@article {pmid42159601,
year = {2026},
author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y},
title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42159601},
issn = {2057-5858},
mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.},
}

Humans
*Mycoplasma pneumoniae/genetics/pathogenicity/metabolism
*Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis
Female
Male
Child, Preschool
Child
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Infant
Severity of Illness Index
Microbiota
Machine Learning
Anti-Bacterial Agents/pharmacology

@article {pmid42159642,
year = {2026},
author = {Ortigoza, PYA and Luiz, FN and Ghellere, GJ and Meyer, RF and Rosa, LH and Passarini, MRZ},
title = {Biogas production using the microbial community present in the soil from Deception Island, maritime Antarctica.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42159642},
issn = {1614-7499},
support = {118/2024//Institutional Program to Support Research Groups/ ; 440218/2023-3//CNPq PROANTAR/ ; },
abstract = {The current energy crisis is increasing the production of sustainable energy, such as biogas, a fuel generated by the anaerobic digestion of organic waste. The use of oat, an agricultural waste, makes the anaerobic digestion more sustainable. Antarctic microbial communities can utilize a wide range of substrates and adapt to different temperatures. Thus, this study evaluated methane production through an innovative approach, using microbial enrichment, and assessed archaeal diversity through metagenomic techniques in Antarctic soils, Deception Island, Maritime Antarctica. Metagenomic analyses showed low archaeal diversity and abundance. The Euryarchaeota (95.2%) and Methanobrevibacter were the most abundant and frequent phylum and genus, respectively. The average biogas production values were 595 LN kg VS[-][1] and 561 LN kg VS[-][1] in tests with individual oat (IO) and oat with enriched mixed culture (O + MC), respectively. However, O + MC showed a higher methane production, 4% (319 LN kg VS[-][1]) more than the results from the IO test with inoculum. Soils from Deception Island may represent a promising source of methanogenic communities capable of producing methane using agricultural waste as an alternative for energy production. Future studies are needed to understand the methane production using soil samples from cold environments.},
}

@article {pmid42159838,
year = {2026},
author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA},
title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42159838},
issn = {1678-4405},
mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.},
}

Animals
*Feces/virology
*Porcupines/virology
Brazil
*Virome
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
*Viruses/classification/genetics/isolation & purification

@article {pmid42159959,
year = {2026},
author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T},
title = {Animal gut microbes and microbiomes in the 21st century and beyond.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42159959},
issn = {1869-1889},
abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.},
}

@article {pmid42160933,
year = {2026},
author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M},
title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142454},
doi = {10.1016/j.jhazmat.2026.142454},
pmid = {42160933},
issn = {1873-3336},
abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.},
}

@article {pmid42161086,
year = {2026},
author = {Ziliani, A and Bovio-Winkler, P and Pabst, M and Cabezas, A and Etchebehere, C and Garcia, HA and López-Vázquez, CM and Brdjanovic, D and van Loosdrecht, MCM and Rubio-Rincón, FJ},
title = {Glycine-mediated microbial interactions in biological phosphorus removal systems.},
journal = {Water research},
volume = {302},
number = {},
pages = {126057},
doi = {10.1016/j.watres.2026.126057},
pmid = {42161086},
issn = {1879-2448},
abstract = {Amino acids are less studied substrates in enhanced biological phosphorus removal (EBPR) systems. Glycine, a prevalent amino acid in wastewater, was used in this study to evaluate its role in EBPR processes. We operated a sequencing batch reactor (SBR) for over three months with glycine as the sole carbon source to investigate phosphorus removal performance and microbial dynamics using chemical and molecular analyses. The reactor supported EBPR activity, with glycine enabling anaerobic phosphorus release followed by aerobic uptake. The dissolved organic carbon to phosphorus (DOC:P) removal ratio of 100:9.9 closely matched values reported for systems dominated by polyphosphate-accumulating organisms (PAOs), and net phosphorus removal (20 mg PO4-P L[-1]) fell within the range reported for laboratory-scale EBPR systems fed with mixed carbon sources. Community analyses showed enrichment of Saccharimonadales alongside putative PAOs, including Ca. Phosphoribacter and Ca. Propionivibrio. Genome-resolved analyses indicate distinct but complementary metabolic potentials, including glycine transformation and lactate-related pathways, suggesting distributed carbon processing within the community. Together, these findings expand the understanding of amino acid utilization in EBPR systems and identify potential metabolic linkages that influence phosphorus removal under glycine-fed conditions.},
}

@article {pmid42161088,
year = {2026},
author = {Liu, Q and Zhang, Y and Gong, H and Zhou, S and Yang, J and Zhu, D and Huang, Z and Zhu, Y and Niu, H and Dai, X},
title = {Microbial-driven molecular transformation of dissolved organic matter in water-jet loom wastewater reclamation: An integrated FT-ICR MS and metagenomic investigation.},
journal = {Water research},
volume = {302},
number = {},
pages = {126124},
doi = {10.1016/j.watres.2026.126124},
pmid = {42161088},
issn = {1879-2448},
abstract = {Water-jet loom wastewater, a major textile effluent in China, contains recalcitrant dissolved organic matter (DOM) derived from synthetic sizing agents and lubricants, whose incomplete removal constrains high-quality water reuse. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics provide high-resolution molecular and genetic insights, optimizing treatment efficacy remains hindered by a fragmented understanding of the intricate links between molecular transformations and their microbial drivers. This study established a reactomic-genomic paradigm coupling potential mass difference (PMD)-based molecular network analysis with metagenomic enzyme annotation in a full-scale membrane bioreactor (MBR) system (10000 m[3]·d[-1]). Over 8,000 molecular formulae were resolved across the treatment train. The results revealed that the dissolved air flotation unit prior to MBR selectively removed hydrophobic lipids and aliphatic/peptide-like compounds, leading to the relative enrichment of lignins/CRAM-like recalcitrant matter. The bioreactor served as the major zone of molecular turnover, with oxidation and depolymerization identified as the dominant transformation classes. These transformations were consistent with the enrichment of a Sphingomonadaceae-associated functional guild and abundant oxygenase-related genes, highlighting the role of microbial oxidation in aromatic transformation. Furthermore, a source-oriented framework revealed MBR effluent DOM as a spatially assembled mixture of three components. The recalcitrant influent-derived fraction dominated total effluent intensity (74.3%), while the bioreactor-emergent fraction constituted a consistent biogenic baseline (12.0%). In contrast, the membrane-associated emergent fraction contributed to molecular diversity (45.4% of unique formulae) but weakly to total intensity (9.7%). These findings indicate that the key challenge for high-quality reuse lies in controlling persistent and compositionally complex DOM. This framework provides a molecular basis for targeted process optimization and supports the transition of textile wastewater treatment from discharge compliance toward chemistry-informed reuse.},
}

@article {pmid42161089,
year = {2026},
author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S},
title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.},
journal = {Placenta},
volume = {181},
number = {},
pages = {168-174},
doi = {10.1016/j.placenta.2026.05.010},
pmid = {42161089},
issn = {1532-3102},
abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.},
}

@article {pmid42161263,
year = {2026},
author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.019},
pmid = {42161263},
issn = {1934-6069},
abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.},
}

@article {pmid42161874,
year = {2026},
author = {, and , },
title = {[Expert consensus on laboratory diagnosis of inflammatory bowel disease (2026)].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {},
pages = {1-17},
doi = {10.3760/cma.j.cn112150-20260413-00324},
pmid = {42161874},
issn = {0253-9624},
support = {82472361//Natural Science Foundation of China/ ; },
abstract = {In recent years, the incidence of inflammatory bowel disease (IBD) in China has shown a significant upward trend. The invasive nature of colonoscopy limits its widespread application in population screening and long-term follow-up, while conventional laboratory parameters still suffer from insufficient sensitivity and specificity. A single test is inadequate for comprehensively assessing the complex pathophysiological processes of IBD. To enhance diagnostic efficacy, it is necessary to establish a multi-index combined evaluation system, integrating comprehensive assessments across dimensions such as inflammatory activity, nutritional metabolism, coagulation function, and infection risk. This consensus integrates relevant hematological and fecal laboratory markers, establishes a stratified application pathway covering initial screening, differential diagnosis, activity monitoring, and efficacy evaluation, and standardizes the clinical application scenarios of indicators such as fecal calprotectin (FC), the anti-Saccharomyces cerevisiae antibody (ASCA)/perinuclear anti-neutrophil cytoplasmic antibody (pANCA) panel, CRP (C-reactive protein)/ESR (erythrocyte sedimentation rate), and NLR (neutrophil-to-lymphocyte ratio). Furthermore, this consensus systematically reviews the clinical potential of cutting-edge technologies, including 16S amplicon sequencing, metagenomic sequencing, and microRNA detection, highlighting their significant prospects in analyzing microbial community structure, identifying occult pathogens, and assessing host regulation. This consensus aims to optimize non-invasive testing strategies for IBD, reduce misdiagnosis and improper treatment, and provide a standardized framework for tiered diagnosis and treatment as well as precision prevention and management.},
}

@article {pmid42162115,
year = {2026},
author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, ÅV and Walter, S and Simon, R},
title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42162115},
issn = {2045-2322},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; },
abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics
Female
*Metagenomics/methods
Adult
Middle Aged
Feces/microbiology
*Metagenome
Case-Control Studies

@article {pmid42162191,
year = {2026},
author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y},
title = {Author Correction: Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.},
journal = {NPJ digital medicine},
volume = {9},
number = {1},
pages = {},
doi = {10.1038/s41746-026-02769-1},
pmid = {42162191},
issn = {2398-6352},
}

@article {pmid42162287,
year = {2026},
author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T},
title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.},
journal = {Archives of virology},
volume = {171},
number = {6},
pages = {},
pmid = {42162287},
issn = {1432-8798},
support = {ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; },
mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation & purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; },
abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.},
}

*Edible Grain/virology
Genome, Viral
Phylogeny
*Hordeum/virology
*Luteoviridae/genetics/classification/isolation & purification
*Plant Diseases/virology
France
*Virome/genetics
Metagenomics

@article {pmid42162448,
year = {2026},
author = {Bharadava, K and Makarani, N and Kaushal, RS},
title = {Co-selection of antimicrobial and heavy metal resistance in aquatic microbial communities at the water interface.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {8},
pages = {},
pmid = {42162448},
issn = {1573-2983},
mesh = {*Metals, Heavy/pharmacology/toxicity ; *Water Microbiology ; *Drug Resistance, Bacterial ; *Water Pollutants, Chemical ; Wastewater/microbiology ; *Drug Resistance, Microbial ; Humans ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; },
abstract = {Antimicrobial resistance (AMR) and heavy metal resistance (HMR) in aquatic ecosystems are increasing global health concerns driven by anthropogenic pollution of water systems. Municipal wastewater, hospital effluents, industrial discharge, agricultural runoff, and aquaculture activities contribute to the persistence and dissemination of resistant microorganisms and resistance genes in aquatic environments. Clinically important waterborne pathogens, including Escherichia coli, Salmonella Typhi, Shigella spp., and Vibrio cholerae, readily acquire resistance under continuous environmental stress conditions. Heavy metals further enhance AMR persistence through co-selection and cross-resistance mediated by mobile genetic elements carrying both antimicrobial and heavy metal resistance genes. This review summarizes the major environmental drivers, molecular mechanisms, and dissemination pathways associated with AMR-HMR interactions in aquatic systems. Recent advances in wastewater-based epidemiology, metagenomic surveillance, and resistance monitoring are highlighted as emerging tools for environmental and public health assessment. Current mitigation approaches, including advanced oxidation processes, membrane bioreactors, nanomaterial-based filtration, and microbial bioremediation, are also evaluated. A multidisciplinary One Health framework is essential for limiting environmental resistance dissemination and protecting human, animal, and ecosystem health.},
}

*Metals, Heavy/pharmacology/toxicity
*Water Microbiology
*Drug Resistance, Bacterial
*Water Pollutants, Chemical
Wastewater/microbiology
*Drug Resistance, Microbial
Humans
*Anti-Bacterial Agents/pharmacology
Bacteria/drug effects/genetics

@article {pmid42162574,
year = {2025},
author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E},
title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.},
journal = {Asian journal of anesthesiology},
volume = {63},
number = {1},
pages = {20-29},
doi = {10.6859/aja.202503_63(1).0003},
pmid = {42162574},
issn = {2468-824X},
mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; },
abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.

METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.

RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.},
}

Animals
*Sevoflurane/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Mice
Female
*Anesthetics, Inhalation/pharmacology
*Dysbiosis/chemically induced/microbiology
*Metagenomics/methods
Feces/microbiology
Longitudinal Studies
Sex Factors

@article {pmid42162897,
year = {2026},
author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J},
title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106706},
doi = {10.1016/j.tvjl.2026.106706},
pmid = {42162897},
issn = {1532-2971},
abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.},
}

@article {pmid42163161,
year = {2026},
author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM},
title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-08132-8},
pmid = {42163161},
issn = {1471-244X},
abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.

METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.

RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p < 0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.

CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.

CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).},
}

@article {pmid42163620,
year = {2026},
author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y},
title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073460107260407065758},
pmid = {42163620},
issn = {1875-5402},
abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.

METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl₁. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.

RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.

DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.

CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.},
}

@article {pmid42164149,
year = {2026},
author = {Scutari, R and Fox, V and Mastropaolo, M and Fini, V and Mussa, M and Bigliano, P and Colagrossi, L and Vrenna, G and Perinzano, A and Scabini, S and Perno, CF and Calcagno, A},
title = {Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1791094},
pmid = {42164149},
issn = {2296-858X},
abstract = {Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1), Candida albicans, Enterococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for Mycobacterium species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of Fusarium pseudograminearum, Mycobacterium canettii, and Ralstonia sp., alongside low-level viral sequences [Epstein-Barr virus (EBV) and HSV-1]. These results reflected the patient's severe immune deficiency, characterized by a marked depletion of CD8[+] T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.},
}

@article {pmid42164154,
year = {2026},
author = {Wang, S and Wang, X and Sun, K and Jin, Z and Ma, J},
title = {Pulmonary sarcoidosis complicated with pulmonary cryptococcosis: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1822801},
pmid = {42164154},
issn = {2296-858X},
abstract = {Pulmonary sarcoidosis is an idiopathic granulomatous disorder primarily affecting the lungs and mediastinal lymph nodes. Pulmonary cryptococcosis, an opportunistic mycosis caused by Cryptococcus species, may occur concurrently with sarcoidosis, presenting substantial diagnostic challenges, particularly in treatment-naïve patients. A 63-years-old previously healthy female presented with insidious-onset dyspnea and low-grade fever. Chest computed tomography (CT) showed mediastinal and hilar lymphadenopathy, accompanied by small nodules in the right lower lobe. She was diagnosed with pulmonary sarcoidosis at a local hospital and started on prednisone, with symptomatic improvement. However, follow-up imaging showed enlargement and cavitation of the right lower lobe nodules. Admission laboratory tests, including inflammatory markers and fungal serology, were all unremarkable. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified sequences of Cryptococcus neoformans. Histopathological examination of mediastinal lymph node specimens confirmed the presence of non-necrotizing granulomas, which is consistent with a diagnosis of sarcoidosis. Meanwhile, the right lower lobe lung biopsy revealed positive staining for Cryptococcus. The patient was treated with fluconazole, resulting in radiological resolution. This case highlights the importance of considering pulmonary cryptococcosis as a potential complication in treatment-naïve sarcoidosis patients who present with abnormal chest shadows. Underlying immune dysregulation in sarcoidosis may obscure both clinical and radiological findings, thereby complicating the diagnostic process.},
}

@article {pmid42164315,
year = {2026},
author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG},
title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag105},
pmid = {42164315},
issn = {2730-6151},
abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.},
}

@article {pmid42164317,
year = {2026},
author = {Domínguez-Huerta, G and Cabello, AM and Santos-Bruña, JJ and Mercado, JM and Ferrera, I},
title = {Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag110},
pmid = {42164317},
issn = {2730-6151},
abstract = {Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon's prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.},
}

@article {pmid42164318,
year = {2026},
author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A},
title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag106},
pmid = {42164318},
issn = {2730-6151},
abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.},
}

@article {pmid42164663,
year = {2026},
author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J},
title = {What a pickle-a metagenomic perspective on the cucumber fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809866},
pmid = {42164663},
issn = {1664-302X},
abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.},
}

@article {pmid42164669,
year = {2026},
author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z},
title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1670904},
pmid = {42164669},
issn = {1664-302X},
abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.},
}

@article {pmid42165181,
year = {2026},
author = {Zhang, B and Zhang, J and Duan, F and Xuan, Z and Sun, T and Lu, L},
title = {Enzymatic Galactosylation of Erythritol Enhances Antibacterial Activity against Cariogenic Streptococcus mutans.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14195},
pmid = {42165181},
issn = {1520-5118},
abstract = {Erythritol is a widely used sweetener with beneficial properties and bioactivities, including the inhibition of Streptococcus mutans, a bacterium that induces dental caries. Galactosylation of compounds is an attractive method for improving antimicrobial activity. In this study, a novel metagenomic β-galactosidase gene, bga7, was successfully expressed in Escherichia coli. The recombinant enzyme was used to galactosylate erythritol, generating a high yield (93.6%) of galactoside product at a concentration of 2 U/mL upon incubation with 20 mM o-nitrophenyl-β-d-galactopyranoside and 0.5 M erythritol at 40 °C and pH 9.0 for 4 h. The product was confirmed to be β-galactosyl-erythritol by MS and NMR analysis. This galactoside demonstrated significantly enhanced inhibition of both the planktonic growth of S. mutans and biofilm formation compared to erythritol alone. Further investigation into the mechanism revealed that the galactoside suppressed the transcriptional levels of four important genes (gtfB, ftf, srtA, and spaP) associated with bacterial adhesion and biofilm formation.},
}

@article {pmid42165232,
year = {2026},
author = {Nap, B and Thinnes, CC and Thiele, I},
title = {Whole-body metabolic modelling and its prospects in precision nutrition.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/S0029665126103061},
pmid = {42165232},
issn = {1475-2719},
abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.},
}

@article {pmid42165805,
year = {2026},
author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM},
title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001731},
pmid = {42165805},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; },
abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/physiology
*Colon/microbiology/virology
Escherichia coli/virology/genetics
Bacteria/genetics/virology/classification
Phage Therapy
Feces/microbiology

@article {pmid42165964,
year = {2026},
author = {Chen, S and Hua, Y and Chen, D and Jiang, X},
title = {Laboratory diagnosis of brucellosis: evolving synergy between serological testing and next-generation sequencing.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42165964},
issn = {1435-4373},
abstract = {BACKGROUND: Brucellosis is an animal‑to‑human infection that is hard to identify in practice; its signs are vague and the laboratory tools used in routine care have clear limits. Bacterial culture is regarded as the reference test; the procedure is slow and has modest sensitivity, and in many hospitals clinicians rely mainly on serologic assays when they make a diagnosis. Over the past decade clinical microbiology laboratories have increasingly used next‑generation sequencing (NGS) as a tool for pathogen identification, especially metagenomic NGS (mNGS). In patients with suspected bru-cellosis clinicians and laboratory staff often see a mismatch between test results, with serological assays suggesting infection but NGS reports failing to detect Brucella, a gap between serology and sequencing that remains a frequent and unresolved problem in routine diagnosis.

OBJECTIVE: This review brings together available data on how serological tests and sequencing-based methods in both metagenomic and targeted formats contribute to the laboratory diagnosis of human brucellosis and where they fall short.

CONCLUSION: It describes biological and technical sources of false-positive serology and false-negative sequencing and sets out a practical integrated way to judge and confirm mismatched findings so that laboratories and clinicians can use conventional and molecular tools together and reach sound decisions when brucellosis is suspected.},
}

@article {pmid42166146,
year = {2026},
author = {Besteman, MS and Alaux, E and Doloman, A and Tahon, G and Ettema, TJG and Sousa, DZ},
title = {Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular AD sludges.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag052},
pmid = {42166146},
issn = {1574-6941},
abstract = {Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate and acetate. This analysis identified multiple interesting novel targets, including Syntrophomonadia families DTU052 and CALXsZ01 as potential butyrate oxidizers; Syntrophia families UBA6807, PHBD01, FEN-1087, and FEN-1099 as potential propionate oxidizers; and, Thermacetogeniaceae genus DTU068 together with Chloroflexota family 4572-78 as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.},
}

@article {pmid42166340,
year = {2026},
author = {Sato, M and Kanaly, RA and Mori, JF},
title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001712},
pmid = {42166340},
issn = {1465-2080},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth & development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth & development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; },
abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Sphingomonadaceae/genetics/metabolism/growth & development
Biodegradation, Environmental
Genome, Bacterial
*Transcriptome
*Achromobacter/genetics/metabolism/growth & development
Soil Microbiology
*Achromobacter denitrificans/genetics/metabolism
Phylogeny
Genomics
Soil Pollutants/metabolism
Gene Expression Profiling
Microbial Consortia

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

@article {pmid42166998,
year = {2026},
author = {Wu, Q and Zheng, Y and Xia, Y and Ge, C and Deng, H and Zhao, Y and Luo, J and Feng, D},
title = {Decoding the seagrass plastisphere: Metagenomic insights into biogeochemical cycling of biogenic elements and ecological consequences.},
journal = {Environment international},
volume = {212},
number = {},
pages = {110311},
doi = {10.1016/j.envint.2026.110311},
pmid = {42166998},
issn = {1873-6750},
abstract = {Seagrass meadow, a crucial blue carbon ecosystem, is increasingly threatened by plastic pollution. Plastic debris in this sensitive ecosystem creates a new microbial habitat known as "plastisphere". However, the functional role of plastisphere, particularly in driving the cycling of key biogenic elements, remains poorly understood. This knowledge gap raises concerns over potential disruptions to elemental fluxes and subsequent ecological consequences. Here, metagenomic analysis was employed to investigate the metabolic profile of in-situ plastisphere in seagrass meadow, with particular focus on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) biotransformation. The obtained results revealed that plastisphere microbes were taxonomically distinct from those in natural environments of the seagrass meadow, and these inhabitants were capable of driving diverse metabolic pathways. However, >75% functional gene similarity indicated a significant functional overlap between the plastisphere and natural environments. This niche enriched genes related to heterotrophic organic C degradation (27.71% ± 3.28%) and oxidation (17.86% ± 2.04%) pathways, organic N metabolism (62.18% ± 8.57%) mainly through GS-GOGAT pathways and denitrification (8.70% ± 4.06%), polyphosphate degradation (22.89% ± 2.20%) and organic P mineralization (17.50% ± 1.70%), as well as assimilatory/dissimilatory sulfate reduction (30.60% ± 3.49%) and thiosulfate disproportionation (13.57% ± 2.89%) metabolic pathways. Metabolic linkage within seagrass plastisphere was facilitated by highly connected taxa including Silicimonas and Erythrobacter, which linked electron-donating processes (including organic C degradation and S oxidation) to electron-accepting pathways (e.g., sulfate/nitrate reduction, C fixation). These interactions established the plastisphere as a potential biogeochemical hotspot, potentially amplifying the risks of CO2/N2O emission, H2S accumulation, nutrient competition with seagrass and potential eutrophication from imbalanced P mobilization, ultimately threatening the health and stability of seagrass ecosystem.},
}

@article {pmid42167281,
year = {2026},
author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC},
title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70327},
doi = {10.1111/1462-2920.70327},
pmid = {42167281},
issn = {1462-2920},
support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; },
mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; },
abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.},
}

*Wetlands
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Greenhouse Gases/analysis/metabolism
Congo
RNA, Ribosomal, 16S/genetics
*Plankton/genetics/classification
Ecosystem
Methane/metabolism
Phylogeny
Carbon Cycle
Biodiversity
Metagenome

@article {pmid41975257,
year = {2026},
author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z},
title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41975257},
issn = {1471-2105},
abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks.

RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis.

CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-026-06444-w.},
}

@article {pmid42156652,
year = {2026},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Computational Microbial and Viral Ecology Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {83-141},
pmid = {42156652},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.},
}

*Metagenomics/methods
*Computational Biology/methods
Metagenome
*Microbiota/genetics
*Viruses/genetics/classification
Virome
Bacteriophages/genetics
Bacteria/genetics
Archaea/genetics

@article {pmid42156658,
year = {2026},
author = {Roma Pi, J and Heinken, A},
title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {233-260},
pmid = {42156658},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; },
abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.},
}

*Metagenomics/methods
Humans
*Gastrointestinal Microbiome/genetics
Precision Medicine/methods
Software
*Microbiota/genetics
*Metagenome
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
RNA, Ribosomal, 16S/genetics
Systems Biology/methods

@article {pmid42156769,
year = {2026},
author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M},
title = {Functional restructuring of the global soil microbiome under multiple stressors.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73231-9},
pmid = {42156769},
issn = {2041-1723},
support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.},
}

@article {pmid42156772,
year = {2026},
author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and , and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E},
title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73193-y},
pmid = {42156772},
issn = {2041-1723},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.},
}

@article {pmid42157110,
year = {2026},
author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F},
title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08962-4},
pmid = {42157110},
issn = {1471-2229},
support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; },
abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.

RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.

CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype × microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.},
}

@article {pmid42157119,
year = {2026},
author = {Li, QX and Luo, LZ},
title = {Cutaneous MAC infection in an immunocompetent patient: a case report confirmed by mNGS.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13549-3},
pmid = {42157119},
issn = {1471-2334},
abstract = {BACKGROUND: Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are rare. Atypical clinical manifestations and the need for precise microbiological identification often result in misdiagnosis and underdiagnosis.

CASE PRESENTATION: A 65-year-old immunocompetent female initially presented with papular urticaria. Her symptoms improved transiently after anti-inflammatory treatment, but the lesions rapidly progressed to generalized erythematous nodules and ulcers accompanied by fever and lymphadenopathy. Routine microbiological culture and histopathological examination yielded negative results, while metagenomic next-generation sequencing (mNGS) identified Mycobacterium avium complex (MAC) as the causative pathogen.Triple antimicrobial therapy (clarithromycin, doxycycline, and levofloxacin) a favorable clinical response. This case indicates that cutaneous non-tuberculous mycobacterial (NTM) infection has atypical clinical manifestations and is frequently misdiagnosed as common cutaneous eruptions. mNGS can serve as a key diagnostic tool for suspected cutaneous NTM infection, effectively reducing misdiagnosis and missed diagnosis and providing a reliable basis for clinical diagnosis and treatment.

CONCLUSION: Cutaneous MAC infection, though rare, may occur in immunocompetent individuals. Clinicians should suspect NTM infection in treatment-refractory skin lesions. mNGS is valuable for etiological diagnosis when conventional tests are negative.},
}

@article {pmid42157131,
year = {2026},
author = {Ji, T and Cheng, R and Lu, M},
title = {mNGS and IL-5: potential early diagnostic clues for clonorchiasis before eosinophil rise - a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13612-z},
pmid = {42157131},
issn = {1471-2334},
support = {2022YFC2303203-01//National Key R&D Program of China/ ; Z-2017-24-2202//Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; },
abstract = {Clonorchiasis, caused by Clonorchis sinensis, often evades early diagnosis in non-endemic regions due to its nonspecific presentation and the delayed appearance of eosinophilia. We report an informative case of a 56-year-old male with acute fever, abdominal pain, and hepatitis, where conventional diagnostics and initial antimicrobial therapy failed. In this case, metagenomic next-generation sequencing (mNGS) of blood identified C. sinensis-specific reads, and cytokine profiling revealed a marked elevation in interleukin-5 (IL-5) before the onset of peripheral eosinophilia. Targeted treatment with praziquantel led to rapid clinical resolution. This case suggests the potential of integrating mNGS and IL-5 monitoring as early diagnostic tools for clonorchiasis, which can allow for intervention prior to classical biomarker emergence.},
}

@article {pmid42157143,
year = {2026},
author = {Sheng, G and Zhao, C and Jiang, L and Zhang, X and Gao, F},
title = {Talaromyces marneffei infection of central nervous system in an immunocompetent child in a nonendemic area: a case report and literature review.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-06996-z},
pmid = {42157143},
issn = {1471-2431},
abstract = {BACKGROUND TALAROMYCES MARNEFFEI: (T. marneffei, formerly Penicillium marneffei) is a rare fatal fungus endemic in Southeast Asia and southern China. T. marneffei infections mainly occur in HIV-infected adults, and commonly involves the skin, lung, and reticuloendothelial system. T. marneffei infections of isolated central nervous system (CNS) in immunocompetent pediatric patients in nonendemic areas have rarely been reported. CASE PRESENTATION: We report a rare case of T. marneffei-induced disseminated encephalomyelitis in an immunocompetent girl from a nonendemic area of Eastern China. The main clinical manifestations were abdominal pain with distension and abnormal gait. Contrast-enhanced magnetic resonance imaging (MRI) revealed both brain and spinal cord lesions. The infection status of T. marneffei was quickly determined via the metagenomic next-generation sequencing (mNGS) of spinal cord biopsy tissue. T. marneffei induced disseminated encephalomyelitis was diagnosed. Following successful antifungal treatment with amphotericin B liposomes and voriconazole, the child recovered gradually. To date, only 3 cases of T. marneffei infection of the central nervous system in non-HIV-infected pediatric patients have been reported in the literature. Among them, one child had inborn errors of immunity, and the other two children were from endemic areas. Moreover, the clinical manifestations of those 3 reported cases were disseminated with common infection sites in the lungs. our patient represents a unique case of an immunocompetent child from a nonendemic area with isolated CNS infection. CONCLUSIONS: We report this rare case and aim to promote pediatric clinicians' recognition of T. marneffei isolated CNS infection in immunocompetent pediatric patients from nonendemic regions. Furthermore, the early use of mNGS is recommended when non-HIV-infected pediatric patients present with unexplained clinical manifestations and poor response to conventional treatments. Timely diagnosis and appropriate antifungal therapy can improve patient prognosis.},
}

@article {pmid42157342,
year = {2026},
author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H},
title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42157342},
issn = {1674-9782},
support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; },
abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.

RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.

CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.},
}

@article {pmid42157352,
year = {2026},
author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H},
title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42157352},
issn = {1297-9716},
support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; },
abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.},
}

Animals
Swine
*Brachyspira hyodysenteriae/physiology
*Swine Diseases/microbiology/metabolism
*Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism
*Metabolome
Colon/metabolism/microbiology
Gastrointestinal Microbiome
*Dysentery/veterinary/microbiology/metabolism
Feces/microbiology
Metabolomics

@article {pmid42157462,
year = {2026},
author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR},
title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70320},
doi = {10.1111/1462-2920.70320},
pmid = {42157462},
issn = {1462-2920},
support = {R01GM085770/NH/NIH HHS/United States ; },
mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; },
abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.},
}

*Geologic Sediments/microbiology
*Polyketides/metabolism
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
Polyketide Synthases/genetics/metabolism
Metagenome
Seawater/microbiology
Biodiversity
Multiomics

@article {pmid42158361,
year = {2026},
author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S},
title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2673265},
pmid = {42158361},
issn = {2993-3935},
abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.},
}

@article {pmid42158572,
year = {2026},
author = {Wong, E and England, J and Jagadeesan, V},
title = {Scedosporium apiospermum Infective Endocarditis With Brain Abscesses in a Lung Transplant Recipient: Review of the Literature and Evaluating the Use of Next-Generation Sequencing.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {8041837},
pmid = {42158572},
issn = {2090-6625},
abstract = {Scedosporium apiospermum is an emerging cause of invasive mold infection in immunocompromised hosts, often with central nervous system involvement and limited susceptibility to amphotericin B. We describe a 36-year-old lung transplant recipient who presented with fever, meningismus, and multiple enhancing brain lesions nine months post-transplant. Cerebrospinal fluid studies, including metagenomic next-generation sequencing (mNGS), were negative. Cardiac imaging revealed a pedunculated right ventricular septal mass, and plasma cell-free DNA (cfDNA) testing (Karius) identified S. apiospermum. Subsequent brain biopsy and thrombectomy confirmed the diagnosis by histopathology and culture. Following surgical removal of the cardiac mass and treatment with voriconazole, the patient improved with near resolution of brain lesions. This case highlights disseminated S. apiospermum endocarditis diagnosed by plasma cfDNA despite negative CSF mNGS, underscoring that site-specific mNGS may be falsely negative in compartmentalized infections. Plasma cfDNA testing can complement conventional and tissue-based diagnostics for early detection of disseminated mold infections in transplant recipients.},
}

@article {pmid42158968,
year = {2026},
author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W},
title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.},
journal = {Cancer medicine},
volume = {15},
number = {5},
pages = {e71946},
doi = {10.1002/cam4.71946},
pmid = {42158968},
issn = {2045-7634},
support = {82200151//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; },
abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.

METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).

RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.

CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Myelodysplastic Syndromes/drug therapy/immunology/microbiology
Male
Female
Aged
Middle Aged
*Dysbiosis/immunology
Case-Control Studies
DNA Methylation/drug effects
Feces/microbiology
Aged, 80 and over
High-Throughput Nucleotide Sequencing
Metabolic Networks and Pathways
Adult

@article {pmid42159114,
year = {2026},
author = {Li, Y and Liu, J and Hu, W and Li, C and Zhang, L and Qiu, S and Zhu, S},
title = {The Value of Second-Generation Metagenomic Sequencing in the Diagnosis of Respiratory Infections.},
journal = {Clinical laboratory},
volume = {72},
number = {5},
pages = {},
doi = {10.7754/Clin.Lab.2025.250525},
pmid = {42159114},
issn = {1433-6510},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Bacteria/genetics/isolation & purification ; Young Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: This study aimed to compare the results of metagenomic next-generation sequencing (mNGS) and conventional culture detection of pathogenic bacteria in bronchoalveolar lavage fluid (BALF) of patients with respiratory tract infections and analyze the influencing factors and clinical significance of mNGS positive detection.

METHODS: We retrospectively analyzed BALF samples from 90 respiratory infection patients at the First People's Hospital of Yongkang City from June 1, 2024, through January 28, 2025, using mNGS and conventional culture testing to compare the positivity rate, pathogen distribution, and consistency of the two methods. The relationship between mNGS detection positivity and clinical indicators of patients and patient prognosis was analyzed.

RESULTS: The positive rate of mNGS detection was 77.78%, while the positive rate of conventional culture detection was 44.44%, and the difference was statistically significant (p < 0.05). mNGS can detect a wider variety of pathogens, mainly gram-negative bacilli, fungi, and atypical pathogens. mNGS has moderate consistency with conventional culture detection results in bacteria, fungi, and atypical pathogens, but low consistency in viruses and para-sites. The positive detection of mNGS is related to factors such as patient age, underlying diseases, peripheral blood white blood cells, and C-reactive protein, which are risk factors affecting the positive detection of mNGS.

CONCLUSIONS: The pathogenic diagnosis of mNGS in BALF of patients with lower respiratory tract infections is su-perior to conventional culture detection; it can detect more and a wider range of pathogens, helping to promote rational drug use and improve patient prognosis in clinical practice.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
Male
Female
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Retrospective Studies
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Aged
Adult
*Bacteria/genetics/isolation & purification
Young Adult
Aged, 80 and over

@article {pmid41804595,
year = {2026},
author = {Long, C and Gui, J and Wang, F and Wang, C and Zhang, L},
title = {Evaluation of the clinical application of MALDI-TOF MS for identification of difficult-to-classify nontuberculous mycobacterial strains isolated in the laboratory.},
journal = {Acta clinica Belgica},
volume = {81},
number = {3},
pages = {293-302},
doi = {10.1080/17843286.2026.2643452},
pmid = {41804595},
issn = {2295-3337},
mesh = {*Nontuberculous Mycobacteria/classification/genetics/isolation & purification ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Reference Standards ; Reagent Kits, Diagnostic/standards ; Molecular Typing/methods/standards ; Sequence Analysis, DNA/standards ; Nanopore Sequencing/methods/standards ; DNA, Bacterial/isolation & purification ; Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods/standards ; China ; Humans ; },
abstract = {OBJECTIVES: This study aims to evaluate the clinical application value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the verification and identification of difficult-to-classify nontuberculous mycobacterial (NTM) strains.

METHODS: From December 2024 to June 2025, 106 suspected NTM isolates were collected from 10 districts in Shenzhen, China. Initial identification was performed using HRM and REBA commercial kits, with targeted nanopore sequencing and mNGS as the composite reference standard. MALDI-TOF MS was used to verify strains unresolved by the kits, and its diagnostic performance was evaluated.

RESULTS: The HRM kit demonstrated concordance with the reference standard in 98 of 106 samples (concordance rate: 89.1%), whereas the REBA kit concorded in 88 samples (concordance rate: 80.0%). The REBA kit exhibited a tendency toward misidentification of NTM species as Mycobacterium tuberculosis. When the reference results were used as a baseline with tNanopore providing parallel validation (achieving ≥95% concordance with reference results), MALDI-TOF MS demonstrated poor performance in identifying difficult-to-classify NTM strains. Specifically, MALDI-TOF MS showed poor concordance in detecting M. abscessus (Kappa = 0.244), while Mycobacterium intracellulare, Mycobacterium kansasii, and Mycobacterium gordonae demonstrated kappa values of 0.543, 0.477, and 0.483, respectively, indicating low concordance overall. Furthermore, 13 species exceeded the detection range of MALDI-TOF MS, resulting in false-positive identifications or detection failures, with Mycobacterium abscessus exhibiting the highest rate of misidentification.

CONCLUSION: The limitations of MALDI-TOF MS in verifying difficult-to-classify NTM strains have been demonstrated. The findings emphasize that PCR-based molecular detection combined with gene sequence analysis remains the most reliable methodological approach for accurately identifying challenging NTM species in clinical practice.},
}

*Nontuberculous Mycobacteria/classification/genetics/isolation & purification
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
*Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Reference Standards
Reagent Kits, Diagnostic/standards
Molecular Typing/methods/standards
Sequence Analysis, DNA/standards
Nanopore Sequencing/methods/standards
DNA, Bacterial/isolation & purification
Metagenomics/methods/standards
High-Throughput Nucleotide Sequencing/methods/standards
China
Humans

@article {pmid41942854,
year = {2026},
author = {Salengros, A and Dechamps, E and Meunier, L and George, IF},
title = {Uncovering the ecophysiological potential of Motilimonas through genomic profiling analysis.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41942854},
issn = {1471-2164},
abstract = {BACKGROUND: The Motilimonas genus was proposed in 2017 and presently include three recognized species isolated from various environments. This genus is still poorly characterized, and its ability to degrade chitin has recently been reported. A genomic profiling analysis was conducted on the seven Motilimonas genomes (family Psychromonadaceae) available in the NCBI database.

RESULTS: The phylogenetic study suggests that Motilimonas sp. E26, Motilimonas sp. 1_MG-2023 G1M02 and Motilimonas sp. Spo1_1 could form a new clade distinct from other already existing clades within the Motilimonas genus (i.e. M. cestriensis, M. pumila and M. eburnea). The genomic features of all Motilimonas genomes are consistent with a moderately copiotrophic lifestyle. For instance, they encode proteins involved in chemotaxis, motility, type IV pili biosynthesis, sugar phosphotransferase systems (PTS) and chitin degradation. Additional shared traits include aerobic respiration, a preference for sugars over organic acids as carbon sources, the use of a “compatible solute” strategy to tolerate osmotic stress in saline environments, and, except for M. cestriensis MKS20[T], the ability to perform nitrate reduction. Furthermore, all Motilimonas genomes encode a diversity of secretion systems. For example, each genome contains one or several complete type I secretion systems (T1SS), one complete T2SS, and four genomes (Motilimonas sp. Spo1_1, M. sp. E26, M. sp. 1_MG-2023 G1M02 and Motilimonas sp. KMU-193) harbor a complete type VI secretion system (T6SS). Notably, only M. pumila PLHSC7-2[T] possesses genes encoding a complete type III secretion system (T3SS).

CONCLUSIONS: These findings provide new insights into the ecological versatility and adaptive strategies of the Motilimonas genus. The next step will involve genome-resolved analyses of metagenomic datasets with the objective to investigate the functional ecology of Motilimonas in a broader range of environments contributing to the better understanding of their ecological distribution.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12781-0.},
}

@article {pmid42059572,
year = {2026},
author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L},
title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.},
journal = {mSystems},
volume = {11},
number = {5},
pages = {e0080025},
doi = {10.1128/msystems.00800-25},
pmid = {42059572},
issn = {2379-5077},
support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; },
mesh = {*Deep Learning ; *Microbiota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Ecosystem ; },
abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.},
}

*Deep Learning
*Microbiota/genetics
*Metagenomics/methods
*Computational Biology/methods
Ecosystem

@article {pmid42151282,
year = {2026},
author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G},
title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49725-3},
pmid = {42151282},
issn = {2045-2322},
support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Università e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Università e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; },
abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.},
}

@article {pmid42151303,
year = {2026},
author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E},
title = {The soil microbiome of the Caatinga drylands in Brazil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50433-1},
pmid = {42151303},
issn = {2045-2322},
support = {20-122//Conrad Prebys Foundation/ ; },
abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.},
}

@article {pmid42151510,
year = {2026},
author = {de Souza Pereira, LF and Tavares, TCS and Martins, DT and Dias Dantas, CW and de Souza, FOR and Prazeres, MCC and Faturi, C and Rogez, HLG and Ramos, RTJ and Cardenas Alegria, OV and Ribeiro Carneiro Nunes, A},
title = {Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42151510},
issn = {1618-1905},
abstract = {The Amazon rainforest represents nearly 40% of the world's tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils-particularly those under fertilization-showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.},
}

@article {pmid42151682,
year = {2026},
author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS},
title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3000},
number = {},
pages = {251-275},
pmid = {42151682},
issn = {1940-6029},
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; },
abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology
*Space Flight
*Microbiota
Weightlessness
*Host Microbial Interactions

@article {pmid42152463,
year = {2026},
author = {Forshee, MD and Nachman, EJ and Shenoy, ER and Danhof, HA and Ermann Lundberg, L and Roos, S and Britton, RA},
title = {Limosilactobacillus reuteri promotes melatonin release from human intestinal organoids via 5'ectonucleotidase activity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2670854},
doi = {10.1080/19490976.2026.2670854},
pmid = {42152463},
issn = {1949-0984},
mesh = {*Melatonin/metabolism ; *Limosilactobacillus reuteri/metabolism/growth & development/enzymology ; Humans ; *Organoids/metabolism/microbiology ; *Intestines/microbiology ; Probiotics ; Adenosine/metabolism ; },
abstract = {Strains of Limosilactobacillus reuteri have been used to prevent or treat various conditions; however, the mechanisms by which they exert beneficial effects are not completely understood. Infant colic is one example in which L. reuteri DSM 17938 reduces clinical symptoms. While the etiology of colic is unknown, abnormal melatonin levels in infants have been suggested as a possible contributor. L. reuteri DSM 17938 has been shown to produce adenosine from AMP via production of the extracellular enzyme 5'ectonucleotidase (5'NT). Adenosine is a potent signaling molecule that impacts several important aspects of host physiology, including the release of melatonin from the pineal gland in the brain. A second major source of melatonin production is enteroendocrine cells in the intestine. We hypothesized that the adenosine generated via the 5'NT activity of L. reuteri DSM 17938, would stimulate melatonin release from human intestinal organoids. Here, we characterized the growth conditions that impact L. reuteri DSM 17938 5'NT activity, including carbon source utilization and required metal cofactors. We found zinc to be an essential cofactor for 5'NT activity by L. reuteri and observed carbon utilization altered 5'NT activity levels. Stachyose and raffinose increased levels of 5'NT activity while sucrose decreased 5'NT activity. We demonstrated that L. reuteri DSM 17938 stimulates melatonin release from pediatric human intestinal organoids in a 5'NT-dependent manner. Surprisingly, adenosine was necessary, but not sufficient, for the induction of epithelial melatonin release, thereby suggesting that an additional secreted factor was also required. Furthermore, L. reuteri BG-R46[®], an evolved strain of DSM 17938 that is known to express higher 5'NT activity, was shown to induce higher levels of melatonin secretion. Taken together, this work identifies zinc and carbon sources as key factors altering L. reuteri 5'NT activity levels and demonstrates that the L. reuteri strains stimulate intestinal melatonin release via 5'NT.},
}

*Melatonin/metabolism
*Limosilactobacillus reuteri/metabolism/growth & development/enzymology
Humans
*Organoids/metabolism/microbiology
*Intestines/microbiology
Probiotics
Adenosine/metabolism

@article {pmid42152762,
year = {2026},
author = {Yang, W and Guo, J},
title = {Unveiling the Hidden Resistome: A Comprehensive Risk Assessment of Latent Antibiotic Resistance Genes in China's Wastewater.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70330},
doi = {10.1111/1462-2920.70330},
pmid = {42152762},
issn = {1462-2920},
support = {2021YFD1600400//National Key Research and Development Program of China/ ; },
mesh = {*Wastewater/microbiology ; China ; Risk Assessment ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Metagenome ; Genes, Bacterial ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; },
abstract = {Wastewater systems are important reservoirs of antibiotic resistance genes (ARGs), but the ecological and health risks of numerous latent ARGs (LARGs) remain unclear. In this study, we analysed 636 wastewater metagenomic samples from China and constructed a database containing 1587 LARGs. Across all environments, LARGs encoding serine-β-lactamases were the most abundant and prevalent. A comprehensive risk assessment, integrating host pathogenicity, gene mobility and environmental prevalence, was performed on 561 LARGs identified in metagenome-assembled genomes. Most LARGs exhibited low levels across all three dimensions, suggesting limited transmission risk. Nevertheless, 37 high-risk LARGs were identified, indicating non-negligible threats. Functional validation showed that the top three extremely high-risk LARGs significantly enhanced host resistance to ampicillin and ciprofloxacin when expressed in Escherichia coli, while AlphaFold3 revealed typical resistance protein folding, further supporting their functional activity. Horizontal gene transfer analysis indicated that these high-risk genes have disseminated from wastewater to natural water bodies such as rivers via plasmid-mediated mechanisms. Collectively, wastewater acts not only as an 'accumulation pool' for LARGs but also as a potential source releasing 'super-risky' resistance gene into the environment. Therefore, urgent efforts are needed to monitor and control these high-risk LARGs and their mobile genetic elements to block their environmental spread.},
}

*Wastewater/microbiology
China
Risk Assessment
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
Metagenome
Genes, Bacterial
Escherichia coli/genetics/drug effects
*Drug Resistance, Microbial/genetics

@article {pmid42152807,
year = {2026},
author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A},
title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.70266},
pmid = {42152807},
issn = {1471-0528},
support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.

DESIGN: Prospective cohort study integrated with mechanistic experiments.

SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).

POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.

METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.

MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.

RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.

CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.},
}

@article {pmid42152996,
year = {2026},
author = {Chauhan, G and Bisht, N and Gautam, P and Arya, M and Kumari, A and Verma, D and Sharma, M},
title = {Cloning and Heterologous Expression of a Novel Thermo-Alkalistable GH-10 Xylanase (rXyn-GM) Retrieved from Tapovan Hot-Spring Soil Metagenome and its Characterization for Kinetic Parameters.},
journal = {Indian journal of microbiology},
volume = {66},
number = {2},
pages = {417-430},
pmid = {42152996},
issn = {0046-8991},
abstract = {UNLABELLED: A cellulase-free xylanase gene of 927 bp size (Xyn-GM) was isolated from the metagenomic library of the Tapovan Hot Spring in Uttarakhand, India. This gene encodes a 308-amino acid xylanase enzyme classified under the glycoside hydrolase family 10 (GH-10). The Xyn-GM gene was introduced into the pET28a (+) vector and expressed in host cells of Escherichia coli BL21 (DE3). The recombinant xylanase (rXyn-GM), with a molecular weight ~ 32.5 kDa, was isolated through a one-step purification process using Ni[2][+]-NTA affinity chromatography. The purified enzyme exhibited broad thermostability (50-100 °C) and pH stability (4.0-11.0), with optimal activity at 70 °C and pH 9.0. Its activity increased by 67% in the presence of 1 mM Mn[2][+]. rXyn-GM retained ~ 65% activity after 2 h at 50 °C and 60 °C and ~ 75% activity at pH 9.0 after 3 h. It showed a preference for beechwood xylan, with kinetic parameters Km 20.9 mg/mL and Vmax 156.25 µmol/mg/min. Furthermore, rXyn-GM catalysed the production of xylo-oligosaccharides from beechwood xylan, suggesting its potential utility as prebiotics in the food and pharmaceutical industries.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01480-1.},
}

@article {pmid42153006,
year = {2026},
author = {Yadav, S and Shipra, },
title = {Impact of Climate Change on Zoonotic Diseases and Antimicrobial Resistance.},
journal = {Indian journal of microbiology},
volume = {66},
number = {2},
pages = {280-291},
pmid = {42153006},
issn = {0046-8991},
abstract = {UNLABELLED: Climate change along with infectious disease and antimicrobial resistance are imposing threat to public health globally. Climate change mediates frequent rise in antimicrobial resistance leading to the emergence of zoonotic vectors. Both climate change and AMR contribute significantly to global morbidity and mortality and impose burden on the healthcare sector. Overexploitation of antimicrobials in various sectors causes broader dissemination of AMR. Therefore, the application of a holistic "One Health Approach" is required to combat both climate change and antimicrobial resistance. Increasing public awareness about the negative consequences of climate change and antimicrobial resistance is essential. Also, the discovery of new antimicrobials has become the need of the present world. The application of metagenomics has the potential to shed light on microbial community dynamics (taxonomic abundance and predominant biochemical pathways) in response to climate change. The application of modern tools like functional metagenomics has the potential to yield new antimicrobial compounds for combating AMR.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01430-3.},
}

@article {pmid42153318,
year = {2026},
author = {Chasapi, MN and Kontis, N and Lehmann, R and Tasneem, R and Patel, NS and Khan, SA and Martínez de Morentin, X and Chasapi, IN and Aplakidou, E and Galaras, A and Aldakheel, L and Su, M and Baltoumas, FA and Venkateswaran, K and Lagani, V and Gómez-Cabrero, D and Tegnér, J and Pavlopoulos, GA and Soares Rosado, A},
title = {Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag236},
pmid = {42153318},
issn = {1477-4054},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; //KAUST Visiting Student Research Program (VSRP)/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; 23592-EMISSION//Research Projects to Support Faculty Members and Researchers/ ; },
mesh = {*Computational Biology/methods ; Culture Techniques ; Environmental Microbiology ; *Extremophiles/genetics/isolation & purification/metabolism ; Machine Learning ; },
abstract = {Life thrives in Earth's most inhospitable environments, from boiling hydrothermal vents to hypersaline lakes and frozen polar deserts, thanks to the remarkable adaptations of extremophilic microorganisms. The study of these organisms has rapidly evolved from early cultivation-based discoveries to a data-rich discipline powered by advanced omics technologies. This review comprehensively outlines the current landscape and future directions in extremophile research, emphasizing the pivotal role of bioinformatics, machine learning (ML), and data-driven approaches. We begin by charting the evolution of methodologies, from innovative in situ cultivation techniques and robust biomolecule extraction protocols to modern multi-omics workflows (metagenomics, transcriptomics, proteomics, and metabolomics) that decode the genetic and functional basis of extremophiles. We then catalogue essential bioinformatics resources and specialized databases critical for annotating extremophile genomes and uncovering their unique adaptive strategies, including protein stabilization and syntrophic metabolic relationships. Finally, we explore the transformative potential of artificial intelligence (AI) and ML in overcoming fundamental challenges in the field. These include predicting the functions of uncharacterized "hypothetical" proteins, identifying novel extremozymes, modeling complex genotype-phenotype relationships, and guiding the targeted engineering of industrially relevant strains. By synthesizing insights across these domains, this review highlights how integrating computational biology and AI is poised to unlock the full biotechnological potential of extremophiles and redefine the boundaries of life itself.},
}

*Computational Biology/methods
Culture Techniques
Environmental Microbiology
*Extremophiles/genetics/isolation & purification/metabolism
Machine Learning

@article {pmid42153323,
year = {2026},
author = {Wang, J and Liu, Y and Liu, F and Hou, T and Chen, S and Liu, S and Liu, Y},
title = {DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag241},
pmid = {42153323},
issn = {1477-4054},
support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Science and Technology Development Plan Project of Jilin Province, China/ ; //Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Algorithms ; *Software ; Computational Biology/methods ; Autoencoder ; },
abstract = {DNA contigs binning is necessary to reconstruct metagenome-assembled genomes. Current metagenomic DNA contigs binning methods often leverage coverage profiles across multiple related metagenomes and have demonstrated strong performance on co-assembled contigs. However, in single-sample scenarios where coverage information is rare, their performance drops significantly, limiting the in-depth development of metagenomics at the individual sample level. To address this issue, we propose DCVBin, a novel single-sample metagenomic contigs binning method that incorporates semantic features extracted from a DNA language model. Specifically, our approach continues pretraining on a DNA language model to capture more domain-specific semantic representations, which are then integrated with 4-mer frequencies using a variational autoencoder. Clustering is subsequently performed using the k-means algorithm, in which the number of clusters is determined by single copy genes. Experimental results on six publicly available datasets demonstrate that DCVBin achieves high-accuracy single-sample metagenomic binning and outperforms other state-of-the-art methods. Furthermore, DCVBin is included into a disease diagnostic framework that is evaluated on a cohort of gut metagenomes from people with colorectal cancer and healthy people. The framework is shown to be accurate in predicting colorectal cancer using gut metagenomes and has identified a list of potential microbial biomarkers.},
}

*Metagenomics/methods
*Metagenome
Humans
Algorithms
*Software
Computational Biology/methods
Autoencoder

@article {pmid42153643,
year = {2026},
author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E},
title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048526},
doi = {10.1128/msystems.00485-26},
pmid = {42153643},
issn = {2379-5077},
abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.},
}

@article {pmid42153646,
year = {2026},
author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV},
title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013926},
doi = {10.1128/msphere.00139-26},
pmid = {42153646},
issn = {2379-5042},
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.},
}

@article {pmid42153961,
year = {2026},
author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17087},
doi = {10.1002/advs.202517087},
pmid = {42153961},
issn = {2198-3844},
support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.},
}

@article {pmid42154322,
year = {2026},
author = {Greaves, JC and Rodriguez, RA},
title = {Revealing the hidden burden: wastewater-based epidemiology for underreported and emerging infectious diseases in communities.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {6},
pages = {},
pmid = {42154322},
issn = {1573-2959},
mesh = {Humans ; *Wastewater/virology/microbiology ; *Communicable Diseases, Emerging/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; },
abstract = {Wastewater-based epidemiology (WBE) has become a transformative tool for infectious disease surveillance, providing population-level insights that complement and extend traditional case-based reporting. This review examines the expanding role of WBE in identifying and characterizing underreported, novel, and emerging human pathogens. Evidence reveals that wastewater analysis consistently detects enteric, respiratory, and neglected pathogens that are often missed by clinical systems, thereby revealing the hidden burden of infection within communities. Sequencing-based studies have identified numerous novel and divergent human viruses, highlighting the extensive diversity of the human virome. The frequent co-detection of multiple viral taxa also suggests that interactions and co-infections may influence viral evolution, disease manifestation, and transmission. Despite methodological challenges in quantification and biological validation, WBE has proven capable of detecting both known and novel pathogens before they are clinically recognized. Future developments in long-read sequencing, bioinformatics, and global data integration will enhance the precision and scope of wastewater genomics, positioning it as a central element of early-warning and One Health surveillance frameworks. By illuminating the unseen spectrum of infectious agents, WBE bridges environmental and clinical domains, offering a scalable and equitable strategy for global pathogen discovery and public health preparedness.},
}

Humans
*Wastewater/virology/microbiology
*Communicable Diseases, Emerging/epidemiology
*Wastewater-Based Epidemiological Monitoring

@article {pmid42154337,
year = {2026},
author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP},
title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42154337},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/metabolism/pathology/microbiology
*alpha-Synuclein/metabolism
Animals
Dysbiosis
*Protein Aggregates

@article {pmid42154370,
year = {2026},
author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG},
title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {42154370},
issn = {1865-8652},
abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.},
}

@article {pmid42154390,
year = {2026},
author = {Khan, I and Irfan, M and Bacha, AS and Khan, I and Ali, Y and Li, Z},
title = {Host-Microbiota Metabolic Interactions in Atherosclerosis: Oral, gut, and Blood Perspectives.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42154390},
issn = {1867-1314},
abstract = {Atherosclerosis is a chronic inflammatory disease influenced by host-microbiota interactions beyond traditional risk factors. Microbial communities in the oral cavity, gut, and blood contribute to vascular dysfunction through metabolic and immune mechanisms, yet an integrated perspective across these compartments remains lacking. This narrative review synthesizes current evidence on the distinct and interconnected roles of oral, gut, and blood microbiotas in atherosclerosis pathogenesis. We critically evaluate key microbial metabolites, trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids, and their mechanisms of host metabolic and immune modulation. We also examine cross-compartment interactions, emerging multi-omics approaches, and the translational potential of microbiota-targeted interventions. Oral pathogens promote systemic inflammation and endothelial activation. Gut-derived metabolites such as TMAO exacerbate foam cell formation and impair reverse cholesterol transport, whereas SCFAs exert protective effects via immune modulation and gut barrier maintenance. Emerging evidence suggests that blood microbial components contribute to vascular inflammation, though methodological challenges remain. Multi-omics integration (metagenomics, metabolomics, host genomics) reveals interconnected metabolic networks linking microbial activity to atherosclerosis. Microbiota-targeted strategies, including dietary modulation, TMA lyase inhibitors, and probiotics, show promise for risk stratification and therapeutic intervention. The human microbiota regulates atherosclerosis through immunometabolic metabolites, offering promising biomarkers and therapeutic targets. However, clinical translation requires addressing interindividual variability, establishing causality, and standardizing methodologies. This review provides an integrated framework for leveraging microbiota-host interactions in precision cardiovascular medicine.},
}

@article {pmid42154500,
year = {2026},
author = {Pouder, E and Alain, K and Mieszkin, S},
title = {Phylogenomic and metabolic insights into iron reduction metabolism in the genus Deferribacter belonging to the order Deferribacterales.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001712},
pmid = {42154500},
issn = {2057-5858},
mesh = {*Phylogeny ; *Iron/metabolism ; Oxidation-Reduction ; Hydrothermal Vents/microbiology ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; },
abstract = {Iron is one of the most important elements of the Earth, yet its bioavailability is limited in oceanic environments. In this context, deep-sea hydrothermal ecosystems represent one of the major sources of iron. While some microorganisms involved in its biogeochemical cycle, particularly in Fe(III)-reduction, have been isolated from these ecosystems, the molecular mechanisms underpinning metabolic pathways remain hypothetical and incomplete. Therefore, this study aims to investigate the global metabolism of bacteria within the Deferribacter genus, isolated from hydrothermal systems and a petroleum reservoir, with a specific focus on the Fe(III)-reduction metabolism to identify genes potentially involved in this pathway. This study revealed a conserved carbon metabolism across the four species, while their energetic metabolism exhibited notable differences. These species appear to be able to use different elements as electron sources, showing their ability to adapt to different ecological (micro)niches, particularly in deep-sea hydrothermal vents. The marker genes known for Fe(III)-reduction were identified, with a contrast between the strains isolated from hydrothermal systems and the one isolated from a petroleum reservoir. To further explore this pattern, the study was extended, including 14 genomes of representative strains and 36 metagenome-assembled genomes affiliated to the Deferribacterales order. Phylogenomic analysis revealed a distribution pattern within this order that correlates with environmental origin. Canonical marker genes of Fe(III)-reduction were also identified, with their distribution primarily aligned with specific ecological niches.},
}

*Phylogeny
*Iron/metabolism
Oxidation-Reduction
Hydrothermal Vents/microbiology
Genome, Bacterial
Metabolic Networks and Pathways/genetics

@article {pmid42154842,
year = {2026},
author = {Wang, D and Wang, N and Liu, J and Zhao, C and Xing, X},
title = {The diagnostic value of fine-needle aspiration cytology in the early diagnosis of pulmonary cryptococcosis.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {68},
number = {},
pages = {e33},
doi = {10.1590/S1678-9946202668033},
pmid = {42154842},
issn = {1678-9946},
mesh = {Humans ; *Cryptococcosis/pathology/diagnosis ; Biopsy, Fine-Needle/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Lung Diseases, Fungal/pathology/diagnosis ; Early Diagnosis ; Adult ; Aged ; Lung/pathology/microbiology ; },
abstract = {Pulmonary cryptococcosis, an invasive fungal infection caused by Cryptococcus spp., is often misdiagnosed as tuberculosis or lung cancer due to overlapping clinical and radiological features, leading to treatment delays. In this descriptive study, we aim to characterize the diagnostic findings and clinical utility of fine-needle aspiration cytology (FNAC) in a series of patients with pulmonary cryptococcosis, within the context of other available diagnostic modalities. We retrospectively analyzed 10 patients with pulmonary cryptococcosis who underwent imaging-guided percutaneous lung aspiration. Wright-Giemsa-stained cytology smears were examined under oil immersion, enabling clear visualization of the characteristic morphological features of Cryptococcus. In this case series, FNAC provided a rapid cytological diagnosis within two hours in all 10 cases, consistent with the results obtained by metagenomic next-generation sequencing (mNGS) and serological testing. In contrast, conventional smear microscopy showed lower detection rates, and histopathology required longer processing times. The use of FNAC facilitated early diagnosis, enabling timely initiation of antifungal therapy and helping to avoid unnecessary surgical interventions. Our findings suggest that cytomorphological evaluation by FNAC is a rapid and valuable diagnostic tool in the early clinical management of pulmonary cryptococcosis, effectively complementing existing diagnostic methods.},
}

Humans
*Cryptococcosis/pathology/diagnosis
Biopsy, Fine-Needle/methods
Retrospective Studies
Male
Female
Middle Aged
*Lung Diseases, Fungal/pathology/diagnosis
Early Diagnosis
Adult
Aged
Lung/pathology/microbiology

@article {pmid42154957,
year = {2026},
author = {Lorca, R and Bretagne, MC and Boizeau, L and Cappy, P and Allenbach, Y and Rodriguez, C and Salem, JE},
title = {Immune checkpoint inhibitor myocarditis: a metagenomic investigation of infectious pathogens.},
journal = {European heart journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/eurheartj/ehag371},
pmid = {42154957},
issn = {1522-9645},
}

@article {pmid42155010,
year = {2026},
author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN},
title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag249},
pmid = {42155010},
issn = {1535-4970},
abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of IPF. However, the role of gut microbiota in IPF pathogenesis is unknown.

OBJECTIVES: Determine associations between gut microbiota, disease severity and lung transplant-free survival in IPF.

METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n = 411). CleanUP-IPF investigated the clinical efficacy of long-term anti-microbials in IPF. 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models and Cox regression models.

MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted (pp) DLCO). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (HR 0.34 95% CI 0.14-0.87, P = .02) in patients not assigned to anti-microbial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long term co-trimoxazole had worse survival (HR 6.09 95% CI 1.36-27.27, P = .02). Survival in pirfenidone treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.

CONCLUSIONS: In exploratory post-hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.},
}

@article {pmid42155550,
year = {2026},
author = {Pandit, S and Hazra, S and Dinda, SK and Bhattacharjee, B and Basu, A and Pradhan, B and Kumar, K and Manna, D},
title = {Advances in the detection of deadly free-living amoebae (FLA).},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {2},
pages = {117465},
doi = {10.1016/j.diagmicrobio.2026.117465},
pmid = {42155550},
issn = {1879-0070},
abstract = {Free-living amoebae (FLA), including Naegleria fowleri, Acanthamoeba castellanii, Balamuthia mandrillaris, and Sappinia pedata, are ubiquitous protozoa capable of causing severe infections such as primary amoebic meningoencephalitis (PAM), granulomatous amoebic encephalitis (GAE), and Acanthamoeba keratitis (AK). Early diagnosis remains challenging due to disease rarity, nonspecific clinical presentation, and limited access to specialized laboratory methods. Rapid and accurate detection is critical for patient management and public health response, particularly amid changing environmental exposures. This review summarizes current diagnostic approaches in clinical and environmental contexts, including specimen handling, microscopy, culture, immunohistochemistry, antigen detection, and molecular methods such as conventional PCR, real-time PCR, multiplex qPCR, LAMP, and metagenomic next-generation sequencing. Environmental surveillance, biomarker discovery, quality assurance, and standardized protocols are also discussed. By evaluating strengths and limitations of available tools, this review highlights diagnostic gaps and future priorities to enhance sensitivity, turnaround time, and global accessibility.},
}

@article {pmid42155712,
year = {2026},
author = {Geng, R and Huang, B and Duan, Z and Zhao, F and Lü, X and Jiang, Z and Yi, Y},
title = {Antimicrobial Efficacy and Food Application Potential of Bacteriocins LL3 and LL4 from Traditional Dairy-Derived Lactococcus lactis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28309},
pmid = {42155712},
issn = {1525-3198},
abstract = {To combat foodborne pathogens like Salmonella, this study employed an activity-based screening followed by metagenomic mining of the active isolates to discover and characterize bacteriocins from Inner Mongolian dairy products. From the 15 active isolates, Lactococcus lactis D63 and D64 were identified as harboring a putative biosynthetic gene cluster (BGC) encoding 2 bacteriocins, LL3 and LL4. Both peptides form amphipathic α-helical structures that disrupt bacterial membranes, leading to intracellular leakage and cell death. They exhibited effective antimicrobial activity, particularly against Salmonella Typhimurium. Crucially, when applied in a simulated milk model under standard refrigeration (4°C), synthesized LL4 demonstrated robust preservative efficacy by effectively controlling S. Typhimurium, showing comparable performance to the commercial preservative Nisin. Genetic analysis revealed that this BGC exhibits low basal transcription under standard laboratory growth conditions and shares high homology with plasmid elements, suggesting it is a mobile genetic element acquired via horizontal gene transfer. This study presents LL3 and LL4 as promising natural preservatives and validates metagenomic mining as an efficient strategy for uncovering antimicrobial genes.},
}

@article {pmid42155775,
year = {2026},
author = {Yao, X and Zhu, Y and Gao, P and Liu, T and Zhang, X and Liu, W and Li, J and Li, D and Zhang, Y and Zhang, Z},
title = {Limitations of endogenous denitrification in low carbon-to-nitrogen wastewater treatment: Insights into carbon allocation imbalance and metabolic adaptation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134915},
doi = {10.1016/j.biortech.2026.134915},
pmid = {42155775},
issn = {1873-2976},
abstract = {Endogenous denitrification (EnD) has been identified as a promising strategy for enhancing nitrogen removal from wastewater with a low carbon-to-nitrogen (C/N) ratio. However, the mechanisms limiting its effectiveness under carbon-starved conditions remain insufficiently understood. This 160-day study compared denitrification performance, carbon allocation, and metabolic responses in two sets of anaerobic/aerobic/anoxic-sequential batch reactors (A/O/A-SBR) under low (3-5) and high (10-15) C/N ratios. Under low C/N, total nitrogen (TN) removal decreased to 69.90 ± 13.31%, with effluent NO3[-]-N accounting for 87.43 ± 14.40% of TN. Concurrently, microbial activity was inhibited. Compared with high C/N ratio, microorganisms under low C/N preferentially allocated limited carbon to extracellular protein (PN) rather than to intracellular polyhydroxyalkanoates or glycogen. PN constitutes 47.39 ± 2.38% of the total internal carbon sources in unit sludge and functions primarily to maintain cellular structural stability. This carbon allocation pattern imposes limitations on the supply of carbon sources available for the EnD process. In addition, despite the enrichment of EnD functional bacteria (15.22 ± 2.03%), functional genes were primarily directed toward survival-related pathways (xenobiotics biodegradation and metabolism and amino acid synthesis). Constraints on energy metabolism further limited carbon utilization and denitrification. Concurrently, while the dispersion of denitrification-related genes under low C/N maintained system stability across multiple bacterial genera, it concomitantly reduced denitrification efficiency. This metabolic shift further limited EnD. This study provides novel insights into constraints on EnD from the perspectives of carbon source allocation and microbial metabolic adaptation, thereby establishing a theoretical foundation for the treatment of low C/N wastewater.},
}

@article {pmid42155781,
year = {2026},
author = {Wang, J and Liu, S and Wang, Z and Guo, Y and Liu, J and Shi, L},
title = {Coupling heterotrophic and hydrogenotrophic partial denitrification via gel-based bio-carriers: microbial mechanisms and metabolic modeling.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134914},
doi = {10.1016/j.biortech.2026.134914},
pmid = {42155781},
issn = {1873-2976},
abstract = {Partial denitrification (PD) has emerged as a pivotal technology for addressing the limited nitrite (NO2[-]) supply that hinders the widespread application of anammox, as it efficiently provides NO2[-]. However, its reliance on organic carbon sources restricts its broad implementation. In this study, a system of heterotrophic coupled with hydrogen-autotrophic PD was established using polyvinyl alcohol gel bio-carriers. Operated under a low COD/NO3[-]-N ratio of 2.00 for 90 days, the system achieved remarkable performances, with a NO2[-] transformation ratio (NTR) of 85.50 ± 3.10% and a nitrate (NO3[-]) removal rate (NRR) of 84.70 ± 5.00%. Metagenomic analysis revealed the effective enrichment ofHydrogenophaga(23.90%) as a key hydrogen-autotrophic denitrifier, which formed a functionally complementary consortium with heterotrophic denitrifiers (e.g.,Dokdonella). The abundance ratio of NO2[-] reduction genes in autotrophic to heterotrophic bacteria was 1.3:1. Furthermore, a putative metabolic model was constructed, which posits a potential cross-feeding interaction characterized by "hydrogen production by heterotrophs and consumption by autotrophs." The hydrogenase (EC:1.12.99.6) was proposed as a potential key gene facilitating this synergy between heterotrophic and autotrophic bacteria. The increased abundance ratio of nitrate reductase to nitrite reductase genes to 2.07 was identified as the key factor promoting the high accumulation of NO2[-]. Material characterization confirmed that the gel carriers possessed a hierarchical porous structure, with a mesopore-dominated pore size distribution conducive to hydrogen diffusion and the aggregation of functional microbial communities, thereby providing a stable micro-environment. This study offers a novel technological pathway for stable NO2[-] supply in the treatment of low-carbon wastewater.},
}

@article {pmid42155841,
year = {2026},
author = {Zhang, M and Sun, H and Ren, Y and Chen, K and Yan, G and Li, B and Huang, Y and Tan, Z and Sun, W},
title = {Thiosulfate drives vanadium natural attenuation in oligotrophic mine tailings: Insights from DNA-SIP and metagenomics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128368},
doi = {10.1016/j.envpol.2026.128368},
pmid = {42155841},
issn = {1873-6424},
abstract = {Vanadium (V) accumulation in mine tailing ponds represents a persistent contamination source, posing severe risks to the surrounding ecosystems. Microbial V(V) reduction represents a key pathway of V detoxification, immobilization and attenuation. While thiosulfate (S2O3[2-]), a prevalent byproduct in tailing ponds, is thermodynamically capable of driving V(V) reduction, the occurrence of the S2O3[2-]-driven V(V) reduction and its underpinning microbial mechanisms remain elusive. Here, we investigated the potential of S2O3[2-] to fuel V(V) natural attenuation in the tailing sediment. Microcosm experiments demonstrated that S2O3[2-] amendment significantly accelerated V(V) reduction rates by 1.8-fold compared to thiosulfate-free controls, confirming a stoichiometric coupling between V(V) reduction and S2O3[2-] oxidation. Pseudomonas, Symbiobacterium and Actinotalea were proposed as the active autotrophic taxa responsible for this coupling process using DNA-stable isotope probing (SIP) combined with metagenomics. Metabolic reconstruction revealed a resilient microbial network based on functional redundancy. These key taxa harbored denitrification-related reductases (NarGHI, NapAB, and NirS/K) and respiratory electron-transfer components (cytochrome c oxidases), together with distinct thiosulfate oxidation genes including thiosulfate dehydrogenase (TsdA/DoxD) and sulfurtransferases (TST/GlpE), indicating potential pathways for the S2O3[2-]-driven V(V) reduction process. These findings expand our understanding of the coupled S-V biogeochemical cycle and highlight the intrinsic natural attenuation capacity of tailing environments. This work provides a mechanistic basis for assessing the environmental fate and mobility of vanadium in oligotrophic habitats.},
}

@article {pmid42156214,
year = {2026},
author = {Wang, H and Chen, N and Feng, C and Mei, D and Gao, H and Liu, T},
title = {Carbon availability dictates the stability of nitrate-vanadium co-remediation in stratified biofilters.},
journal = {Water research},
volume = {302},
number = {},
pages = {126137},
doi = {10.1016/j.watres.2026.126137},
pmid = {42156214},
issn = {1879-2448},
abstract = {Thermodynamic hierarchies constrain the bioremediation of groundwater co-contaminated with nitrate (NO3[-]) and pentavalent vanadium (V(V)), denitrification preferentially consumes electron donors that would otherwise support metal reduction. Here, we show that spatial stratification of lignocellulosic residues (wheat straw → corn straw → corncob) can transiently alleviate competition between these competing processes, although system performance remains ultimately governed by carbon availability and kinetics. Over 330 days of operation, the stratified biofilter exhibited a biphasic response: (i) a carbon-sufficient phase (0 - 88 d) that enabled synergistic co-removal, increasing NO3[-] and V(V) loading capacities by up to 6.3-fold and 4.0-fold, respectively, relative to single-substrate controls; and (ii) a carbon-limited phase (88 - 330 d) in which denitrification persisted (>50% removal) while V(V) reduction collapsed (≈0%). Spatially resolved metagenomics (n = 15) revealed the mechanism as a thermodynamic "metabolic triage": under carbon limitation, microbial communities maintained denitrification pathways but selectively down-regulated V-reduction modules (sulfite reductase and multiheme cytochromes) by 59% - 69%. While distinct functional niches emerged-characterized by rapid efflux (top), deep reduction (middle), and sequestration (bottom), spatial organization alone could not override thermodynamic limits. Our findings establish that sustained metal co-remediation requires dynamic carbon management strategies to actuate latent genetic potential, providing a design framework for overcoming competitive inhibition in engineered aquifers.},
}

@article {pmid42156216,
year = {2026},
author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B},
title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.},
journal = {Water research},
volume = {302},
number = {},
pages = {126133},
doi = {10.1016/j.watres.2026.126133},
pmid = {42156216},
issn = {1879-2448},
abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.},
}

@article {pmid42156414,
year = {2026},
author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and , and Guarner, F and Ehrlich, SD},
title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44895-6},
pmid = {42156414},
issn = {2045-2322},
support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; },
abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.},
}

@article {pmid42156610,
year = {2026},
author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z},
title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {42156610},
issn = {1437-7772},
support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; },
abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.},
}

@article {pmid42156647,
year = {2026},
author = {Ravikrishnan, A},
title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {1-23},
pmid = {42156647},
issn = {1940-6029},
abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.},
}

@article {pmid42156648,
year = {2026},
author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A},
title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {25-32},
pmid = {42156648},
issn = {1940-6029},
abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.},
}

@article {pmid42156649,
year = {2026},
author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D},
title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {33-46},
pmid = {42156649},
issn = {1940-6029},
abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.},
}

@article {pmid42156650,
year = {2026},
author = {Miliotis, G and Tumeo, A},
title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {47-73},
pmid = {42156650},
issn = {1940-6029},
abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.},
}

@article {pmid42143599,
year = {2026},
author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S},
title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70140},
pmid = {42143599},
issn = {1943-3670},
support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jusélius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; },
abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.

METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.

RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).

CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.

PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.},
}

@article {pmid42143831,
year = {2026},
author = {Deng, Y and Yuan, X and Xu, Y and Jiang, H and Xue, J and Jiang, Y and Wang, Y},
title = {Acetoclastic methanogenesis associated with arsenic methylation in a reducing aquifer: Pathway-specific patterns and mechanistic insights.},
journal = {Water research},
volume = {301},
number = {},
pages = {126114},
doi = {10.1016/j.watres.2026.126114},
pmid = {42143831},
issn = {1879-2448},
abstract = {The distribution of methylated arsenic (MeAs) in reducing groundwater systems remains incompletely understood, in part due to uncertainties regarding how specific methanogenic pathways may influence arsenic biomethylation, a critical issue in arsenic biogeochemistry and risk assessment. To explore this question, we integrated hydrogeochemical characterization, carbon isotopic tracing, metagenomic analysis, and pathway-specific enrichment experiments, focusing on MeAs-rich alluvial-lacustrine aquifers in the central Yangtze River Basin. A strong positive correlation between arsM and mcrA abundances (r = 0.84, p < 0.001) points to a co-occurrence of genetic potential for arsenic methylation and methanogenesis in the studied aquifer. Metagenome-assembled genome (MAG) analysis showed a pathway-specific distribution of arsM gene, a higher proportion of acetoclastic methanogen MAGs harbored complete arsM genes (14.29 %), compared to methylotrophic (9.09 %) and hydrogenotrophic (0.00 %) methanogens. In pathway-specific enrichment assays under controlled laboratory conditions, acetoclastic cultures exhibited the highest capacity for stepwise arsenic methylation (MMA and DMA production), with methylation efficiency reaching approximately 10.2 %, whereas methylotrophic cultures produced only transient MMA and hydrogenotrophic cultures showed minimal methylation. These observations provide insights into pathway-dependent differences in methanogen-associated arsenic methylation, highlighting a possible biogeochemical link between methanogenesis and arsenic cycling in the studied aquifer. These findings contribute to understanding potential controls on MeAs occurrence in reducing groundwater and provide a basis for further investigations in comparable hydrogeological settings.},
}

@article {pmid42144568,
year = {2026},
author = {Rui, Z and Wang, X and Yu, C},
title = {Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70924},
pmid = {42144568},
issn = {1526-4998},
support = {QKEZDZX[2024]010//the Guizhou Provincial Major Scientific and Technological Program/ ; theNationalNaturalScienceFoundationofChina//32160375/ ; },
abstract = {BACKGROUND: Fusarium oxysporum causes damping-off disease in Pinus massoniana seedlings. While Trichoderma koningiopsis can enhance seedling resistance by regulating rhizosphere plant growth-promoting rhizobacteria (PGPR), the specific bacterial compositions and their role in disease resistance remained undefined. To elucidate this mechanism, we used amplicon and metagenomic sequencing to identify T. koningiopsis-assembled PGPR. Synthetic PGPR communities were constructed from isolated strains to validate their effects on disease suppression and growth promotion.

RESULTS: Microbial community analysis indicated that T. koningiopsis reshaped the bacterial community: Actinospica, Dyella, and Streptomyces decreased in presence, and Bacillus and Arthrobacter increased. A total of 153 PGPR strains were isolated from the T. koningiopsis-inoculated treatment. Of these, eight strains demonstrated significant inhibitory effects against F. oxysporum, ranging from 33.81% to 59.52%. Four synthetic communities (SynComs) (C1, C2, HT, and 2K) were further constructed, exhibiting superior inhibitory effects against F. oxysporum compared to individual strains. Compared to the control, the C2 and HT SynComs increased seedling height by 10.18% and 9.44%, and reduced disease incidence by 50% and 36.67%, respectively. These treatments also enhanced protective enzyme activity and alleviated membrane damage. At the molecular level, the C2 and HT SynComs boost plant resistance by modulating the plant hormone and mitogen-activated protein kinase (MAPK) signaling pathways, thereby activating the expression of crucial resistance genes such as PR1, FLS2, and CAT1.

CONCLUSION: Trichoderma koningiopsis alters the composition of rhizosphere PGPR community. The synthetic PGPR community assembled under the influence of T. koningiopsis effectively enhances damping-off resistance and promotes the growth of Masson pine seedlings. © 2026 Society of Chemical Industry.},
}

@article {pmid42145141,
year = {2026},
author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R},
title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {15353141261449964},
doi = {10.1177/15353141261449964},
pmid = {42145141},
issn = {1556-7125},
abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.},
}

@article {pmid42145647,
year = {2026},
author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H},
title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.06.26352545},
pmid = {42145647},
abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.},
}

@article {pmid42146067,
year = {2026},
author = {Cooper, G and Ayotte, SH and Du, ML and Wood, JD and Opp, B and Bothner, B and Peyton, BM},
title = {Arsenic detoxification within thermo-alkaline biofilms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783099},
pmid = {42146067},
issn = {1664-302X},
abstract = {INTRODUCTION: The fundamental principles driving community composition and dynamics of microbial mats in thermoalkaline springs are largely uncharacterized. High in not only temperature but also arsenic (As), the microbial populations of Yellowstone National Parks (YNP), USA thermal springs require unique detoxification mechanisms to survive and carry out basic biological functions.

METHODS: While many studies have focused on which microorganisms are present, few studies have integrated the use of metagenome sequencing, imaging techniques, and mass spectrometry to gain insight into how structure and function of the mat dwelling organisms might be impacted by the high arsenical species in the ecosystem.

RESULTS: Here, we demonstrate via metagenome sequencing that community composition, including microbial genera Roseiflexus, Thermus, and Synechococcus, and as detoxification abilities change with mat depth and distance from the springs. Arsenical speciation confirmed the generation of bioarsenicals by mat-dwelling microorganisms. Microscopy revealed stratification of microorganisms in the mat, potentially reflecting their arsenic redox capabilities.

DISCUSSION: These data demonstrate how microbial mats are modular, stratified systems that shape and are shaped by environmental and geochemical gradients. Together, these findings characterize novel complexity and associations between geochemical cycles of metals and metabolic adaptations necessary for microorganisms to inhabit thermal springs. In conclusion, these findings demonstrate physiochemical heterogeneity of microbial mats in YNP.},
}

@article {pmid42146533,
year = {2026},
author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV},
title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721144},
pmid = {42146533},
issn = {2692-8205},
abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.},
}

@article {pmid42146661,
year = {2026},
author = {Miller, CJ and Pope, CE and Lavitt, MH and Caverly, LJ and LiPuma, JJ and Penewit, K and Lewis, JD and Salipante, SJ and Hoffman, LR},
title = {The Unified Human Virome Database: A toolkit for expanded human virome analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.01.722327},
pmid = {42146661},
issn = {2692-8205},
abstract = {Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes from human gastrointestinal, airway, skin, and urogenital sample metagenomes. We developed an associated toolkit that uses UHVDB to characterize viruses and their potential activity from metagenomes, then applied this toolkit to 1,983 airway sample metagenomes from people with cystic fibrosis. Over half of detected viruses lacked evidence of potential activity and were detected transiently. UHVDB is nearly three times larger than prior viral databases and its ability to identify likely active viruses enables rigorous analysis of viruses from diverse human sample types, expanding the capacity to define virus contributions to health and disease.},
}

@article {pmid42146906,
year = {2026},
author = {Orletskaia, VA and Olekhnovich, EI},
title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0065},
pmid = {42146906},
issn = {2001-0370},
abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.},
}

@article {pmid42147179,
year = {2026},
author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S},
title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9092464/v1},
pmid = {42147179},
issn = {2693-5015},
abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.},
}

@article {pmid42148043,
year = {2026},
author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS},
title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.},
journal = {Environmental health perspectives},
volume = {134},
number = {1},
pages = {75-90},
doi = {10.1021/EHP.6c00064},
pmid = {42148043},
issn = {1552-9924},
mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics & numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; },
abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.},
}

Humans
Uganda
Female
*Gastrointestinal Microbiome
*Air Pollution, Indoor/statistics & numerical data/adverse effects
Adult
*Virome
Middle Aged

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0411725},
doi = {10.1128/spectrum.04117-25},
pmid = {42148573},
issn = {2165-0497},
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}