag028},
pmid = {41622108},
issn = {1537-1719},
abstract = {Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfiler's utility beyond traditional phylogenetic profiling, as well as its ability to efficiently handle massive datasets, by analyzing the functional diversification of the methyl-accepting chemotaxis protein (MCP) family comprising over 400,000 genomic and metagenomic sequences, and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.},
}

@article {pmid41621540,
year = {2026},
author = {Sun, H and Han, Y and Ren, S and Zhang, X and Li, X and Bi, P and Chen, L and Zhu, L and Yang, G and Ma, J and He, Q},
title = {Convergent enrichment of communities involved in Fe-N metabolism in anammox and activated sludge: Insights into genome-resolved metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134125},
doi = {10.1016/j.biortech.2026.134125},
pmid = {41621540},
issn = {1873-2976},
abstract = {The coupled process of ferric ammonium oxidation (Feammox) and nitrate-dependent ferrous oxidation (NDFO) is a cost-effective nitrogen removal strategy, yet insufficient molecular evidence supports its microbial mechanisms. This study successfully established anaerobic Fe-N coupling systems using anammox sludge and activated sludge as inoculum. Batch experiments and microbial community analysis revealed that two systems achieved similar nitrogen removal, dominated by anammox and Feammox performed by anammox bacteria (AnAOB), with a minor NDFO contribution, and convergently enriched core functional guilds under identical environmental pressures. Genome-resolved metagenomics further indicated that the porin-cytochrome protein complex associated with extracellular electron transfer co-occurred with anammox genes in Brocadia sapporoensis, suggesting its potential Feammox capability. Meanwhile, the iron oxidation gene Cyc2 co-occurred with mtr pathway homologs and complete denitrification genes in IGN3 sp900696555, suggesting its role in NDFO. This genomic evidence supports their dual metabolic capabilities, providing new insights into nitrogen removal in the coupled Feammox-NDFO process.},
}

@article {pmid41621514,
year = {2026},
author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G},
title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150646},
doi = {10.1016/j.ijbiomac.2026.150646},
pmid = {41621514},
issn = {1879-0003},
abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.},
}

@article {pmid41621269,
year = {2026},
author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L},
title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.},
journal = {Water research},
volume = {293},
number = {},
pages = {125448},
doi = {10.1016/j.watres.2026.125448},
pmid = {41621269},
issn = {1879-2448},
abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.},
}

@article {pmid41620987,
year = {2026},
author = {Tian, H and Liu, J and Li, L and Ge, J},
title = {From Interface to Cell: The Complex Interaction and Transfer Process Coupling Mechanism between Microplastics and Antibiotic Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11841},
pmid = {41620987},
issn = {1520-5851},
abstract = {Microplastic-phase interfaces (MPPIs) were established as critical vectors for accelerating antibiotic resistance gene (ARG) dissemination. Through integrated anaerobic/aerobic wastewater treatment system experiments combined with physicochemical characterization, metagenomic sequencing, and molecular dynamics simulations (MD), we elucidated MP-ARG interaction mechanisms from the interfacial to the cellular scale. Polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) MPPIs underwent significant aging during 60 days of exposure, resulting in elemental enrichment (C/O/P), the formation of C═C/C-H/C-O/C-OH functional groups, and elevated oxidation. These transformations enhanced extracellular polymeric substance production (184.81 mg/g MLSS) and selectively enriched antibiotic-resistant bacteria, ARGs, and mobile genetic elements (MGEs), promoting horizontal gene transfer. XDLVO theory revealed spontaneous microbial adhesion (ΔGadh = -23.63 mJ/m[2]) driven by Lifshitz-van der Waals (LW) and acid-base interactions. MD demonstrated direct MP penetration into the membrane via dominant LW forces (-1200 kJ/mol) and increased permeability. Concurrently, compared with sewage water (SW), MPPIs induced a 2.06-fold overproduction of reactive oxygen species, which upregulated genes encoding efflux pumps (acrF, 3.2-fold), outer membrane porins (OmpF, 4.1-fold), and conjugative transfer genes (traF, 3.8-fold). Material-specific (PET > PE > PP) and oxygen-driven redox mechanisms governed ARG dissemination: aerobic conditions favored radical-driven oxidation and MGE entrapment, whereas anaerobic systems enhanced hydrophobic adhesion.},
}

@article {pmid41620752,
year = {2026},
author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M},
title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02325-1},
pmid = {41620752},
issn = {2049-2618},
support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; },
abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.},
}

@article {pmid41620643,
year = {2026},
author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R},
title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623356},
doi = {10.1080/19490976.2026.2623356},
pmid = {41620643},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation & purification ; *Social Class ; },
abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.},
}

*Gastrointestinal Microbiome
Humans
*Socioeconomic Factors
Bacteria/classification/genetics/isolation & purification
*Social Class

@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09639-2},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}

@article {pmid41620049,
year = {2026},
author = {Xia, Q and Li, J and Li, Q and Hu, Z and Wu, H and Xie, H and Lu, J and Liu, H and Zhang, J},
title = {Immobile iron-rich particles enhance simultaneous nitrogen removal and phosphorus retention in treatment wetlands.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134129},
doi = {10.1016/j.biortech.2026.134129},
pmid = {41620049},
issn = {1873-2976},
abstract = {Eutrophication control requires cost-effective and sustainable technologies capable of simultaneously removing nitrogen and phosphorus from wastewater treatment plant (WWTP) effluents. Widely used post-treatment systems, treatment wetlands (TWs) typically exhibit limited nutrient removal because of imbalances in electron supply and demand, and rapid saturation of substrate adsorption capacity. In this study, immobile iron-rich particles (IIRPs) were introduced into TWs via a drainage-injection strategy to enhance nutrient removal from municipal WWTP effluent. Following the start-up phase, the IIRP-amended TWs consistently achieved effluent concentrations that met the target quasi-Class IV surface water quality standards (TN ≤ 10 mg L[-1]; TP ≤ 0.3 mg L[-1]) for 300 days of continuous operation. The enhanced NH4[+]-N and TN removal with iron-rich particles amendment could not be attributed to nitrification or anammox, as evidenced using qPCR, metagenomic binning, and removal profiles. Instead, Fe-N redox-coupling processes, including Fe(III) reduction-driven and Fe(II) oxidation-driven nitrogen-removal pathways, contributed to enhanced nitrogen removal. The IIRPs amendment increased the equilibrium phosphorus adsorption capacity of wetland substrate by threefold, and the improved phosphorus retention was attributed to Fe-P interactions. These findings reveal a coupled Fe-N-P mechanism that enables efficient and stable nutrient removal and provide a mechanistic foundation for developing low-carbon, sustainable strategies to upgrade existing TWs for advanced wastewater polishing.},
}

@article {pmid41620043,
year = {2026},
author = {Chang, XL and Xing, BS and Qin, Y and Xie, J and Li, ZB and Wang, XC and Chen, R and Li, YY},
title = {Sustained performance and microbial succession in novel artificial rumen system coupling dynamic membrane with methanogenic granules for acid absorption.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134119},
doi = {10.1016/j.biortech.2026.134119},
pmid = {41620043},
issn = {1873-2976},
abstract = {Artificial rumen systems promise for converting lignocellulosic biomass into renewable products but face challenges in long-term operation. This study developed a novel artificial rumen system combined fermentation with acid absorption using methanogenic granules and a dynamic membrane. Over 480 days, volatile fatty acids (VFAs) were effectively separated by the dynamic membrane and immediately absorbed by granules, simulating natural ruminant acid absorption. Despite increasing the organic loading rate from 3.27 to 8.18 g-VS/L/day, stable VFA yields of 0.21-0.24 g-COD/g-VS were maintained. After 440 days, removal efficiencies for cellulose, hemicellulose, and lignin reached 62.7 %, 52.1 %, and 40.7 %, respectively. The acid absorption unit efficiently converted VFAs into biomethane (302-304 mL/g COD), showing high bioenergy potential. Metagenomic analysis confirmed key rumen microbes (Firmicutes, Bacteroidetes) were dominant, with enrichment of low-abundance species like Prevotella and Solobacterium that secreted lignocellulose-degrading enzymes. The system enables long-term biomass conversion and supports future high-load artificial rumen engineering.},
}

@article {pmid41619990,
year = {2026},
author = {Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Qin, Y and Liu, S and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H},
title = {Antimicrobial Resistance and Genomic Characterization of Escherichia coli Isolated from Mink in Northern China.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108328},
doi = {10.1016/j.micpath.2026.108328},
pmid = {41619990},
issn = {1096-1208},
abstract = {Escherichia coli (E. coli) is one of the most common commensal bacteria in the intestinal tract of humans and animals. It serves as a major reservoir of antimicrobial resistance genes and may facilitate their horizontal transfer among different hosts. In this study, 212 fecal samples were collected from mink across four northern provinces of China, a total of 110 E. coli isolates were recovered (isolation rate, 51.89%). Preliminary antimicrobial screening was conducted using four clinically critical antibiotics, including ceftazidime (CAZ), polymyxin B (PMB), meropenem (MEM), and tigecycline (TGC), with CAZ resistance being the most prevalent, followed by PMB, MEM, and TGC. Further antimicrobial susceptibility testing against ten commonly used antibiotics in 49 representative isolates revealed universal multidrug resistance (MDR), including 100% resistance to imipenem, tetracycline, enrofloxacin, florfenicol, and sulfamethoxazole. Genetic screening identified multiple resistance genes such as aac(3')-IIa, blaCTX-M, tet(A), and mcr-1. Conjugation assays demonstrated that CAZ resistance was the most transferable. Virulence profiling revealed a low prevalence of classical pathogenic virulence factors, with only six virulence gene types detected, consistent with the results of Galleria mellonella infection assays. Whole-genome sequencing of 41 representative isolates revealed 87 unique antibiotic resistance genes (ARGs) types spanning 14 antibiotic classes including alinically important determinants such as blaCTX-M, tet, and mcr, and 71 unique virulence genes assigned to 65 functions. Metagenomic analysis further identified diverse ARGs within the mink gut microbiota, with 21 shared between whole-genome and metagenomic sequencing. Correlation analysis suggested co-occurrence patterns among ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), particularly between ARGs and MGEs. Overall, mink-derived E. coli exhibited extensive MDR but limited classical pathogenic virulence, and the mink gut microbiota may represent an important reservoir and transmission hub for resistance genes in intensive farming ecosystems.},
}

@article {pmid41619833,
year = {2026},
author = {Tran, LNB and Zhuo, R and Singha, M and Sekhon, H and Yang, S and Fishbein, GA and Tymchuk, C and Allyn, PR},
title = {First Reported Case of Capnocytophaga cynodegmi Infective Endocarditis: A Diagnostic Odyssey.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108446},
doi = {10.1016/j.ijid.2026.108446},
pmid = {41619833},
issn = {1878-3511},
abstract = {Capnocytophaga cynodegmi, a commensal of canine and feline oral flora, is rarely implicated in human infections, with most cases limited to localized soft tissue infections. We present the first case of C. cynodegmi-associated infective endocarditis (IE) in a 39-year-old man with bicuspid aortic valve and alcohol use disorder. The patient presented with sepsis, aortic valve vegetations, and systemic complications, including heart failure and shock liver. Despite negative blood and valve cultures, metagenomic sequencing of plasma (Karius test) initially detected Capnocytophaga canimorsus, while targeted Next-Generation Sequencing (NGS) of explanted valve tissue confirmed C. cynodegmi (100% match). The patient underwent valve replacement and completed a 6-week course of ampicillin-sulbactam with clinical recovery. This case underscores the diagnostic challenges of fastidious pathogens and demonstrates the potential of C. cynodegmi to cause life-threatening IE. It highlights the necessity of advanced molecular diagnostics, such as NGS, in atypical cases of IE. Clinicians should consider zoonotic Capnocytophaga spp. in culture-negative IE, particularly in high-risk patients with animal exposure or valvular abnormalities.},
}

@article {pmid41619830,
year = {2026},
author = {Zheng, C and Zhang, Y and Wang, Y and Sun, Y and Wei, F and Zhang, Y and Ma, Y and Cai, M},
title = {Two-case cluster of rapidly progressive influenza B and Staphylococcus aureus pneumonia with one death.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108442},
doi = {10.1016/j.ijid.2026.108442},
pmid = {41619830},
issn = {1878-3511},
abstract = {The synergistic interaction between Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible Staphylococcus aureus (MSSA) and influenza virus can cause fulminant necrotizing pneumonia. We report a cluster of two cases involving epidemiologically linked construction workers illustrating this life-threatening synergy. After shared occupational exposure, one patient died of rapidly progressive pneumonia, while the other survived after prolonged intensive care. As conventional diagnostics failed, metagenomic next-generation sequencing (mNGS) of sputum and bronchoalveolar lavage fluid (BALF) identified co-infection with PVL-positive sequence type 22 (ST22) MSSA and influenza B virus (IBV) in case 2, guiding a successful shift to targeted therapy. This report demonstrates the extreme virulence of PVL-positive MSSA-influenza co-infection, highlights the diagnostic value of mNGS in severe treatment-refractory pneumonia, and emphasizes the need for effective respiratory protection in high-risk occupational environments.},
}

@article {pmid41619556,
year = {2026},
author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y},
title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157875},
doi = {10.1016/j.phymed.2026.157875},
pmid = {41619556},
issn = {1618-095X},
abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.

PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.

METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.

RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.

CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.},
}

@article {pmid41619541,
year = {2026},
author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Alifrangis, M and Aarestrup, FM and Sonda, T},
title = {Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.},
journal = {Virology},
volume = {617},
number = {},
pages = {110813},
doi = {10.1016/j.virol.2026.110813},
pmid = {41619541},
issn = {1096-0341},
abstract = {Human adenoviruses (HAdVs) are important pathogens that are associated with a wide array of clinical diseases, particularly in the pediatric population. Despite numerous reports of HAdV infections in Tanzania, there are currently no whole genome sequences from this region available in global public databases. This gap presents challenges to our efforts to understand their dissemination and evolution over time. This study employed nanopore-based metagenomic sequencing to detect and sequence the whole genomes of HAdV strains in Tanzanian infants with diarrhea. We present the first whole genome of HAdV-A18 from Africa, representing only the third worldwide. Additionally, it includes the first complete genomes of HAdV-F40, HAdV-F41, and HAdV-B3 obtained from Tanzania. In addition, this study provides information on the enteric adenovirus lineages circulating in Tanzania. These findings provide crucial genomic insights into the diversity of viruses in sub-Saharan Africa and underscore the importance of genomic surveillance to deepen our understanding of adenovirus transmission and evolution.},
}

@article {pmid41619490,
year = {2026},
author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L},
title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106506},
doi = {10.1016/j.psj.2026.106506},
pmid = {41619490},
issn = {1525-3171},
abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.},
}

@article {pmid41619482,
year = {2026},
author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L},
title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106527},
doi = {10.1016/j.psj.2026.106527},
pmid = {41619482},
issn = {1525-3171},
abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.},
}

@article {pmid41619464,
year = {2026},
author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A},
title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181482},
doi = {10.1016/j.scitotenv.2026.181482},
pmid = {41619464},
issn = {1879-1026},
abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.},
}

@article {pmid41619271,
year = {2026},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1539},
pmid = {41619271},
issn = {2152-5250},
abstract = {Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.},
}

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/classification
Animals
*Microbiota
Male
*Lice Infestations/epidemiology/parasitology
Female
Child
Child, Preschool
*Genetic Variation
RNA, Ribosomal, 16S/genetics
Vulnerable Populations
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units). Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

@article {pmid41618858,
year = {2026},
author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W},
title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14269},
doi = {10.1002/advs.202514269},
pmid = {41618858},
issn = {2198-3844},
support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; },
abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.},
}

@article {pmid41618766,
year = {2026},
author = {Yan, Y and Li, F and Huang, T and Cheng, Y and Liao, Y and Liu, H},
title = {Intraocular infection of Moraxella nonliquefaciens accompanied by secondary angle-closure glaucoma: A case report.},
journal = {The Journal of international medical research},
volume = {54},
number = {1},
pages = {3000605251411736},
doi = {10.1177/03000605251411736},
pmid = {41618766},
issn = {1473-2300},
mesh = {Humans ; *Glaucoma, Angle-Closure/microbiology/etiology/diagnosis ; *Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis ; *Moraxella/isolation & purification ; *Endophthalmitis/microbiology/complications ; Trabeculectomy/adverse effects ; Anti-Bacterial Agents/therapeutic use ; *Eye Infections, Bacterial/microbiology/complications ; Male ; Female ; Aged ; Vitrectomy ; Vancomycin/therapeutic use/administration & dosage ; },
abstract = {Infectious endophthalmitis after ocular surgery is a rare complication that can result in severe vision loss. Moraxella nonliquefaciens is an opportunistic pathogen that rarely causes ocular infections. We report a rare case of Moraxella nonliquefaciens endophthalmitis complicated by secondary angle-closure glaucoma occurring years after trabeculectomy and cataract surgery. Cycloplegia resulted in deepening of the anterior chamber and opening of the angles. Metagenomic next-generation sequencing of the aqueous humor identified Moraxella nonliquefaciens. Following multiple intravitreal vancomycin injections and vitrectomy with posterior capsulectomy, direct communication between the anterior chamber and the vitreous cavity was established, leading to resolution of the condition. The patient's visual acuity was fully restored. We hypothesize that persistent infection with Moraxella nonliquefaciens may damage the lens zonules, resulting in zonular laxity and weakness; however, this represents only one possible mechanistic explanation and may play a secondary role in the development of secondary angle-closure glaucoma. Ophthalmologists should be aware that patients with Moraxella nonliquefaciens endophthalmitis may be at risk of zonular laxity and secondary angle-closure glaucoma, particularly years after trabeculectomy and cataract surgery. Prompt recognition and intervention may be vision-saving.},
}

Humans
*Glaucoma, Angle-Closure/microbiology/etiology/diagnosis
*Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis
*Moraxella/isolation & purification
*Endophthalmitis/microbiology/complications
Trabeculectomy/adverse effects
Anti-Bacterial Agents/therapeutic use
*Eye Infections, Bacterial/microbiology/complications
Male
Female
Aged
Vitrectomy
Vancomycin/therapeutic use/administration & dosage

@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Artiles, RF and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00824-w},
pmid = {41618437},
issn = {2042-6410},
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}

@article {pmid41618433,
year = {2026},
author = {Wang, Y and Zuo, W and Huang, J and Sun, F and Du, Y},
title = {Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03970-x},
pmid = {41618433},
issn = {1474-760X},
support = {EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; },
abstract = {BACKGROUND: Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) provides a powerful approach to study microbial communities by linking genomic content with spatial interactions. Hi-C complements shotgun sequencing by revealing taxonomic composition, functional interactions, and genomic organization within a single sample. However, aligning Hi-C reads to metagenomic contigs is challenging due to variable insert sizes of Hi-C paired-end reads, multi-species complexity, and gaps in assemblies. Although several benchmark studies have evaluated general alignment tools and Hi-C data alignment, none have specifically focused on metagenomic Hi-C data.

RESULTS: We evaluated seven alignment strategies commonly used in Hi-C analyses: BWA MEM -5SP, BWA MEM default, BWA aln default, Bowtie2 default, Bowtie2 -very-sensitive-local, Minimap2 default, and Chromap Hi-C default. We benchmarked these tools on one synthetic dataset and seven real-world environments. Performance was assessed based on the number of inter-contig Hi-C read pairs and their impact on downstream tasks, such as binning quality.

CONCLUSIONS: We show that BWA MEM -5SPgenerally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.},
}

@article {pmid41618383,
year = {2026},
author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A},
title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {25},
pmid = {41618383},
issn = {1297-9716},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Swine Diseases/microbiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; *Brachyspira hyodysenteriae/physiology ; Feces/microbiology ; Disease Susceptibility/veterinary/microbiology ; },
abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.},
}

Animals
Swine
*Gastrointestinal Microbiome
*Swine Diseases/microbiology
*Gram-Negative Bacterial Infections/veterinary/microbiology
*Brachyspira hyodysenteriae/physiology
Feces/microbiology
Disease Susceptibility/veterinary/microbiology

@article {pmid41618136,
year = {2026},
author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX},
title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04750-0},
pmid = {41618136},
issn = {1471-2180},
support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41618101,
year = {2026},
author = {Park, SJ and Özdinç, BE and Coker, KG and Walsh, DM and Fox, DJ and Evans, S and Farahnik, J and Moffat, K and Boomgaarden, M and Mischley, LK},
title = {Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01271-5},
pmid = {41618101},
issn = {2373-8057},
abstract = {Previous studies suggest there are distinct gut microbial and functional variations in patients with Parkinson's disease (PwPD) that may reveal potential microbiome signatures or biomarkers to aid in early detection of the disease. In this case-control study, we used whole genome sequencing to compare the stool samples of 55 PwPD to 42 healthy controls (HC) from a public database (BioProject Accession PRJEB39223). For bacterial phyla, we observed a greater relative abundance in Firmicutes and Actinobacteria among PwPD, while that of Bacteroidetes was lower. For phages, PwPD had a greater relative abundance of Siphoviridae, Tectiviridae, and Podoviridae, while Microviridae was lower. Moreover, we described 10 functional pathways that most significantly differed between PwPD and HC (all P < 0.0001). In conclusion, significant differences were observed in gut bacteria, phages, and functional pathways between PwPD and HC that both support and conflict with previous case-control studies and warrant further validation.},
}

@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06706-5},
pmid = {41617733},
issn = {2052-4463},
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}